# BugSigDB 2022-04-17, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
Study,Study design,PMID,DOI,URL,Authors list,Title,Journal,Year,Experiment,Location of subjects,Host species,Body site,UBERON ID,Condition,EFO ID,Group 0 name,Group 1 name,Group 1 definition,Group 0 sample size,Group 1 sample size,Antibiotics exclusion,Sequencing type,16S variable region,Sequencing platform,Statistical test,Significance threshold,MHT correction,LDA Score above,Matched on,Confounders controlled for,Pielou,Shannon,Chao1,Simpson,Inverse Simpson,Richness,Signature page name,Source,Curated date,Curator,Revision editor,Description,Abundance in Group 1,MetaPhlAn taxon names,NCBI Taxonomy IDs,State,Reviewer
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,adenoma,EFO:0000232,controls,conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,144,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,5 September 2018,Levi Waldron,"WikiWorks743,WikiWorks753","Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae",2|1239|91061;2|1224|1236;2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|162289;2|1239|186801|186802|186803|189330;2|1239|909932|1843488|909930|33024;2|1224|28216|80840|995019|40544;2|201174|1760|2037;2|201174|1760|2037|2049;2|1224|28216|80840|506;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|909932|1843489|31977;2|1224|1236|91347;2|201174|1760|85007|1653;2|1239|91061|186826|33958|2759736|57037;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186817,Complete,Fatima
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,adenoma,EFO:0000232,controls,conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,144,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Table 2 + Supplemental Table S5 + S3+ S4,5 September 2018,Levi Waldron,WikiWorks743,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Cyanobacteria",2|1239|526524|526525|2810280|100883;2|1117,Complete,Shaimaa Elsafoury
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,Hyperplastic Polyp,EFO:1000299,controls,hyperplastic polyp cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,40,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,5 September 2018,Levi Waldron,WikiWorks743,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae",2|1239|186801|186802|186803|207244;2|1239|91061|186826|33958|2759736|57037,Complete,Shaimaa Elsafoury
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,Hyperplastic Polyp,EFO:1000299,controls,hyperplastic polyp cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,40,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2 + Supplemental Table S5 + S3+ S4,5 September 2018,Levi Waldron,WikiWorks743,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales",2|1224|1236;2|1239|526524|526525|2810280|100883;2|1224|1236|91347,Complete,Shaimaa Elsafoury
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,Colon Sessile Serrated Adenoma/Polyp,EFO:1000189,controls,Sessile serrated adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,33,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,5 September 2018,Levi Waldron,WikiWorks743,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria",2|1239|526524;2|1224|1236,Complete,Shaimaa Elsafoury
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,adenoma,EFO:0000232,controls,Proximal conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,87,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S6 + S3,5 September 2018,Marianthi Thomatos,WikiWorks743,"Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae",2|201174|1760|2037;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300;2|1239|186801|186802|31979|1485;2|976|200643|171549|171551|836;2|1239|91061;2|1239|91061|186826;2|1239|1737404|1737405|1570339|162289;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1737406;2|1239|1737404|1737405|1570339|165779;2|976|200643|171549|1853231|283168;2|1239|909932|1843489|31977;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|189330;2|1224|28216|80840|995019|40544;2|1239|909932|1843488|909930|33024;2|1224|28216|80840|506;2|1224|1236|91347;2|1224|1236;2|976|200643|171549|1853231,Complete,Shaimaa Elsafoury
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,adenoma,EFO:0000232,controls,Proximal conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,87,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Table S6 + S3,5 September 2018,Marianthi Thomatos,WikiWorks743,"Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",decreased,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,2|1239|526524|526525|2810280|100883,Complete,Shaimaa Elsafoury
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 5,United States of America,Homo sapiens,feces,UBERON:0001988,adenoma,EFO:0000232,controls,Distal conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,55,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S6 + S3,5 September 2018,Marianthi Thomatos,"WikiWorks743,Fatima","Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Synergistetes",2|1239|186801|186802|990719;2|1239|186801;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|544448|31969;2|508458,Complete,Fatima
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 6,United States of America,Homo sapiens,feces,UBERON:0001988,adenoma,EFO:0000232,controls,Non-advanced conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,121,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S6 + S3,5 September 2018,Marianthi Thomatos,WikiWorks743,"Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|201174|1760|2037|2049|1654;2|976|200643|171549|1853231|283168;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958|2759736|57037;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|189330;2|1239|909932|1843489|31977;2|1224|28216|80840|995019|40544;2|1224|28216|80840|506;2|1239|909932|1843488|909930|33024,Complete,Shaimaa Elsafoury
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 7,United States of America,Homo sapiens,feces,UBERON:0001988,adenoma,EFO:0000232,controls,advanced conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,22,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Supplemental Table S7 + S3,5 September 2018,Marianthi Thomatos,WikiWorks743,"Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae",2|201174|1760|2037;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653|1716;2|976|200643|171549|171551|836;2|1239|1737404|1737405|1737406;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|1236|135625|712|724;2|201174|1760|85007|1653,Complete,Shaimaa Elsafoury
Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,Experiment 7,United States of America,Homo sapiens,feces,UBERON:0001988,adenoma,EFO:0000232,controls,advanced conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,22,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Supplemental Table S7 + S3,5 September 2018,Marianthi Thomatos,WikiWorks743,"Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Cyanobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria",2|976|200643|171549|2005519;2|1117;2|1239|186801|186802|990719;2|1239|186801|186802|186803|140625;2|1239|186801|186802|186803|28050;2|1224|28211,Complete,Shaimaa Elsafoury
Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,normal adjacent tissues,squamous cell carcinoma tissues,Not stated,121,121,NA,16S,1234,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3 +text,5 September 2018,Nidhi Saini,WikiWorks743,Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|1239|1737404|1737405|1737406;2|1239|1737404|1737405|1570339|543311,Complete,Shaimaa Elsafoury
Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,normal adjacent tissues,squamous cell carcinoma tissues,Not stated,121,121,NA,16S,1234,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks743,Significant taxa by Wilcoxon signed-rank in paired tumor and normal tissue. Box plots representing relative abundances of taxa observed to be significantly different between tumor (orange) and adjacent normal (blue) samples by paired Wilcoxon signed-rank testing after correction for FDR.,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|201174;2|201174|1760;2|201174|1760|2037;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654,Complete,Shaimaa Elsafoury
Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,Experiment 2,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,T0-T2 low tumor stages patients,T3-T4 high tumor stages patients,Not stated,NA,NA,NA,16S,1234,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks743,"Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.",increased,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,2|1239|1737404|1737405|1570339|543311,Complete,Shaimaa Elsafoury
Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,Experiment 2,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,T0-T2 low tumor stages patients,T3-T4 high tumor stages patients,Not stated,NA,NA,NA,16S,1234,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks743,"Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria",2|201174|1760|2037|2049|1654;2|201174,Complete,Shaimaa Elsafoury
Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,Experiment 3,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,T0-T2 stages patients,T3-T4 stages patients,Not stated,NA,NA,NA,16S,1234,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks743,"Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.",increased,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,2|1239|1737404|1737405|1570339|543311,Complete,Shaimaa Elsafoury
Study 2,case-control,28173873,10.1186/s13073-017-0405-5,NA,"Wang H, Funchain P, Bebek G, Altemus J, Zhang H, Niazi F, Peterson C, Lee WT, Burkey BB , Eng C",Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas,Genome medicine,2017,Experiment 3,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,T0-T2 stages patients,T3-T4 stages patients,Not stated,NA,NA,NA,16S,1234,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 +text,10 January 2021,Shaimaa Elsafoury,WikiWorks743,"Relative abundances of differentially represented taxa stratified by T-stage. Box plots representing relative abundances of phylum Actinobacteria (top), genus Actinomyces (middle), and genus Parvimonas (bottom) stratified by T-stage.",decreased,k__Bacteria|p__Actinobacteria,2|201174,Complete,Shaimaa Elsafoury
Study 3,case-control,27015276,10.1371/journal.pone.0152126,NA,"Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB , Goedert JJ","Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations",PloS one,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,adenocarcinoma of colon and rectum patients,Not stated,89,42,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks743,Fecal microbes independently associated with colorectal cancer,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836,Complete,Shaimaa Elsafoury
Study 3,case-control,27015276,10.1371/journal.pone.0152126,NA,"Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB , Goedert JJ","Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations",PloS one,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,adenocarcinoma of colon and rectum patients,Not stated,89,42,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,10 January 2021,Nidhi Saini,WikiWorks743,Fecal microbes independently associated with colorectal cancer,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|186801;2|1239|186801|186802|186803,Complete,Shaimaa Elsafoury
Study 4,case-control,27625705,10.1186/s13099-016-0124-2,NA,"Aly AM, Adel A, El-Gendy AO, Essam TM , Aziz RK",Gut microbiome alterations in patients with stage 4 hepatitis C,Gut pathogens,2016,Experiment 1,Egypt,Homo sapiens,feces,UBERON:0001988,Hepatitis,HP:0012115,male healthy controls,HCV stage 4 male patients,Not stated,8,6,3 months,16S,4,Illumina,LEfSe,0.1,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Table 2 and Fig 5,10 January 2021,Shaimaa Elsafoury,WikiWorks743,Genera that are statistically signifcantly diferent between the two groups hcv patients and healthy participants  (non-parametric t test). All participants were male.,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes",2|1224|1236|2887326|468|469;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465;2|1239|909932|1843488|909930|33024;2|1224|1236|72274;2|1224|1236|2887326|468;2|976|200643|171549;2|976|200643;2|976,Complete,Shaimaa Elsafoury
Study 4,case-control,27625705,10.1186/s13099-016-0124-2,NA,"Aly AM, Adel A, El-Gendy AO, Essam TM , Aziz RK",Gut microbiome alterations in patients with stage 4 hepatitis C,Gut pathogens,2016,Experiment 1,Egypt,Homo sapiens,feces,UBERON:0001988,Hepatitis,HP:0012115,male healthy controls,HCV stage 4 male patients,Not stated,8,6,3 months,16S,4,Illumina,LEfSe,0.1,FALSE,2,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Table 2 and Fig 5,10 January 2021,Shaimaa Elsafoury,WikiWorks743,Genera that are statistically signifcantly diferent between the two groups hcv patients and healthy participants  (non-parametric t test). All participants were male.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Tenericutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales,k__Bacteria|p__Lentisphaerae",2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|1263;2|976|200643|171549|1853231|574697;2|201174;2|201174|1760;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953;2|976|200643|171549|171551;2|544448|31969;2|544448;2|1224|1236|135622|267888|53246;2|1224|1236|135622|267888;2|1224|1236|135623;2|1239|909932|1843489|31977|39948;2|256845|1313211|278082|255528;2|256845|1313211|278082;2|256845,Complete,Shaimaa Elsafoury
Study 5,case-control,23071781,10.1371/journal.pone.0047305,NA,"Pragman AA, Kim HB, Reilly CS, Wendt C , Isaacson RE",The lung microbiome in moderate and severe chronic obstructive pulmonary disease,PloS one,2012,Experiment 1,United States of America,Homo sapiens,lung,UBERON:0002048,chronic obstructive pulmonary disease,EFO:0000341,controls,Chronic obstructive pulmonary disease,Not stated,10,22,2 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 2,10 September 2018,Fatima Zohra,"WikiWorks743,Lwaldron,Fatima",Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales",2|1239|91061|186826|186827|46123;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|1239|91061|186826|186827;2|1224|1236|135624|84642;2|1224|1236|135624;2|1224|1236|135624|84642|642;2|1239|186801|186802|186803|653683;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|118747;2|1239|186801|186802|186803|830;2|1224|29547|213849|72294|194;2|1224|29547|213849|72294;2|1224|29547|213849;2|976|117743|200644|49546|1016;2|1239|186801|186802|186803|43996;2|1239|909932|909929|1843491|82202;2|201174|84998|84999|84107;2|201174|84998|1643822|1643826|84162;2|1224|28221|213118|213119;2|1224|28221|213118;2|1224|28221|213118|213121|893;2|1239|909932|1843489|31977|39948;2|976|200643|171549|2005520|156973;2|1224|29547;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|52228;2|1239|186801|186802|186803;2|1239|91061|186826;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|201174|1760|85006|1268;2|1224|28211|356|119045|186650;2|1224|28216|206351|481;2|1224|28216|206351;2|201174|1760|85009|85015|1839;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186803|265975;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186804|1257;2|976|200643|171549|171552|838;2|1224|28211|204441;2|201174|1760|85006|1268|32207;2|1239|909932|909929|1843491|970;2|1224|1236|91347|1903411|613;2|1239|526524|526525|128827|123375;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|195950;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|201174|84998|84999,Complete,Fatima
Study 5,case-control,23071781,10.1371/journal.pone.0047305,NA,"Pragman AA, Kim HB, Reilly CS, Wendt C , Isaacson RE",The lung microbiome in moderate and severe chronic obstructive pulmonary disease,PloS one,2012,Experiment 1,United States of America,Homo sapiens,lung,UBERON:0002048,chronic obstructive pulmonary disease,EFO:0000341,controls,Chronic obstructive pulmonary disease,Not stated,10,22,2 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 2,10 September 2018,Fatima Zohra,WikiWorks743,Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus|s__Candidatus Blastococcus massiliensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Nakamurellales|f__Nakamurellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae|g__Thermoactinomyces,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter",2|1239|186801|186802|31979|1485;2|201174|1760|1643682|85030|38501|1470358;2|201174|1760|1643682|85030|88138;2|201174|1760|1643684|85031;2|1239|91061|1385|186824|2023;2|1239|91061|1385|186824;2|1224|1236|91347|543|544;2|201174|1760|85006|1268|1663,Complete,Shaimaa Elsafoury
Study 5,case-control,23071781,10.1371/journal.pone.0047305,NA,"Pragman AA, Kim HB, Reilly CS, Wendt C , Isaacson RE",The lung microbiome in moderate and severe chronic obstructive pulmonary disease,PloS one,2012,Experiment 2,United States of America,Homo sapiens,lung,UBERON:0002048,chronic obstructive pulmonary disease,EFO:0000341,moderate Chronic obstructive pulmonary disease,Severe,Not stated,8,14,2 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,NA,age,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 2,8 July 2019,Shaimaa Elsafoury,WikiWorks743,Metastats Analysis of Differential Abundance of moderate and severe COPD Lung microbiome compared to controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobulbaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Pontibacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|1224|1236|135624;2|1224|28221|213118;2|1224|1236|135624|84642;2|1224|28221|213118|213121;2|201174|1760|85009|85015|1839;2|1239|91061|1385|186817|289201;2|1239|186801|186802|31979|1485;2|1224|28211|356|119045|186650;2|1224|1236|135624|84642|642,Complete,Shaimaa Elsafoury
Study 6,prospective cohort,28467925,10.1016/j.cmet.2017.04.001,NA,"Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC , Nelson KE",Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease,Cell metabolism,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,mild/moderate fibrosis,advanced fibrosis,"Based on clinical, magnetic resonance, histology assessment; Mild/Moderate NAFLD: fibrosis 0-2. Advanced NAFLD: fibrosis 3-4",72,14,NA,WMS,NA,Illumina,Random Forest Analysis,0.05,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,"WikiWorks743,Lwaldron",relative abundances of top 4 phyla found in all samples and representative species from the first 3 phyla.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|186803|39491,Complete,Fatima
Study 7,case-control,20603222,10.1016/j.anaerobe.2010.06.008,NA,"Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, Liu M, Molitoris DR , Green JA",Pyrosequencing study of fecal microflora of autistic and control children,Anaerobe,2010,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,non-sibling control,severely autistic,"Cases were diagnosed with autistic spectrum disorder. Moreover, they were evaluated for autism and their diagnoses were validated based on impairment in social skills, impairment in language skills and verbal communication, sensory disturbances, repetitive stereotypical behaviors, and gastrointestinal disturbances.",8,11,within preceding month,16S,NA,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 1,Table 2 + Table 3 +  Table 5 + Table 6 + Table 8,11 September 2018,Marianthi Thomatos,WikiWorks743,Significant fecal microflora of autistic and control children,increased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Alkaliflexus,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria",2|1239|526524|526525|2810281|191303;2|976|200643|171549|815|816;2|976|200643|1970189|558415|286729;2|1224|28221|213115|194924|872;2|1239|186801|186802|216572|258514;2|976|200643|171549|2005525|375288;2|1224|28221|213115|194924|872|901;2|1224|28221|213115|194924|872|876;2|1224|28221|213115|194924|872|58621;2|976|200643|171549|815|909656|821;2|976;2|1224,Complete,Shaimaa Elsafoury
Study 7,case-control,20603222,10.1016/j.anaerobe.2010.06.008,NA,"Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, Liu M, Molitoris DR , Green JA",Pyrosequencing study of fecal microflora of autistic and control children,Anaerobe,2010,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,non-sibling control,severely autistic,"Cases were diagnosed with autistic spectrum disorder. Moreover, they were evaluated for autism and their diagnoses were validated based on impairment in social skills, impairment in language skills and verbal communication, sensory disturbances, repetitive stereotypical behaviors, and gastrointestinal disturbances.",8,11,within preceding month,16S,NA,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,increased,Signature 2,Table 2 + Table 3 +  Table 5 + Table 6 + Table 8,11 September 2018,Marianthi Thomatos,"WikiWorks743,Lwaldron",Significant fecal microflora of autistic and control children,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum",2|201174;2|1239|186801|186802|31979|114627;2|1239|186801|186802|216572|52784;2|1239|186801|186802|543314|109326;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1683;2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|216572|253238;2|1239;2|1239|1737404|1737405|1570339|31983;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1243;2|1239|186801|186802|186806|113286;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|46255;2|1239|186801|186802|216572|1535,Complete,Fatima
Study 8,case-control,20140211,10.1371/journal.pone.0009085,NA,"Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sørensen SJ, Hansen LH , Jakobsen M",Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults,PloS one,2010,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Control,Diabetes Type 2,The diabetic group had elevated concentration of plasma glucose as determined by a fasting oral glucose tolerance test (OGTT),10,10,NA,16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 2 + Text,20 September 2018,Phyu Han,WikiWorks743,Relative abundances (%) of bacteria were determined in feces from human adults with type 2 diabetes and non-diabetic adult (all are males),increased,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,2|1224|28216,Complete,Shaimaa Elsafoury
Study 8,case-control,20140211,10.1371/journal.pone.0009085,NA,"Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sørensen SJ, Hansen LH , Jakobsen M",Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults,PloS one,2010,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Control,Diabetes Type 2,The diabetic group had elevated concentration of plasma glucose as determined by a fasting oral glucose tolerance test (OGTT),10,10,NA,16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 2 + Text,21 September 2018,Phyu Han,WikiWorks743,Relative abundances (%) of bacteria were determined in feces from human adults with type 2 diabetes and non-diabetic adult (all are males),decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia",2|1239;2|1239|186801,Complete,Shaimaa Elsafoury
Study 9,case-control,29190829,10.1371/journal.pone.0188873,NA,"Thompson KJ, Ingle JN, Tang X, Chia N, Jeraldo PR, Walther-Antonio MR, Kandimalla KK, Johnson S, Yao JZ, Harrington SC, Suman VJ, Wang L, Weinshilboum RL, Boughey JC, Kocher JP, Nelson H, Goetz MP , Kalari KR",A comprehensive analysis of breast cancer microbiota and host gene expression,PloS one,2017,Experiment 1,United States of America,Homo sapiens,breast,UBERON:0000310,breast carcinoma,EFO:0000305,Control,Breast Cancer,Not stated,668,72,NA,16S,345,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 +text,4 October 2018,Phyu Han,"WikiWorks743,Lwaldron",Species compositions of the Breast Caner and Non-cancerous Adjacent tissues,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus|s__Alkalihalobacillus alcalophilus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium|s__Brachybacterium muris,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Furfurilactobacillus|s__Furfurilactobacillus rossiae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium phlei,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycolicibacterium|s__Mycolicibacterium fortuitum",2|1239|91061|1385|186817|2675234|1445;2|201174|1760|85006|85020|43668|219301;2|1239|91061|186826|33958|2767882|231049;2|1224|1236|91347|543|590|28901;2|201174|1760|85007|1762|1866885|1771;2|201174|1760|85007|1762|1866885|1766,Complete,Fatima
Study 9,case-control,29190829,10.1371/journal.pone.0188873,NA,"Thompson KJ, Ingle JN, Tang X, Chia N, Jeraldo PR, Walther-Antonio MR, Kandimalla KK, Johnson S, Yao JZ, Harrington SC, Suman VJ, Wang L, Weinshilboum RL, Boughey JC, Kocher JP, Nelson H, Goetz MP , Kalari KR",A comprehensive analysis of breast cancer microbiota and host gene expression,PloS one,2017,Experiment 1,United States of America,Homo sapiens,breast,UBERON:0000310,breast carcinoma,EFO:0000305,Control,Breast Cancer,Not stated,668,72,NA,16S,345,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3 +text,4 October 2018,Phyu Han,"WikiWorks743,Lwaldron",Species compositions of the Breast Caner and Non-cancerous Adjacent tissues,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium barkeri",2|1224|1236|2887326|468|469|40216;2|1224|1236|91347|543|561|562;2|1224|28216|80840|119060|48736|329;2|201174|1760|85006|85023|33882|33917,Complete,Fatima
Study 10,case-control,29234019,10.1038/s41598-017-17351-9,NA,"Curty G, Costa RL, Siqueira JD, Meyrelles AI, Machado ES, Soares EA , Soares MA",Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions,Scientific reports,2017,Experiment 1,Brazil,Homo sapiens,uterus,UBERON:0000995,cervical glandular intraepithelial neoplasia,EFO:1000165,Normal tissue HIV patients,Cervical Intraepithelial Lesion HIV patients,Cases were identified by HIV rapid or ELISA test and subsequent Western blot following recommendations for HIV diagnosis by the Brazilian Ministry of Health.,42,38,NA,16S,3456,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,6 October 2018,Phyu Han,WikiWorks743,Bacteria that presented higher relative abundance in cervical lesions using LEfse,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,2|1239|186801|186802|186803|437755,Complete,Shaimaa Elsafoury
Study 10,case-control,29234019,10.1038/s41598-017-17351-9,NA,"Curty G, Costa RL, Siqueira JD, Meyrelles AI, Machado ES, Soares EA , Soares MA",Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions,Scientific reports,2017,Experiment 2,Brazil,Homo sapiens,uterus,UBERON:0000995,cervical glandular intraepithelial neoplasia,EFO:1000165,Normal tissue HIV patients,Cervical Intraepithelial Lesion HIV patients,Cases were identified by HIV rapid or ELISA test and subsequent Western blot following recommendations for HIV diagnosis by the Brazilian Ministry of Health.,42,38,NA,16S,3456,Illumina,LEfSe,0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,18 July 2019,Shaimaa Elsafoury,WikiWorks743,Bacteria that presented higher relative abundance in cervical lesions using LEfse,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Schlegelella|s__Schlegelella thermodepolymerans",2|201174|1760|85004|31953|2701|2702;2|1239|91061|186826|186827|1375;2|201174|1760|85004|31953|1678|1681;2|1224|28216|80840|80864|215579|215580,Complete,Shaimaa Elsafoury
Study 11,time series / longitudinal observational,29234019,10.1038/s41598-017-17351-9,NA,"Curty G, Costa RL, Siqueira JD, Meyrelles AI, Machado ES, Soares EA , Soares MA",Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions,Scientific reports,2017,Experiment 1,Brazil,Homo sapiens,uterus,UBERON:0000995,cervical glandular intraepithelial neoplasia,EFO:1000165,HIV pateints with normal tissue at 6 months,HIV patients with lesion at 12 months,Cases were identified by HIV rapid or ELISA test and subsequent Western blot following recommendations for HIV diagnosis by the Brazilian Ministry of Health.,5,5,NA,16S,3456,Illumina,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,17 July 2019,Shaimaa Elsafoury,WikiWorks743,Gardnerella vaginalis abundance longitudinal analysis at six and twelve months postpartum in paired samples,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,2|201174|1760|85004|31953|2701|2702,Complete,Shaimaa Elsafoury
Study 12,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S, Seo SS, Kwon M, Lee JK , Kim MK","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,Experiment 1,South Korea,Homo sapiens,uterus,UBERON:0000995,human papilloma virus infection,EFO:0001668,HPV clearance,HPV persistent,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",15,16,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,6 November 2018,Phyu Han,WikiWorks743,Mulivariate odd ratios of species according to different types of HPV,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,2|976|200643|171549|2005525|375288|387661,Complete,Shaimaa Elsafoury
Study 12,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S, Seo SS, Kwon M, Lee JK , Kim MK","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,Experiment 2,South Korea,Homo sapiens,uterus,UBERON:0000995,human papilloma virus infection,EFO:0001668,HPV negative,HPV clearance,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",10,15,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,6 November 2018,Phyu Han,WikiWorks743,Mulivariate odd ratios of species according to different types of HPV,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma|s__Ureaplasma urealyticum",2|201174|1760|85004|31953|2701|2702;2|544448|31969|2085|2092|2129|2130,Complete,Shaimaa Elsafoury
Study 12,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S, Seo SS, Kwon M, Lee JK , Kim MK","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,Experiment 3,South Korea,Homo sapiens,uterus,UBERON:0000995,human papilloma virus infection,EFO:0001668,HPV presistent and clearance,HPV negative,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",31,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,6 November 2018,Phyu Han,WikiWorks743,Mulivariate odd ratios of species according to different types of HPV,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,2|1239|91061|186826|33958|1578|47770,Complete,Shaimaa Elsafoury
Study 12,time series / longitudinal observational,30341386,10.1038/s41598-018-33750-y,NA,"Arokiyaraj S, Seo SS, Kwon M, Lee JK , Kim MK","Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study",Scientific reports,2018,Experiment 4,South Korea,Homo sapiens,uterus,UBERON:0000995,human papilloma virus infection,EFO:0001668,HPV presistent and negative,HPV clearance,"HPV DNA was detected using the Digene HC2 high-risk DNA test (Qiagen, Gaithersburg, MD, USA) with signal amplification and chemiluminescence for 13 types of HR-HPV scored in RLU/PC. A positive result indicated a concentration of 1 pg/ml or higher than the RLU/cutoff ratio (RLU of the specimen/mean RLU of 2 positive controls).",26,15,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,"age,contraception,menopause,smoking behavior",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 2,29 July 2019,Shaimaa Elsafoury,WikiWorks743,Mulivariate odd ratios of species according to different types of HPV,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,2|1239|186801|186802|186803|28050|39485,Complete,Shaimaa Elsafoury
Study 13,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C, Liu Y, Gao W, Pan Y, Gao Y, Shen J , Xiong H",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,Experiment 1,China,Homo sapiens,uterus,UBERON:0000995,cervical glandular intraepithelial neoplasia,EFO:1000165,Cervical Intraepithelial Neoplasis -1,Cervical Intraepithelial Neoplasis +2,NA,126,40,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,1 December 2018,Phyu Han,WikiWorks743,LEfSe showing the differences in the 18 most abundant species according to Cervical Intraepithelial Neoplasia (CIN) status,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus",2|1239|91061|186826|33958|1578|47770;2|976|200643|171549|815|816|817;2|1239|91061|186826|1300|1301|1311;2|1224|29547|213849|72294|194|827,Complete,Shaimaa Elsafoury
Study 13,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C, Liu Y, Gao W, Pan Y, Gao Y, Shen J , Xiong H",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,Experiment 1,China,Homo sapiens,uterus,UBERON:0000995,cervical glandular intraepithelial neoplasia,EFO:1000165,Cervical Intraepithelial Neoplasis -1,Cervical Intraepithelial Neoplasis +2,NA,126,40,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,1 December 2018,Phyu Han,WikiWorks743,LEfSe showing the differences in the 18 most abundant species according to Cervical Intraepithelial Neoplasia (CIN) status,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Photobacterium|s__Photobacterium damselae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae",2|1224|1236|135623|641|657|38293;2|1239|91061|186826|33958|1578|109790;2|201174|1760|2037|2049|2767327|82135,Complete,Shaimaa Elsafoury
Study 13,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C, Liu Y, Gao W, Pan Y, Gao Y, Shen J , Xiong H",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,Experiment 2,China,Homo sapiens,uterus,UBERON:0000995,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV -ve among pateints with Cervical Intraepithelial Neoplasia different severity status,HPV +ve,NA,130,36,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,22 July 2019,Shaimaa Elsafoury,WikiWorks743,LEfSe showing the differences in the 18 most abundant species according to HPV infection,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas stutzeri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius",2|1239|91061|186826|1300|1301|1311;2|976|200643|171549|815|816|817;2|1224|1236|72274|135621|286|316;2|1239|186801|186802|186804|1257|1261,Complete,Shaimaa Elsafoury
Study 13,"cross-sectional observational, not case-control",29608253,10.1002/cam4.1471,NA,"Zhang C, Liu Y, Gao W, Pan Y, Gao Y, Shen J , Xiong H",The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia,Cancer medicine,2018,Experiment 2,China,Homo sapiens,uterus,UBERON:0000995,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV -ve among pateints with Cervical Intraepithelial Neoplasia different severity status,HPV +ve,NA,130,36,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,22 July 2019,Shaimaa Elsafoury,WikiWorks743,LEfSe showing the differences in the 18 most abundant species according to HPV infection,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,2|1239|91061|186826|33958|1578|1584,Complete,Shaimaa Elsafoury
Study 14,case-control,28875948,10.1088/1752-7163/aa7c24,NA,"Seerangaiyan K, van Winkelhoff AJ, Harmsen HJM, Rossen JWA , Winkel EG",The tongue microbiome in healthy subjects and patients with intra-oral halitosis,Journal of breath research,2017,Experiment 1,Netherlands,Homo sapiens,oral gland,UBERON:0010047,halitosis,HP:0100812,Control,Oral Halitosis,"IOH patient group was selected based on an organoleptic score of >= 2 from the mouth and nose =< 1, having a VSC level > 160 ppb, and H2S > 4 nmol/ L (96 ppb) and CH3SH > 0.5 nmol/L (12 ppb) and a DPSI of =< 2",5,10,3 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 4,4 December 2018,Phyu Han,WikiWorks743,Significant differentially abundant OTU of intr-aoral halitosis and Control,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|135625|712|416916|739;2|1224|29547|213849|72294|194;2|976|200643|171549|2005525|195950;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186804|1257;2|1239|909932|909929|1843491|970;2|32066|203490|203491|1129771|32067;2|1239|186801|186802|186807|2740;2|1239|186801|186802;2|1239|1737404|1737405|1570339|543311;2|203691|203692|136|2845253|157;2|976|117743|200644|49546|1016;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 14,case-control,28875948,10.1088/1752-7163/aa7c24,NA,"Seerangaiyan K, van Winkelhoff AJ, Harmsen HJM, Rossen JWA , Winkel EG",The tongue microbiome in healthy subjects and patients with intra-oral halitosis,Journal of breath research,2017,Experiment 1,Netherlands,Homo sapiens,oral gland,UBERON:0010047,halitosis,HP:0100812,Control,Oral Halitosis,"IOH patient group was selected based on an organoleptic score of >= 2 from the mouth and nose =< 1, having a VSC level > 160 ppb, and H2S > 4 nmol/ L (96 ppb) and CH3SH > 0.5 nmol/L (12 ppb) and a DPSI of =< 2",5,10,3 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 4,4 December 2018,Phyu Han,WikiWorks743,Significant differentially abundant OTU of intra-oral halitosis and Control,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207|2047;2|1239|186801|186802|186803|437755;2|1239|186801|186802|186803|265975;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 15,"cross-sectional observational, not case-control",28932201,10.3389/fphys.2017.00675,NA,"Zheng J, Xiao X, Zhang Q, Mao L, Yu M, Xu J , Wang T",The Placental Microbiota Is Altered among Subjects with Gestational Diabetes Mellitus: A Pilot Study,Frontiers in physiology,2017,Experiment 1,China,Homo sapiens,uterus,UBERON:0000995,gestational diabetes,EFO:0004593,controls,Gestational diabetes mellitus,"GDM was diagnosed when the fasting plasma glucose ≥5.1 mmol/L or 1 h post-OGTT glycemia ≥10.0 mmol/L or 2 h post-OGTT glycemia ≥8.5 mmol/L, according to the criteria set by International Association of Diabetes and Pregnancy Study Groups (IADPSG)",10,10,9 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2+ Figure 4+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks743,Phlotypes in placental microbiota significantly different between GDM and NDM groups,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae",2|1224;2|1224|28216|206389|2008794|33057;2|1224|28216|80840;2|1224|28211|356;2|1224|28216|80840|506,Complete,Shaimaa Elsafoury
Study 15,"cross-sectional observational, not case-control",28932201,10.3389/fphys.2017.00675,NA,"Zheng J, Xiao X, Zhang Q, Mao L, Yu M, Xu J , Wang T",The Placental Microbiota Is Altered among Subjects with Gestational Diabetes Mellitus: A Pilot Study,Frontiers in physiology,2017,Experiment 1,China,Homo sapiens,uterus,UBERON:0000995,gestational diabetes,EFO:0004593,controls,Gestational diabetes mellitus,"GDM was diagnosed when the fasting plasma glucose ≥5.1 mmol/L or 1 h post-OGTT glycemia ≥10.0 mmol/L or 2 h post-OGTT glycemia ≥8.5 mmol/L, according to the criteria set by International Association of Diabetes and Pregnancy Study Groups (IADPSG)",10,10,9 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2+ Figure 4+ Supplemental Table S2,10 January 2021,Fatima Zohra,WikiWorks743,Phlotypes in placental microbiota significantly different between GDM and NDM groups,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Armatimonadetes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Sulfuricellaceae|g__Sulfuricella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Rhodanobacteraceae|g__Dyella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Acidobacteria|c__Holophagae|o__Holophagales,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales,k__Bacteria|p__Ignavibacteriae|c__Ignavibacteria|o__Ignavibacteriales,k__Bacteria|p__Chlorobi,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Acidobacteria|c__Holophagae|o__Holophagales|f__Holophagaceae|g__Geothrix,k__Bacteria|p__Ignavibacteriae|c__Ignavibacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae",2|976;2|67819;2|1239|91061|1385|186822|55080;2|1224|28216|32003|2772226|935200;2|1239|91061|186826|33958|1578;2|1224|1236|135614|1775411|231454;2|976|200643|171549;2|1239|526524|526525;2|57723|533205|574975;2|1224|2008785|119069;2|1134404|795747|795748;2|1090;2|976|200643;2|57723|533205|574975|574976|44675;2|1134404|795747;2|1239|91061|186826|33958;2|1224|2008785|119069|206349;2|1239|91061|1385|186822,Complete,Shaimaa Elsafoury
Study 16,laboratory experiment,28199741,10.1111/jpi.12399,NA,"Xu P, Wang J, Hong F, Wang S, Jin X, Xue T, Jia L , Zhai Y",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,normal chow diet,high fat diet,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 6B + Data S1,18 September 2018,Marianthi Thomatos,WikiWorks743,Differential abundant taxa in gut microbiota in response to melatonin treatment,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Acetitomaculum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|186803|31980;2|976|200643|171549|171552;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|248744;2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|572511,Complete,Shaimaa Elsafoury
Study 16,laboratory experiment,28199741,10.1111/jpi.12399,NA,"Xu P, Wang J, Hong F, Wang S, Jin X, Xue T, Jia L , Zhai Y",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,normal chow diet,high fat diet,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 6B + Data S1,18 September 2018,Marianthi Thomatos,WikiWorks743,Differential abundant taxa in gut microbiota in response to melatonin treatment,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Tenericutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|976|200643|171549|815|816;2|976|200643|171549|1853231|283168;2|1239|186801|186802|543314|109326;2|976|200643|171549|1853231|574697;2|1239|186801|186802|990719;2|1224|29547|213849|72293|209;2|1239|186801|186802|990719|990721;2|1224|28221|213115|194924|35832;2|544448;2|1239|186801|186802|216572|459786,Complete,Shaimaa Elsafoury
Study 16,laboratory experiment,28199741,10.1111/jpi.12399,NA,"Xu P, Wang J, Hong F, Wang S, Jin X, Xue T, Jia L , Zhai Y",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,Experiment 2,United States of America,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,high fat diet,high fat diet + melatonin,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 1,Figure 6B + Data S1,18 September 2018,Marianthi Thomatos,WikiWorks743,Differential abundant taxa in gut microbiota in response to melatonin treatment,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Geodermatophilales|f__Antricoccaceae|g__Antricoccus",2|1224|1236|91347|1903414|583;2|976|200643|171549|1853231|283168;2|1224|29547|213849|72293|209;2|1239|186801|186802|543314|109326;2|1224|28221|213115|194924|872;2|1224|28221|213115|194924;2|976|200643|171549|1853231|574697;2|74201|203494|48461|1647988|239934;2|201174|1760|1643682|2805401|1920251,Complete,Shaimaa Elsafoury
Study 16,laboratory experiment,28199741,10.1111/jpi.12399,NA,"Xu P, Wang J, Hong F, Wang S, Jin X, Xue T, Jia L , Zhai Y",Melatonin prevents obesity through modulation of gut microbiota in mice,Journal of pineal research,2017,Experiment 2,United States of America,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,high fat diet,high fat diet + melatonin,Obesity is (BMI ≥ 30kg/m2),5,5,NA,16S,34,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,increased,NA,NA,Signature 2,Figure 6B + Data S1 + Figure 7,18 September 2018,Marianthi Thomatos,WikiWorks743,Differential abundant taxa in gut microbiota in response to melatonin treatment,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter marmotae",2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|244127;2|1224|29547|213849|72293|209|152490,Complete,Shaimaa Elsafoury
Study 17,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang HY, Zhang X, Yu ZH, Zhang Z, Deng M, Zhao JH , Ruan B",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,anxiety disorder,EFO:0006788,healthy controls,treatment active Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,36,40,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 1,10 January 2021,Fatima Zohra,WikiWorks743,Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and generalized anxiety disorder groups,increased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] innocuum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia",2|32066;2|976;2|32066|203490|203491|203492|848;2|1239|186801|186802|186803|2316020|33038;2|976|200643|171549|815|816;2|1239|186801|186802|216572|946234;2|32066|203490;2|32066|203490|203491|203492;2|32066|203490|203491;2|1239|186801|186802|186803|1432051;2|1239|526524|526525|128827|1505663;2|1239|526524|526525|128827|1505663|1522;2|976|200643|171549|815;2|976|200643|171549;2|976|200643,Complete,Shaimaa Elsafoury
Study 17,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang HY, Zhang X, Yu ZH, Zhang Z, Deng M, Zhao JH , Ruan B",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,anxiety disorder,EFO:0006788,healthy controls,treatment active Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,36,40,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 1,10 January 2021,Fatima Zohra,"WikiWorks743,Lwaldron",Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and generalized anxiety disorder groups,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|1224|28216|80840|506;2|1224|28216;2|1224|28221|213115|194924|35832;2|1224|28216|80840;2|1239|186801|186802|31979|580596;2|1239|186801|186802|990719;2|1239|186801;2|201174|84998|84999|84107;2|201174|84998|84999;2|1224|28221;2|1224|28221|213115|194924;2|1224|28221|213115;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|28050|39485;2|1239|186801|186802|186803;2|1239|186801|186802|541000;2|1239|186801|186802|186807;2|1239|186801|186802|186803|46205;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|216572|292632;2|1224|28216|80840|995019|40544;2|1239|186801|186802|186803|39491,Complete,Fatima
Study 17,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang HY, Zhang X, Yu ZH, Zhang Z, Deng M, Zhao JH , Ruan B",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,anxiety disorder,EFO:0006788,healthy controls,treatment naiive Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,17,12,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 2,24 July 2019,Shaimaa Elsafoury,WikiWorks743,Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and treatment naiive generalized anxiety disorder groups,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] innocuum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria",2|1239|91061|186826|33958|1578;2|32066|203490|203491|203492|848;2|1239|186801|186802|186803|2316020|33038;2|976|200643|171549|815|816;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|976|200643|171549|815;2|976|200643|171549;2|976|200643;2|976;2|1224|1236|91347|543;2|1224|1236|91347;2|976|200643|171549|2005525|375288;2|1239|91061|186826|33958;2|1239|526524|526525|128827|1505663;2|1239|186801|186802|186803|2316020|33039;2|1239|526524|526525|128827|1505663|1522;2|1239|186801|186802|216572|946234;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066,Complete,Shaimaa Elsafoury
Study 17,"cross-sectional observational, not case-control",30029052,10.1016/j.jpsychires.2018.07.007,NA,"Jiang HY, Zhang X, Yu ZH, Zhang Z, Deng M, Zhao JH , Ruan B",Altered gut microbiota profile in patients with generalized anxiety disorder,Journal of psychiatric research,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,anxiety disorder,EFO:0006788,healthy controls,treatment naiive Generalized Anxiety disorder,The active state of GAD was defined as a baseline Hamilton Anxiety Rating Scale HAMA score ≥14 upon admission to the hospital. The remissive state was defined as a HAMA score < 7 after 3 months of treatment.,17,12,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 2,24 July 2019,Shaimaa Elsafoury,"WikiWorks743,Fatima",Comparison of relative abundance at the bacterial phylum and genus levels between healthy controls and treatment naiive generalized anxiety disorder groups,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium xylanophilum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|1239|186801|186802|216572|244127;2|976|200643|171549|2005519|397864;2|1239|186801|186802|31979|580596;2|976|200643|171549|1853231|574697;2|1239|186801|186802|990719;2|1239|186801;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|186801|186802;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|186806|1730|39497;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|28050|39485;2|1239|186801|186802|186803;2|1239|186801|186802|186803|437755;2|1239|186801|186802|541000;2|1224|28216|80840|75682|846;2|1224|28216|80840|75682;2|1224|28216|80840|995019|577310;2|1239|186801|186802|186807;2|1239|186801|186802|186807|2740;2|976|200643|171549|171552;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|216572|292632;2|1239|186801|186802|186803|39491,Complete,Fatima
Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,Experiment 1,Denmark,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,BL6- Low Fat,Sv129- Low Fat,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Data S4,S7,S8,S9,S10,S11,S13,S14",3 December 2019,Shaimaa Elsafoury,"WikiWorks743,Lwaldron","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus,k__Bacteria|p__Chloroflexi,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium hathewayi CAG:224,k__Bacteria|p__Cyanobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Planctomycetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Synergistetes,k__Bacteria|p__Thermotogae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] hylemonae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse",2|1239|186801|186802|216572|244127;2|976|200643|171549|815|816;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|830;2|1239|186801|186802|186803|830|43305;2|200795;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1263067;2|1117;2|1239|186801|186802|186803|189330;2|1239|91061|186826|81852|1350|1351;2|1239|186801|186802|186806|1730;2157|28890;2|1239|186801|186802|216572|216851;2|1239;2|32066;2|1239|186801|186802|186803|658087;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2767887|1605;2|1239|186801|186802|186803|248744|168384;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|459786|351091;2|203682;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1017280|106588;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|841|166486;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|216572|1263;2|203691;2|1239|186801|186802|216572|292632;2|508458;2|200918;2|1239|186801|186802|186803|1506553|89153;2|1239|186801|186802|186803|1506553|29347;2|1239|186801|186802|31979|49082|49118,Complete,Chloe
Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,Experiment 1,Denmark,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,BL6- Low Fat,Sv129- Low Fat,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,7,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Data S4,S7,S8,S9,S10,S11,S13,S14",3 December 2019,Shaimaa Elsafoury,"WikiWorks743,Fatima","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Chlorobi,k__Bacteria|p__Fibrobacteres,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",2|201174;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759;2|1090;2|65842;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|195950;2|74201;2|1239|526524|526525|128827|1573535|1735,Complete,Chloe
Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,Experiment 2,Denmark,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,BL6-High Fat without enomithacin,Sv129-High Fat without enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,8,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Data S4,S7,S8,S9,S10,S11,S13,S14",3 December 2019,Shaimaa Elsafoury,"WikiWorks743,Fatima","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium hathewayi CAG:224,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus animalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Candidatus Arthromitus|s__Candidatus Arthromitus sp. SFB-mouse",2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1263067;2|1239|91061|186826|81852|1350|1351;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958|2767887|1605;2|1239|186801|186802|186803|248744|168384;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|841|166486;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|186803|1506553|29347;2|1239|186801|186802|31979|49082|49118,Complete,Fatima
Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,Experiment 2,Denmark,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,BL6-High Fat without enomithacin,Sv129-High Fat without enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,8,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Data S4,S7,S8,S9,S10,S11,S13,S14",3 December 2019,Shaimaa Elsafoury,"WikiWorks743,Fatima","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Planctomycetes,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis",2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|203682;2|74201;2|1239|526524|526525|128827|1573535|1735,Complete,Fatima
Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,Experiment 3,Denmark,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,BL6-High Fat with enomithacin,Sv129-High Fat with enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,9,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Data S4,S7,S8,S9,S10,S11,S13,S14",3 December 2019,Shaimaa Elsafoury,WikiWorks743,"Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Cyanobacteria,k__Bacteria|p__Chlorobi,k__Bacteria|p__Fibrobacteres",2|976|200643|171549|815|816;2|976;2|1117;2|1090;2|65842,Complete,Shaimaa Elsafoury
Study 18,laboratory experiment,28390422,10.1186/s40168-017-0258-6,NA,"Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L , Kristiansen K",High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice,Microbiome,2017,Experiment 3,Denmark,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,BL6-High Fat with enomithacin,Sv129-High Fat with enomithacin,"(BL6): C57BL/6JBomTac mouse strain, (Sv129):  the obesity-resistant mouse strain 129S6/SvEvTac . LF:  (LF)low-fat diet, (HF) high fat diet without indomethacin,  (HFI) high fat diet supplemented with indomethacin.",10,9,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Data S4,S7,S8,S9,S10,S11,S13,S14",3 December 2019,Shaimaa Elsafoury,"WikiWorks743,Fatima,Kwekuamoo","Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin",decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium leptum CAG:27,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Planctomycetes,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis",2|201174;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|216572|244127;2|1239|186801|186802|31979|1485|1263068;2|32066;2|1239|526524|526525|128827|1573535|1735;2|203682;2|74201;2|1239|186801|186802|186804|2743582|89152,Complete,Fatima
Study 19,"cross-sectional observational, not case-control",29352709,10.1016/j.schres.2018.01.002,NA,"Shen Y, Xu J, Li Z, Huang Y, Yuan Y, Wang J, Zhang M, Hu S , Liang Y",Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study,Schizophrenia research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia,The patients were examined and diagnosed according to the ICD-10 by two trained psychiatric physicians.,53,64,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 4, S3",10 January 2021,Fatima Zohra,WikiWorks743,"Microbial composition at phylum, genus and species level in healthy and schizophrenia cohorts",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1224|1236;2|1224;2|1224|1236|135624;2|1224|1236|135624|83763|83770;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|135624|83763;2|32066|203490;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|32066|203490|203491;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|906;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1224|1236|91347|543|544;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930|904;2|1224|28221|213115|194924|872,Complete,Shaimaa Elsafoury
Study 19,"cross-sectional observational, not case-control",29352709,10.1016/j.schres.2018.01.002,NA,"Shen Y, Xu J, Li Z, Huang Y, Yuan Y, Wang J, Zhang M, Hu S , Liang Y",Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study,Schizophrenia research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,Schizophrenia,The patients were examined and diagnosed according to the ICD-10 by two trained psychiatric physicians.,53,64,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 4, S3",10 January 2021,Fatima Zohra,WikiWorks743,"Microbial composition at phylum, genus and species level in healthy and schizophrenia cohorts",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|572511;2|1224|28216|80840|506;2|1239|186801|186802;2|1239|186801;2|1239;2|1239|186801|186802|186803,Complete,Shaimaa Elsafoury
Study 20,case-control,26600078,10.1002/hep.28356,NA,"Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P , Diehl AM",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,Non-NASH,"NASH","NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular inflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",22,35,2 months,16S,4,Illumina,Logistic Regression,0.1,FALSE,NA,NA,"blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 1,Table 2 + text,10 January 2021,Shaimaa Elsafoury,WikiWorks743,Relative significant Abundance of Gut Microbiome Taxa in Patients With NASH and Without NASH,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 20,case-control,26600078,10.1002/hep.28356,NA,"Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P , Diehl AM",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,Non-NASH,"NASH","NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular inflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",22,35,2 months,16S,4,Illumina,Logistic Regression,0.1,FALSE,NA,NA,"blood pressure,body mass index,diabetes mellitus,hypertriglyceridemia,metabolic syndrome",NA,NA,NA,NA,NA,NA,Signature 2,Table 2 + text,10 January 2021,Shaimaa Elsafoury,WikiWorks743,Relative significant Abundance of Gut Microbiome Taxa in Patients With NASH and Without NASH,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,Shaimaa Elsafoury
Study 20,case-control,26600078,10.1002/hep.28356,NA,"Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P , Diehl AM",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,Experiment 2,France,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,mild fibrosis (F 0-1),significant fibrosis (F>2),"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular nflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",30,27,2 months,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,NA,"blood pressure,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks743,Relative significant Abundance of Gut Microbiome Taxa in Patients With Significant F 2 Fibrosis and No/Mild Fibrosis (F0/F1 Stage),increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|216572|1263;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 20,case-control,26600078,10.1002/hep.28356,NA,"Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P , Diehl AM",The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota,"Hepatology (Baltimore, Md.)",2016,Experiment 2,France,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,mild fibrosis (F 0-1),significant fibrosis (F>2),"NAFLD was defined as liver steatosis on liver biopsy after exclusion of concomitant steatosis-inducing drugs, excessive alcohol consumption (>210 g/week in men or >140 g/week in women), chronic hepatitis B or C infection, and histological evidence of other concomitant chronic liver disease. NASH was defined as the presence of each of the three following conditions: steatosis grade 1; lobular nflammation grade 1; and ballooning grade 1. “Significant fibrosis” was defined as fibrosis stage F2.",30,27,2 months,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,NA,"blood pressure,body mass index",NA,NA,NA,NA,NA,NA,Signature 2,Table 3,10 January 2021,Shaimaa Elsafoury,WikiWorks743,Relative significant  Abundance of Gut Microbiome Taxa in Patients With Significant F 2 Fibrosis and No/Mild Fibrosis (F0/F1 Stage),decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
Study 21,"cross-sectional observational, not case-control",25763184,10.1186/s40168-015-0072-y,NA,"Ross MC, Muzny DM, McCormick JB, Gibbs RA, Fisher-Hoch SP , Petrosino JF",16S gut community of the Cameron County Hispanic Cohort,Microbiome,2015,Experiment 1,United States-Mexico Border,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,Human Microbiome Project samples,Cameron County Hispanic Cohort samples,NA,213,63,NA,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.02,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,4 October 2018,Marianthi Thomatos,WikiWorks743,Relative abundance comparision between Cameron County Hispanic Cohort (CCHC) and Human microbiome project (HMP) subject stool samples,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|1239;2|201174;2|1239|186801|186802|186803;2|1239|909932|1843489|31977;2|201174|84998|84999|84107;2|1239|186801|186802|541000;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186803|841;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|39948,Complete,Shaimaa Elsafoury
Study 21,"cross-sectional observational, not case-control",25763184,10.1186/s40168-015-0072-y,NA,"Ross MC, Muzny DM, McCormick JB, Gibbs RA, Fisher-Hoch SP , Petrosino JF",16S gut community of the Cameron County Hispanic Cohort,Microbiome,2015,Experiment 1,United States-Mexico Border,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,Human Microbiome Project samples,Cameron County Hispanic Cohort samples,NA,213,63,NA,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.02,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,4 October 2018,Marianthi Thomatos,WikiWorks743,Relative abundance comparision between Cameron County Hispanic Cohort (CCHC) and Human microbiome project (HMP) subject stool samples,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976;2|976|200643|171549|815;2|976|200643|171549|171550;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
Study 22,"cross-sectional observational, not case-control",28429209,10.1007/s10517-017-3700-7,NA,"Petrov VA, Saltykova IV, Zhukova IA, Alifirova VM, Zhukova NG, Dorofeeva YB, Tyakht AV, Kovarsky BA, Alekseev DG, Kostryukova ES, Mironova YS, Izhboldina OP, Nikitina MA, Perevozchikova TV, Fait EA, Babenko VV, Vakhitova MT, Govorun VM , Sazonov AE",Analysis of Gut Microbiota in Patients with Parkinson's Disease,Bulletin of experimental biology and medicine,2017,Experiment 1,Russian Federation,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's,NA,66,89,NA,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3,18 October 2018,Fatima Zohra,WikiWorks743,Differences in the content of bacterial taxa in PD patients and control subjects at the genus and species level,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella|s__Christensenella hongkongensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans",2|1239|91061|186826|33958|1578;2|1239|186801|186802|990719|990721;2|1239|186801|186802|990719|270497;2|1239|186801|186802|216572|119852;2|201174|1760|85004|31953|1678;2|1239|186801|186802|990719|990721|626937;2|1239|186801|186802|990719|990721|270498;2|1239|91061|186826|33958|2742598|97478;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|100175|100176,Complete,Shaimaa Elsafoury
Study 22,"cross-sectional observational, not case-control",28429209,10.1007/s10517-017-3700-7,NA,"Petrov VA, Saltykova IV, Zhukova IA, Alifirova VM, Zhukova NG, Dorofeeva YB, Tyakht AV, Kovarsky BA, Alekseev DG, Kostryukova ES, Mironova YS, Izhboldina OP, Nikitina MA, Perevozchikova TV, Fait EA, Babenko VV, Vakhitova MT, Govorun VM , Sazonov AE",Analysis of Gut Microbiota in Patients with Parkinson's Disease,Bulletin of experimental biology and medicine,2017,Experiment 1,Russian Federation,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Parkinson's,NA,66,89,NA,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3,18 October 2018,Fatima Zohra,WikiWorks743,Differences in the content of bacterial taxa in PD patients and control subjects at the genus and species level,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus|s__Candidatus Stoquefichus massiliensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus",2|1239|186801|186802|186803|189330;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|216851;2|976|200643|171549|815|909656|204516;2|1239|186801|186802|186803|572511|536633;2|1239|526524|526525|128827|1470349|1470350;2|976|200643|171549|815|909656|310298;2|1239|186801|186802|216572|1263|40519;2|1239|186801|186802|186803|189330|88431;2|976|200643|171549|815|909656|357276;2|976|200643|171549|171552|838|165179;2|976|200643|171549|815|909656|310297;2|1239|186801|186802|186803|33042|33043,Complete,Shaimaa Elsafoury
Study 23,case-control,29051531,10.1038/s41598-017-13601-y,NA,"Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, Bendlin BB , Rey FE",Gut microbiome alterations in Alzheimer's disease,Scientific reports,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healhty controls,Alzheimer's,NA,25,25,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,unchanged,unchanged,NA,Signature 1,Figure 2+figure 1,25 October 2018,Fatima Zohra,"WikiWorks743,Kwekuamoo",Bacterias differentially represented in faeces from AD participants compared to controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|976|200643|171549|171550|239759;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|28221|213115|194924|35832;2|1239|186801|186802|186803|572511;2|1239|91061|1385|1378;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171550,Complete,Shaimaa Elsafoury
Study 23,case-control,29051531,10.1038/s41598-017-13601-y,NA,"Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, Bendlin BB , Rey FE",Gut microbiome alterations in Alzheimer's disease,Scientific reports,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,Alzheimer's disease,MONDO:0004975,Healhty controls,Alzheimer's,NA,25,25,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,unchanged,unchanged,NA,Signature 2,Figure 2+figure 1,25 October 2018,Fatima Zohra,"WikiWorks743,Fatima,Kwekuamoo",Bacterias differentially represented in faeces from AD participants compared to controls,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium",2|201174;2|201174|84998|1643822|1643826|447020;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2|1239;2|1239|186801|186802|541000;2|1239|186801|186802|186804;2|1239|526524|526525|2810281;2|1239|186801;2;2|1239|186801|186802|543314|86331,Complete,Fatima
Study 24,case-control,30204780,10.1371/journal.pone.0203503,NA,"Wang T, Yu L, Xu C, Pan K, Mo M, Duan M, Zhang Y , Xiong H",Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function,PloS one,2018,Experiment 1,China,Homo sapiens,saliva-secreting gland,UBERON:0001044,chronic fatigue syndrome,EFO:0004540,Healthy controls,Chronic Fatigue patients,NA,45,46,2 months for healthy control only,16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3b,25 October 2018,Shaimaa Elsafoury,"WikiWorks743,Fatima",LEfSe analysis identified the most differentially abundant taxa between healthy controls and CFS patients.Only taxa with LDA > 3 are shown.,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalibacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella",2|1239|91061|1385|186817|331654;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|29547|213849|72294|194;2|1224|29547|213849|72294;2|1224|29547|213849;2|1224|29547;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|91061|1385|1378,Complete,Fatima
Study 24,case-control,30204780,10.1371/journal.pone.0203503,NA,"Wang T, Yu L, Xu C, Pan K, Mo M, Duan M, Zhang Y , Xiong H",Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function,PloS one,2018,Experiment 1,China,Homo sapiens,saliva-secreting gland,UBERON:0001044,chronic fatigue syndrome,EFO:0004540,Healthy controls,Chronic Fatigue patients,NA,45,46,2 months for healthy control only,16S,34,Illumina,LEfSe,0.05,FALSE,3,"age,body mass index,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3b,25 October 2018,Shaimaa Elsafoury,WikiWorks743,LEfSe analysis identified the most differentially abundant taxa between healthy controls and CFS patients.Only taxa with LDA > 3 are shown.,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1224|1236;2|1239|909932|1843489|31977;2|1239|909932;2|1239|909932|909929;2|1239|909932|1843489|31977|29465;2|1224|1236|135625|712|724;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1224|1236|2887326|468|475;2|1224|1236|72274|135621|351;2|1224|1236|72274|135621|286,Complete,Shaimaa Elsafoury
Study 25,prospective cohort,23153041,10.1186/gb-2012-13-11-r101,NA,"Zeeuwen PL, Boekhorst J, van den Bogaard EH, de Koning HD, van de Kerkhof PM, Saulnier DM, van Swam II, van Hijum SA, Kleerebezem M, Schalkwijk J , Timmerman HM",Microbiome dynamics of human epidermis following skin barrier disruption,Genome biology,2012,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,psoriasis,EFO:0000676,Female,Psoriasis Male,"tape stripping method involves the repeated application of adhesive tape to the skin surface, thereby removing stratum corneum layers, it creates a superficial wound showing slight skin irritation (erythema) and loss of barrier function (transepidermal water loss)",6,6,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 4,25 October 2018,WikiWorks743,WikiWorks743,Difference in microbial community composition of upper buttok skin between males and females,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Sporacetigenium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|186827;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|31979;2|1239|1737404|1737405|1570339|150022;2|1239|186801|186802|186804;2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|186804|360541;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|1760|2037;2|201174|1760|85006|85020;2|201174|1760|85006|85020|43668;2|201174|1760|85006|1268|32207;2|201174;2|201174|1760;2|201174|1760|85006|85023;2|201174|1760|85006|85023|33882;2|201174|1760|85006|145357|57495;2|976|117743;2|976|117743|200644;2|976|117743|200644|49546;2|976|117743|200644|49546|1016;2|1224|1236|2887326|468|469;2|201174|1760|85006|85020|36739;2|1239|91061|186826|186827|171412,Complete,Shaimaa Elsafoury
Study 25,prospective cohort,23153041,10.1186/gb-2012-13-11-r101,NA,"Zeeuwen PL, Boekhorst J, van den Bogaard EH, de Koning HD, van de Kerkhof PM, Saulnier DM, van Swam II, van Hijum SA, Kleerebezem M, Schalkwijk J , Timmerman HM",Microbiome dynamics of human epidermis following skin barrier disruption,Genome biology,2012,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,psoriasis,EFO:0000676,Female,Psoriasis Male,"tape stripping method involves the repeated application of adhesive tape to the skin surface, thereby removing stratum corneum layers, it creates a superficial wound showing slight skin irritation (erythema) and loss of barrier function (transepidermal water loss)",6,6,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 4,25 October 2018,WikiWorks743,WikiWorks743,Difference in microbial community composition of upper buttok skin between males and females,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|201174|1760|85009|31957;2|201174|1760|85009|31957|1743;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|2701;2|1224;2|1224|1236;2|1224|1236|72274;2|1224|1236|2887326|468;2|1224|28211|356|212791;2|201174|1760|85006|85019;2|201174|1760|85006|85019|1696,Complete,Shaimaa Elsafoury
Study 26,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F , Camargo A",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,sex design,EFO:0001752,male,female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,39,36,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Table 2,25 October 2018,Marianthi Thomatos,WikiWorks743,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,increased,"k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae",2|1224|28221|213115|194924|35832;2|976|200643|171549|815|816|47678,Complete,Shaimaa Elsafoury
Study 26,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F , Camargo A",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,sex design,EFO:0001752,male,female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,39,36,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text + Table 2,25 October 2018,Marianthi Thomatos,WikiWorks743,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,2|976|200643|171549|815|909656|310297,Complete,Shaimaa Elsafoury
Study 26,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F , Camargo A",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,male,BMI >33 female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,13,13,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 2 +Table 2,25 October 2018,Marianthi Thomatos,WikiWorks743,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 26,"cross-sectional observational, not case-control",27228093,10.1371/journal.pone.0154090,NA,"Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F , Camargo A",Intestinal Microbiota Is Influenced by Gender and Body Mass Index,PloS one,2016,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,male,BMI >33 female,three groups according to the BMI: BMI < 30; BMI between 30- 33; and BMI > 33.,13,13,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text + Figure2 + Table 2,25 October 2018,Marianthi Thomatos,WikiWorks743,Intestinal Microbiota Is Influenced by Gender and Body Mass Index,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,2|976|200643|171549|815|909656|310297,Complete,Shaimaa Elsafoury
Study 27,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C , Kang JX",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,foster mother fat1 pre HFD,foster mother wild-type pre HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure S4",31 October 2018,Marianthi Thomatos,WikiWorks743,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales",2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|128827;2|1239|186801|186802|186807;2|1239|186801|186802|186807|2740;2|1239|186801|186802|216572|946234;2|1239|526524|526525;2|1239|526524;2|976|200643|171549|1853231|574697;2|1239|186801|186802|541000;2|1239|186801|186802|31979|580596;2|976|200643|171549|2005525|375288;2|1239;2|1239|186801;2|1239|186801|186802,Complete,Shaimaa Elsafoury
Study 27,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C , Kang JX",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,foster mother fat1 pre HFD,foster mother wild-type pre HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure S4",31 October 2018,Marianthi Thomatos,WikiWorks743,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Candidatus Saccharibacteria|g__Candidatus Saccharimonas",2|976;2|976|200643;2|976|200643|171549;2|1224|29547|213849;2|1224|29547;2|1224;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|28221;2|1224|28221|213115;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|976|200643|171549|2005519|397864;2|1224|29547|213849|72293;2|1224|29547|213849|72293|209;2|1224|28221|213115|194924;2|976|200643|171549|1853231|283168;2|1224|28221|213115|194924|872;2|1239|526524|526525|128827|174708;2|976|200643|171549|171550|28138;2|95818|1331051,Complete,Shaimaa Elsafoury
Study 27,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C , Kang JX",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,Experiment 2,United States of America,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,foster mother fat1 post HFD,foster mother wild-type post HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure S4",31 October 2018,Marianthi Thomatos,WikiWorks743,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",increased,"k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaerales|f__Lentisphaeraceae|g__Lentisphaera,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria",2|256845|1313211|278082|255528|172900;2|256845|1313211|278081|566277|256846;2|256845|1313211|278082|255528;2|1239|526524|526525|128827;2|256845|1313211|278082;2|1239|186801|186802|31979|1485;2|1239|526524|526525;2|1239|526524;2|976|200643|171549|171550|28138;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|946234;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186807|2740;2|1239|186801|186802|186807;2|1239|91061|186826;2|1239|91061;2|976|200643|171549|1853231|574697;2|1239|186801|186802|541000;2|1239|186801|186802|186803;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1239;2|1239|186801;2|1239|186801|186802;2|256845|1313211,Complete,Shaimaa Elsafoury
Study 27,laboratory experiment,29793531,10.1186/s40168-018-0476-6,NA,"Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C , Kang JX",Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota,Microbiome,2018,Experiment 2,United States of America,Mus musculus,feces,UBERON:0001988,obesity,EFO:0001073,foster mother fat1 post HFD,foster mother wild-type post HFD,fat-1 mice: with a balanced tissue n-6/n-3 ratio (~ 1:1) and wild-type (WT) mice: with a high n-6/ n-3 ratio similar to the Western diet (> 10:1).,15,9,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2.4,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure S4",31 October 2018,Marianthi Thomatos,WikiWorks743,"Pre-High fat diet (HFD) and Post-HF diet differential abundance in offspring according to foster mother genotype at lactation, wild type (WT) or fat-1 (balanced tissue n-6/n-3)",decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Candidatus Saccharibacteria|g__Candidatus Saccharimonas",2|1224|29547;2|1224|29547|213849;2|1224;2|1224|28221;2|1224|28221|213115;2|1224|29547|213849|72293;2|1224|29547|213849|72293|209;2|1224|28221|213115|194924;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|1853231|283168;2|95818|1331051,Complete,Shaimaa Elsafoury
Study 28,case-control,27338587,10.1186/s40168-016-0171-4,NA,"Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE , Hanson MR",Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,Healthy controls,CFS cases,"Subjects with ME/CFS were established patients of a ME/ CFS specialist, Susan Levine, M.D. and fit the Fukuda diag- nostic criteria",39,48,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,figure 5,8 November 2018,Shaimaa Elsafoury,WikiWorks743,taxonomy of differentially abundant microbiota between  ME/CFS and healthy individuals,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|1239|186801|186802|216572|119852;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|1300|1357;2|1239|186801|186802|216572|244127;2|1239|526524|526525|2810280|100883,Complete,Shaimaa Elsafoury
Study 28,case-control,27338587,10.1186/s40168-016-0171-4,NA,"Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE , Hanson MR",Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,Healthy controls,CFS cases,"Subjects with ME/CFS were established patients of a ME/ CFS specialist, Susan Levine, M.D. and fit the Fukuda diag- nostic criteria",39,48,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,figure 5,8 November 2018,Shaimaa Elsafoury,WikiWorks743,taxonomy of differentially abundant microbiota between  ME/CFS and healthy individuals,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239|186801|186802|186807|2740;2|1224|1236|135625|712|724;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|31979|1485;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|1224|1236|135625|712|416916;2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107|102106;2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
Study 29,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L , Ruan B",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,Healthy Controls,Active Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,29,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,unchanged,Signature 1,Figure 2,8 November 2018,Fatima Zohra,WikiWorks743,Taxonomic differences of fecal microbiota between Healthy Controls and Active Major Depressive Disorder groups,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1239|186801|186802|216572|946234;2|976|200643|171549|1853231|574697;2|1224|1236|91347;2|1224|1236|91347|543;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|976|200643|171549|171550|239759;2|976|200643|171549|171550,Complete,Shaimaa Elsafoury
Study 29,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L , Ruan B",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,Healthy Controls,Active Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,29,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,unchanged,NA,unchanged,Signature 2,Figure 2,8 November 2018,Fatima Zohra,WikiWorks743,Taxonomic differences of fecal microbiota between Healthy Controls and Active Major Depressive Disorder groups,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851;2|1239|909932|1843489|31977|39948;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|186802|216572|1263;2|1224|1236|135625|712|724;2|1239|186801|186802|186804;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,Shaimaa Elsafoury
Study 29,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L , Ruan B",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,Healthy Controls,Responded Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,17,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 3,8 November 2018,Fatima Zohra,WikiWorks743,Taxonomic differences of fecal microbiota between Healthy Controls and Responded Major Depressive Disorder groups,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|976|200643|171549|1853231|574697;2|976|200643|171549|171551,Complete,Shaimaa Elsafoury
Study 29,case-control,25882912,10.1016/j.bbi.2015.03.016,NA,"Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L , Ruan B",Altered fecal microbiota composition in patients with major depressive disorder,"Brain, behavior, and immunity",2015,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,Healthy Controls,Responded Major Depressive Disorder,The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.,30,17,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 3,8 November 2018,Fatima Zohra,WikiWorks743,Taxonomic differences of fecal microbiota between Healthy Controls and Responded Major Depressive Disorder groups,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|186801|186802|216572|1263;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|1236|135625|712|724;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,Experiment 1,Belgium,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,Belgian controls,Norweigan controls,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,17,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,table 1,12 November 2018,Shaimaa Elsafoury,WikiWorks743,Differentiately abundant mictobiota between Norwegian controls and Belgian controls.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",2|1239|186801|186802|186803|841;2|1239|526524|526525|128827|61170,Complete,Shaimaa Elsafoury
Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,Experiment 1,Belgium,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,Belgian controls,Norweigan controls,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,17,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,table 1,12 November 2018,Shaimaa Elsafoury,WikiWorks743,Differentiately abundant mictobiota between Norwegian controls and Belgian controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|815|816;2|976|200643|171549|171550|239759;2|976|200643|171549|2005519|397864;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,Experiment 2,Belgium,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,Norweigan controls,Norweigan CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,17,25,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,table 2,12 November 2018,Shaimaa Elsafoury,WikiWorks743,Differentiately abundant mictobiota between Norwegian CFS patients and Norwegian controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor",2|976|200643|171549|171550|239759;2|1239|186801|186802|31979|420345,Complete,Shaimaa Elsafoury
Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,Experiment 2,Belgium,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,Norweigan controls,Norweigan CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,17,25,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,table 2,12 November 2018,Shaimaa Elsafoury,WikiWorks743,Differentiately abundant mictobiota between Norwegian CFS patients and Norwegian controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Syntrophococcus",2|1239|186801|186802|186803|841;2|1239|526524|526525|128827|61170;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|84036,Complete,Shaimaa Elsafoury
Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,Experiment 3,Belgium,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,Belgian controls,Belgian CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,18,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,table 3,12 November 2018,Shaimaa Elsafoury,WikiWorks743,Differentiately abundant mictobiota between Belgian CFS patients and Belgian controls,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,2|1239|186801|186802|31979|420345,Complete,Shaimaa Elsafoury
Study 30,case-control,23791918,10.1016/j.anaerobe.2013.06.002,NA,"Frémont M, Coomans D, Massart S , De Meirleir K",High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients,Anaerobe,2013,Experiment 3,Belgium,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,Belgian controls,Belgian CFS/ME patients,Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al,19,18,4 weeks,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,table 3,12 November 2018,Shaimaa Elsafoury,WikiWorks743,Differentiately abundant mictobiota between Belgian CFS patients and Belgian controls,decreased,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,2|201174|84998|1643822|1643826|553372,Complete,Shaimaa Elsafoury
Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,50,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,14 November 2018,Shaimaa Elsafoury,"WikiWorks743,Fatima",Differentiately abundant mictobiota between CFS/ME and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis",2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|207244|105841;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|186803|2719313|333367;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1017280|106588;2|1239|186801|186802|186803|1506553|29347;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|2316020|33038;2|1239|526524|526525|2810280|100883|100884,Complete,Fatima
Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,50,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,14 November 2018,Shaimaa Elsafoury,"WikiWorks743,Fatima,Lwaldron",Differentiately abundant mictobiota between CFS/ME and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.",2|976|200643|171549|171550|239759|28117;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|33042|116085;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|91061|1385|1378;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1239|186801|186802|186803;2|976|200643|171549|2005525|375288|823;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|216572|216851|1971605,Complete,Fatima
Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients with IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,21,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,15 November 2018,Shaimaa Elsafoury,WikiWorks743,Differentiately abundant mictobiota between CFS/ME with IBS and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes",2|1239|186801|186802|186803|207244|105841;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979;2|1239|186801|186802|186803|2719313|208479;2|1239|186801|186802|186803|207244,Complete,Shaimaa Elsafoury
Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients with IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,21,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,15 November 2018,Shaimaa Elsafoury,"WikiWorks743,Lwaldron",Differentiately abundant mictobiota between CFS/ME with IBS and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum",2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|33042|116085;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186803;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|186803|572511|40520,Complete,Shaimaa Elsafoury
Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients without IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,29,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c,12 December 2018,Shaimaa Elsafoury,"WikiWorks743,Fatima,Lwaldron",Differentiately abundant mictobiota between CFS/ME without IBS and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",2|1224|1236|72274|135621|351;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|2810280|100883|100884;2|1239|186801|186802|186803|189330|88431;2|201174|84998|1643822|1643826|84111;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|1017280|106588;2|1224|1236|72274;2|1224|1236|72274|135621|286;2|1239|186801|186802|186803|1506553|29347;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|31979|1485|1506,Complete,Fatima
Study 31,case-control,28441964,10.1186/s40168-017-0261-y,NA,"Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M , Lipkin WI",Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome,Microbiome,2017,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,controls,CFS/ME patients without IBS,Cases met the 1994 CDC Fukuda and the 2003 Canadian consensus criteria for ME/CFS,50,29,3 months for controls only,WMS,NA,Illumina,LEfSe,0.2,TRUE,2,"age,ethnic group,geographic area,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3c,12 December 2018,Shaimaa Elsafoury,WikiWorks743,Differentiately abundant mictobiota between CFS/ME without IBS and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea",2|1239|186801|186802|186803|33042|116085;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|189330,Complete,Shaimaa Elsafoury
Study 32,prospective cohort,28636668,10.1371/journal.pone.0179739,NA,"Borgo F, Riva A, Benetti A, Casiraghi MC, Bertelli S, Garbossa S, Anselmetti S, Scarone S, Pontiroli AE, Morace G , Borghi E","Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests",PloS one,2017,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,Controls,Aonerxia Nervosa patients,"The severity of eating disorder and psychopathology tests were assessed by means of the Symptom Checklist 90 (general psychopathology), Eating Disorder Inventory 2 (eating disorder), State Trait Anxiety Inventory (anxiety disorder) and Beck Depression Inventory (depressive symptoms). Psychologists and psychiatrists (all extensively trained in the use of the instruments) conducted clinical evaluations.",15,15,1 month,16S,NA,Illumina,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 +text,14 November 2018,Fatima Zohra,WikiWorks743,Significant differential abundance in anorexia nervosa vs controls,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii",2|1224;2|1224|1236|91347|543;2157|28890|183925|2158|2159|2172|2173,Complete,Shaimaa Elsafoury
Study 32,prospective cohort,28636668,10.1371/journal.pone.0179739,NA,"Borgo F, Riva A, Benetti A, Casiraghi MC, Bertelli S, Garbossa S, Anselmetti S, Scarone S, Pontiroli AE, Morace G , Borghi E","Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests",PloS one,2017,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,Controls,Aonerxia Nervosa patients,"The severity of eating disorder and psychopathology tests were assessed by means of the Symptom Checklist 90 (general psychopathology), Eating Disorder Inventory 2 (eating disorder), State Trait Anxiety Inventory (anxiety disorder) and Beck Depression Inventory (depressive symptoms). Psychologists and psychiatrists (all extensively trained in the use of the instruments) conducted clinical evaluations.",15,15,1 month,16S,NA,Illumina,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 +text,14 November 2018,Fatima Zohra,WikiWorks743,Significant differential abundance in anorexia nervosa vs controls,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239;2|1239|186801|186802|541000;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|841;2|1239|186801|186802|31979|1485,Complete,Shaimaa Elsafoury
Study 33,"cross-sectional observational, not case-control",26261039,10.1186/s12876-015-0330-2,NA,"Kasai C, Sugimoto K, Moritani I, Tanaka J, Oya Y, Inoue H, Tameda M, Shiraki K, Ito M, Takei Y , Takase K","Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing",BMC gastroenterology,2015,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,obese,BMI ≥25 kg/m2,4,6,current use,16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Table 2, Table 4 & Table 5",24 November 2018,Marianthi Thomatos,"WikiWorks743,Fatima","Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, using  Next generation sequencing",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum",2|1239|186801|186802|186803|572511|53443;2|1239|186801|186802|186803|33042|116085;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|186803|572511|40520,Complete,Fatima
Study 33,"cross-sectional observational, not case-control",26261039,10.1186/s12876-015-0330-2,NA,"Kasai C, Sugimoto K, Moritani I, Tanaka J, Oya Y, Inoue H, Tameda M, Shiraki K, Ito M, Takei Y , Takase K","Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing",BMC gastroenterology,2015,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,obese,BMI ≥25 kg/m2,4,6,current use,16S,34,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Table 2, Table 4 & Table 5",24 November 2018,Marianthi Thomatos,WikiWorks743,"Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, using  Next generation sequencing",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecichinchillae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Bacteroidetes",2|1239|186801|186802|216572|946234|292800;2|976|200643|171549|815|816|871325;2|976|200643|171549|815|816|818;2|1239|186801|186802|186803|572511|418240;2|1239|186801|186802|186803|2719313|208479;2|976,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 1,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,32,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 3,28 November 2018,Fatima Zohra,WikiWorks743,Differentially abundant features of Bipolar disorder individuals in comparison to HC,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia",2|201174;2|201174|84998|84999;2|201174|84998|84999|84107;2|201174|84998,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 1,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,32,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 3,28 November 2018,Fatima Zohra,WikiWorks743,Differentially abundant features of Bipolar disorder individuals in comparison to HC,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 2,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,low IL-6,Bipolar patients with high IL-6,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),7 December 2018,Fatima Zohra,WikiWorks743,Microbiota composition in relation to inflammatory markers among bipolar patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 3,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,low total cholesterol,Bipolar patients with high total cholesterol,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),7 December 2018,Fatima Zohra,WikiWorks743,Microbiota composition in relation to lipid levels among bipolar patients,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 4,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,low LDL,Bipolar patients with high LDL,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),3 October 2019,Shaimaa Elsafoury,WikiWorks743,Microbiota composition in relation to lipid levels among bipolar patients,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 5,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,low TRP,Bipolar patients with high TRP,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),7 December 2018,Fatima Zohra,WikiWorks743,Microbiota composition in relation to tryptophan metabolites among bipolar patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|201174|84998|84999|84107;2|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 6,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,low TBARS level,Bipolar patients with high TBARS level,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),7 December 2018,Fatima Zohra,WikiWorks743,Microbiota composition in relation to markers of oxidative stress among bipolar patients,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,2|1239|186801|186802|186806|1730,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 7,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,low MDA level,Bipolar patients with high MDA level,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),7 December 2018,Fatima Zohra,WikiWorks743,Microbiota composition in relation to markers of oxidative stress among bipolar patients,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 8,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,low BMI,Bipolar patients with high BMI,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),7 December 2018,Fatima Zohra,WikiWorks743,Microbiota composition in relation to BMI among bipolar patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 9,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,no metabolic syndrome,Bipolar patients with metabolic syndrome,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),7 December 2018,Fatima Zohra,WikiWorks743,Microbiota composition in relation to metabolic syndrome among bipolar patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|201174|84998|84999|84107,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 10,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,healthier bipolar patients,Bipolar patients with depressive syndrome,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text (results),7 December 2018,Fatima Zohra,WikiWorks743,Microbiota composition in relation to depressive syndrome among bipolar patients,increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 10,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,healthier bipolar patients,Bipolar patients with depressive syndrome,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,NA,NA,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,text (results),7 December 2018,Fatima Zohra,WikiWorks743,Microbiota composition in relation to depressive syndrome among bipolar patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|31979;2|1239|186801|186802|186803|841,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 11,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,27,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,7 December 2018,Fatima Zohra,WikiWorks743,Differentially abundant features of Bipolar disorder individuals in comparison to HC after exclusion obese and diabetic patients,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia",2|201174;2|201174|84998|84999;2|201174|84998|84999|84107;2|201174|84998,Complete,Shaimaa Elsafoury
Study 34,"cross-sectional observational, not case-control",30051546,10.1111/bdi.12682,NA,"Painold A, Mörkl S, Kashofer K, Halwachs B, Dalkner N, Bengesser S, Birner A, Fellendorf F, Platzer M, Queissner R, Schütze G, Schwarz MJ, Moll N, Holzer P, Holl AK, Kapfhammer HP, Gorkiewicz G , Reininghaus EZ",A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode,Bipolar disorders,2019,Experiment 11,Austria,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,Controls,Bipolar disorder,cases followed the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)21 diagnosis of bipolar I disorder,10,27,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 1,7 December 2018,Fatima Zohra,WikiWorks743,Differentially abundant features of Bipolar disorder individuals in comparison to HC after exclusion obese and diabetic patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
Study 35,case-control,30280027,10.7717/peerj.5649,NA,"Zhou Z, Ling G, Ding N, Xun Z, Zhu C, Hua H , Chen X",Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing,PeerJ,2018,Experiment 1,China,Homo sapiens,oral gland,UBERON:0010047,Sjogren syndrome,EFO:0000699,Control,PSS,NA,23,22,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,sex",NA,decreased,decreased,unchanged,NA,decreased,NA,Signature 1,Figure 3,28 November 2018,Rimsha Azhar,WikiWorks743,Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria",2|1239|909932|1843489|31977|29465;2|1239|909932|909929;2|1239|909932|1843489|31977;2|1224|1236;2|1224,Complete,Shaimaa Elsafoury
Study 35,case-control,30280027,10.7717/peerj.5649,NA,"Zhou Z, Ling G, Ding N, Xun Z, Zhu C, Hua H , Chen X",Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing,PeerJ,2018,Experiment 1,China,Homo sapiens,oral gland,UBERON:0010047,Sjogren syndrome,EFO:0000699,Control,PSS,NA,23,22,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,"age,sex",NA,decreased,decreased,unchanged,NA,decreased,NA,Signature 2,Figure 3,28 November 2018,Rimsha Azhar,WikiWorks743,Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Actinobacteria",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|201174|1760|85006|1268|32207;2|976|200643|171549|171551|836;2|1239|186801|186802|186804|1257;2|1224|28216;2|201174|1760|2037|2049;2|1224|1236|135625|712;2|1224|28216|206351|481;2|1224|28216|206351;2|201174|1760|85006|1268;2|976|200643|171549|171551;2|201174|1760|2037;2|32066|203490;2|32066;2|32066|203490|203491;2|1239|186801;2|1239|186801|186802;2|1224|1236|135625;2|201174,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control adult,obese adolescent,NA,25,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2,1 December 2018,Marianthi Thomatos,WikiWorks743,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",2|201174|1760|2037|2049|1654;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|216572|216851|853;2|201174|1760|85009|31957|1912216|1747,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control adult,obese adolescent,NA,25,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2,1 December 2018,Marianthi Thomatos,WikiWorks743,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,2|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,contorl adolescent,obese adult,NA,20,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 2,1 December 2018,Marianthi Thomatos,WikiWorks743,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|31979;2|1239|186801|186802|186803;2|1239|186801|186802|216572|216851|853;2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,contorl adolescent,obese adult,NA,20,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 2,1 December 2018,Marianthi Thomatos,WikiWorks743,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|976|200643|171549|815|816|47678;2|976|200643|171549|2005519;2|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 3,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control adult,control adolescent,NA,12,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Table 2,9 March 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae",2|1239|186801|186802|216572|119852;2|976|200643|171549|815|816|47678;2|976|200643|171549|2005519,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 3,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control adult,control adolescent,NA,12,12,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Table 2,9 March 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota markers in obese adolescent and adult patterns: age-dependent differential patterns,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|186803;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 4,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,obese adult,obese adolescent,NA,20,25,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S4,7 October 2019,Shaimaa Elsafoury,WikiWorks743,"U Mann-Whitney test on OTUs at family/species level for the CTRL_ado, CTRL_adult, ob_ado, ob_adult groups.",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes",2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|447020;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|216572|216851|853;2|201174;2|1239,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 5,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control adolescent,obese adolescent,NA,12,25,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S4,7 October 2019,Shaimaa Elsafoury,WikiWorks743,"U Mann-Whitney test on OTUs at family/species level for the CTRL_ado, CTRL_adult, ob_ado, ob_adult groups.",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes",2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186803;2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465|29466;2|201174;2|1239,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 5,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control adolescent,obese adolescent,NA,12,25,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S4,7 October 2019,Shaimaa Elsafoury,WikiWorks743,"U Mann-Whitney test on OTUs at family/species level for the CTRL_ado, CTRL_adult, ob_ado, ob_adult groups.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes",2|976|200643|171549|815|816|47678;2|976|200643|171549|2005519;2|1239|186801|186802|216572|119852;2|976,Complete,Shaimaa Elsafoury
Study 36,case-control,29922272,10.3389/fmicb.2018.01210,NA,"Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G , Putignani L",Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns,Frontiers in microbiology,2018,Experiment 6,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control adult,obese adult,NA,12,20,2 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S4,7 October 2019,Shaimaa Elsafoury,WikiWorks743,"U Mann-Whitney test on OTUs at family/species level for the CTRL_ado, CTRL_adult, ob_ado, ob_adult groups.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",2|1239|186801|186802|216572|216851|853;2|201174|1760|85009|31957|1912216|1747,Complete,Shaimaa Elsafoury
Study 37,case-control,23733170,10.1007/s00248-013-0245-9,NA,"Wu N, Yang X, Zhang R, Li J, Xiao X, Hu Y, Chen Y, Yang F, Lu N, Wang Z, Luan C, Liu Y, Wang B, Xiang C, Wang Y, Zhao F, Gao GF, Wang S, Li L, Zhang H , Zhu B",Dysbiosis signature of fecal microbiota in colorectal cancer patients,Microbial ecology,2013,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,Healthy controls,CRC patients,NA,20,19,3 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,6 December 2018,Shaimaa Elsafoury,"WikiWorks743,Fatima",Cladogram of Colorectal cancer and healthy microbiota,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Tissierellia",2|1239|1737404|1737405|1570339|165779;2|1224|29547|213849|72294|194;2|1224|29547|213849|72294;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|236752;2|32066|203490|203491|203492;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|91061|1385|1378;2|1239|526524|526525|128827|61170;2|1224|28216|206351|481|32257;2|32066|203490|203491|1129771|32067;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186804|1257;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1239|526524|526525|128827|123375;2|1239|91061|1385|90964;2|1239|1737404,Complete,Fatima
Study 37,case-control,23733170,10.1007/s00248-013-0245-9,NA,"Wu N, Yang X, Zhang R, Li J, Xiao X, Hu Y, Chen Y, Yang F, Lu N, Wang Z, Luan C, Liu Y, Wang B, Xiang C, Wang Y, Zhao F, Gao GF, Wang S, Li L, Zhang H , Zhu B",Dysbiosis signature of fecal microbiota in colorectal cancer patients,Microbial ecology,2013,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,Healthy controls,CRC patients,NA,20,19,3 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,6 December 2018,Shaimaa Elsafoury,WikiWorks743,Cladogram of Colorectal cancer and healthy microbiota,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|186826|33958|1243;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 1,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,child head,teen head,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3, S4",9 July 2019,Rimsha Azhar,WikiWorks743,"Identification of significant microbial genera and species associated with different body sites (head, neck and underarm)",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",2|201174|1760|85009|31957|1912216;2|201174|1760|85009|31957|1912216|1747,Complete,Shaimaa Elsafoury
Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 1,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,child head,teen head,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S3, S4",9 July 2019,Rimsha Azhar,WikiWorks743,"Identification of significant microbial genera and species associated with different body sites (head, neck and underarm)",decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",2759|4751|5204|1538075|162474|742845|55193;2|1239|91061|1385|90964|1279;2759|4751|5204|1538075|162474|742845|55193|76773;2|1239|91061|1385|90964|1279|1290;2|1239|91061|1385|90964|1279|1282,Complete,Shaimaa Elsafoury
Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 2,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,child neck,teen neck,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3, S4",9 July 2019,Rimsha Azhar,WikiWorks743,"Identification of significant microbial genera and species associated with different body sites (head, neck and underarm)",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",2|201174|1760|85009|31957|1912216;2759|4751|5204|1538075|162474|742845|55193;2|201174|1760|85009|31957|1912216|1747;2759|4751|5204|1538075|162474|742845|55193|76773,Complete,Shaimaa Elsafoury
Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 2,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,child neck,teen neck,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S3, S4",9 July 2019,Rimsha Azhar,WikiWorks743,"Identification of significant microbial genera and species associated with different body sites (head, neck and underarm)",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis",2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964|1279|1290,Complete,Shaimaa Elsafoury
Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 3,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,child underarm,teen underarm,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure S3, S4",9 July 2019,Rimsha Azhar,WikiWorks743,"Identification of significant microbial genera and species associated with different body sites (head, neck and underarm)",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa",2|1239|91061|1385|90964|1279|1282;2759|4751|5204|1538075|162474|742845|55193|76773,Complete,Shaimaa Elsafoury
Study 38,"cross-sectional observational, not case-control",30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 3,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,child underarm,teen underarm,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure S3, S4",9 July 2019,Rimsha Azhar,WikiWorks743,"Identification of significant microbial genera and species associated with different body sites (head, neck and underarm)",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,2|1239|91061|1385|90964|1279|1290,Complete,Shaimaa Elsafoury
Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 1,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,after excercise,youth underarm before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,30,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,8 October 2019,Shaimaa Elsafoury,WikiWorks743,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,2|1239|91061|1385|90964|1279|1282,Complete,Shaimaa Elsafoury
Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 1,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,after excercise,youth underarm before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,30,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1& S3,8 October 2019,Shaimaa Elsafoury,WikiWorks743,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,2|1224|28211|204455|31989|265,Complete,Shaimaa Elsafoury
Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 2,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,after excercise,youth Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,30,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,8 October 2019,Shaimaa Elsafoury,WikiWorks743,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri",2|1224|1236|2887326|468|469;2|201174|1760|85009|31957|1912216|33011;2|1224|1236|2887326|468|469|108981,Complete,Shaimaa Elsafoury
Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 3,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,after excercise,Children underarm before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,8 October 2019,Shaimaa Elsafoury,WikiWorks743,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,2|1224|28211|204455|31989|265,Complete,Shaimaa Elsafoury
Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 4,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,after excercise,Children Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,8 October 2019,Shaimaa Elsafoury,WikiWorks743,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 4,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,after excercise,Children Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1& S3,8 October 2019,Shaimaa Elsafoury,WikiWorks743,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,2|201174|1760|85009|31957|1912216,Complete,Shaimaa Elsafoury
Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 5,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,after excercise,teen underarm before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,8 October 2019,Shaimaa Elsafoury,WikiWorks743,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,2|1224|28211|204455|31989|265,Complete,Shaimaa Elsafoury
Study 39,time series / longitudinal observational,30497517,10.1186/s40168-018-0588-z,NA,"Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J , Nagarajan N",Understanding the microbial basis of body odor in pre-pubescent children and teenagers,Microbiome,2018,Experiment 6,Philippines,Homo sapiens,skin of body,UBERON:0002097,body odor measurement,EFO:0008386,after excercise,teen Neck before,Malodor is a phenotype that is well known to arise from specific interactions between host-derived odor precursors and the microbial metabolism that they support,15,15,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1& S3,8 October 2019,Shaimaa Elsafoury,WikiWorks743,List of microbes at the genus level that show significant correlation with odor intensity in at least one age group,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,2|1224|1236|2887326|468|469,Complete,Shaimaa Elsafoury
Study 40,case-control,28863139,10.1371/journal.pone.0183509,NA,"Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J, Timmerman HM, Smeekens SP, Netea MG, Buitelaar JK, Franke B, van Hijum SAFT , Arias Vasquez A",Gut microbiome in ADHD and its relation to neural reward anticipation,PloS one,2017,Experiment 1,Netherlands,Homo sapiens,feces,UBERON:0001988,attention deficit hyperactivity disorder,EFO:0003888,Controls,ADHD,cases were diagnosed based on DSM-IV symptoms using the Schedule for Affective Disorders and Schizophrenia for School-Age Children,77,19,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,9 December 2018,Fatima Zohra,WikiWorks743,Differential abundance of microbial taxa for ADHD cases versus healthy controls,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales",2|201174;2|201174|1760;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|84998|1643822|1643826|84111;2|201174|1760|85004|31953|1678|28026;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|1853231|283168;2|976|200643|171549|171551;2|976|200643|171549|171550;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550|239759;2|976|200643|171549|815|909656|821;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|820;2|1224|28221;2|1224|28221|213115,Complete,Shaimaa Elsafoury
Study 40,case-control,28863139,10.1371/journal.pone.0183509,NA,"Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J, Timmerman HM, Smeekens SP, Netea MG, Buitelaar JK, Franke B, van Hijum SAFT , Arias Vasquez A",Gut microbiome in ADHD and its relation to neural reward anticipation,PloS one,2017,Experiment 1,Netherlands,Homo sapiens,feces,UBERON:0001988,attention deficit hyperactivity disorder,EFO:0003888,Controls,ADHD,cases were diagnosed based on DSM-IV symptoms using the Schedule for Affective Disorders and Schizophrenia for School-Age Children,77,19,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.1,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 3,9 December 2018,Fatima Zohra,WikiWorks743,Differential abundance of microbial taxa for ADHD cases versus healthy controls,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus",2|1239;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186803|33042|33043;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|35829;2|1239|186801|186802|186803|33042,Complete,Shaimaa Elsafoury
Study 41,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E, Maukonen J, Hyytiäinen T, Kieseppä T, Orešič M, Sabunciyan S, Mantere O, Saarela M, Yolken R , Suvisaari J",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,psychosis,EFO:0005407,Controls,FIrst episode Psychosis,NA,16,28,3 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,10 December 2018,Fatima Zohra,WikiWorks743,Taxonomic differences of fecal microbiota between first episode psychosis patients and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Chromatiales|f__Halothiobacillaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Tropherymataceae|g__Tropheryma,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Saccharophagus,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Haloferacales|f__Halorubraceae|g__Halorubrum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Deferribacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Chromatiales|f__Halothiobacillaceae|g__Halothiobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Deferribacter|s__Deferribacter desulfuricans,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cenocepacia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulfosporosinus|s__Desulfosporosinus acidiphilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Chromatiales|f__Halothiobacillaceae|g__Halothiobacillus|s__Halothiobacillus neapolitanus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Saccharophagus|s__Saccharophagus degradans,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Thiotrichales|f__Francisellaceae|g__Francisella|s__Francisella hispaniensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Tropherymataceae|g__Tropheryma|s__Tropheryma whipplei,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella canis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Haloferacales|f__Halorubraceae|g__Halorubrum|s__Halorubrum lacusprofundi,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Chromatiales|f__Chromatiaceae|g__Nitrosococcus|s__Nitrosococcus halophilus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella|s__Bartonella clarridgeiae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium",2|1224|28211|356|118882;2|1239|91061|186826|33958;2|1224|1236|135613|255526;2|201174|1760|85006|2805591|2038;2|1224|28211|356|118882|528;2|1224|1236|1706369|1706371|316625;2157|28890|183963|1644055|1963271|56688;2|1239|91061|186826|33958|1578;2|200930|68337|191393|191394|53572;2|1224|1236|135613|255526|109262;2|1239|91061|186826|33958|1578|1579;2|200930|68337|191393|191394|53572|197162;2|1224|28216|80840|119060|32008|95486;2|1239|186801|186802|186807|79206|885581;2|1224|1236|135613|255526|109262|927;2|1224|1236|1706369|1706371|316625|86304;2|1224|1236|72273|34064|262|622488;2|201174|1760|85006|2805591|2038|2039;2|1224|28211|356|118882|234|36855;2|1239|91061|186826|33958|1578|33959;2157|28890|183963|1644055|1963271|56688|2247;2|1239|91061|186826|33958|2742598|1598;2|1224|1236|135613|1046|1227|133539;2|1224|28211|356|772|773|56426;2|1224|28211|356|118882|234|529;2|1239|91061|1385;2|1224|28211|356;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|1578|1596;2|201174|1760|85004|31953|1678|1689,Complete,Shaimaa Elsafoury
Study 41,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E, Maukonen J, Hyytiäinen T, Kieseppä T, Orešič M, Sabunciyan S, Mantere O, Saarela M, Yolken R , Suvisaari J",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,psychosis,EFO:0005407,Controls,FIrst episode Psychosis,NA,16,28,3 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,10 December 2018,Fatima Zohra,"WikiWorks743,Lwaldron",Taxonomic differences of fecal microbiota between first episode psychosis patients and healthy controls,decreased,"k__Bacteria|p__Cyanobacteria|o__Nostocales|f__Nostocaceae|g__Anabaena,k__Bacteria|p__Chlorobi|c__Chlorobia|o__Chlorobiales|f__Chlorobiaceae|g__Chlorobium|s__Chlorobium chlorochromatii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Gallionellaceae|g__Gallionella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Gallionellaceae|g__Gallionella|s__Gallionella capsiferriformans,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosomonas|s__Nitrosomonas sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosospira,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosospira|s__Nitrosospira multiformis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Archaea|p__Euryarchaeota|c__Thermococci|o__Thermococcales|f__Thermococcaceae|g__Thermococcus|s__Thermococcus gammatolerans,k__Bacteria|p__Cyanobacteria|o__Nostocales|f__Nostocaceae|g__Trichormus|s__Trichormus variabilis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Xenorhabdus|s__Xenorhabdus nematophila,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc gelidum|s__Leuconostoc gelidum subsp. gasicomitatum",2|1117|1161|1162|1163;2|1090|191410|191411|191412|1091|337090;2|1224|28216|32003|90627|96;2|1224|28216|32003|90627|96|370405;2|1239|909932;2|1224|28216|32003|206379|914|42353;2|1224|28216|32003|206379|35798;2|1224|28216|32003|206379|35798|1231;2|1239|909932|909929;2157|28890|183968|2258|2259|2263|187878;2|1117|1161|1162|264688|264691;2|1239|909932|1843489|31977;2|1224|1236|91347|1903414|626|628;2|1239|91061|186826|33958|1243|1244|115778,Complete,Shaimaa Elsafoury
Study 41,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E, Maukonen J, Hyytiäinen T, Kieseppä T, Orešič M, Sabunciyan S, Mantere O, Saarela M, Yolken R , Suvisaari J",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,psychosis,EFO:0005407,Controls,FIrst episode Psychosis (physically active),NA,16,15,3 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 1+results (text),10 December 2018,Fatima Zohra,WikiWorks743,Taxonomic differences of fecal microbiota between physically active psychosis patients and healthy controls,increased,"k__Archaea|p__Crenarchaeota|c__Thermoprotei|o__Thermoproteales|f__Thermoproteaceae,k__Archaea|p__Crenarchaeota|c__Thermoprotei|o__Thermoproteales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2157|28889|183924|2266|2267;2157|28889|183924|2266;2|1239|91061|186826|33958,Complete,NA
Study 41,case-control,28442250,10.1016/j.schres.2017.04.017,NA,"Schwarz E, Maukonen J, Hyytiäinen T, Kieseppä T, Orešič M, Sabunciyan S, Mantere O, Saarela M, Yolken R , Suvisaari J",Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response,Schizophrenia research,2018,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,psychosis,EFO:0005407,Controls,FIrst episode Psychosis (physically active),NA,16,15,3 months,16S,NA,Illumina,LEfSe,0.05,FALSE,2,"age,region of residence,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 1+results (text),10 December 2018,Fatima Zohra,WikiWorks743,Taxonomic differences of fecal microbiota between physically active psychosis patients and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932;2|1239|909932|909929;2|1239|909932|1843489|31977,Complete,NA
Study 42,case-control,30483228,10.3389/fmicb.2018.02682,NA,"Guo C, Li Y, Wang P, Li Y, Qiu C, Li M, Wang D, Zhao R, Li D, Wang Y, Li S, Dai W , Zhang L",Alterations of Gut Microbiota in Cholestatic Infants and Their Correlation With Hepatic Function,Frontiers in microbiology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,extrahepatic cholestasis,EFO:1000933,healthy infants,cholestasis infants,NA,37,43,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2+ text,13 December 2018,Christina Brown,WikiWorks743,Differentially abundundant gut microbiota in cholestatic infants vs healthy infants,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|1239|91061|186826|1300|1301;2|1239|91061|186826|81852|1350;2|1239|91061|1385|90964|1279;2|1239|909932|1843489|31977|906;2|1224|28211|356|69277|28100;2|1239|909932|909929|1843491|158846,Complete,Shaimaa Elsafoury
Study 42,case-control,30483228,10.3389/fmicb.2018.02682,NA,"Guo C, Li Y, Wang P, Li Y, Qiu C, Li M, Wang D, Zhao R, Li D, Wang Y, Li S, Dai W , Zhang L",Alterations of Gut Microbiota in Cholestatic Infants and Their Correlation With Hepatic Function,Frontiers in microbiology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,extrahepatic cholestasis,EFO:1000933,healthy infants,cholestasis infants,NA,37,43,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2 + text,13 December 2018,Christina Brown,WikiWorks743,Differentially abundundant gut microbiota in cholestatic infants vs healthy infants,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|201174|1760|85004|31953|1678;2|976|200643|171549|815|816;2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|207244;2|201174|84998|84999|84107|102106,Complete,Shaimaa Elsafoury
Study 43,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H , Sawalha AH",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,Experiment 1,Turkey,Homo sapiens,oral gland,UBERON:0010047,Behcet's syndrome,EFO:0003780,controls,behcet's disease,NA,15,31,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Table 4,13 December 2018,Rimsha Azhar,WikiWorks743,The LEfSe analysis revealed 22 OTUs with a consistent and significant overabundance in either patients or controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|1224|1236|135625|712|724|729;2|976|200643|171549|171552|1283313,Complete,Shaimaa Elsafoury
Study 43,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H , Sawalha AH",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,Experiment 1,Turkey,Homo sapiens,oral gland,UBERON:0010047,Behcet's syndrome,EFO:0003780,controls,behcet's disease,NA,15,31,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Table 4,13 December 2018,Rimsha Azhar,WikiWorks743,The LEfSe analysis revealed 22 OTUs with a consistent and significant overabundance in either patients or controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella enoeca",2|976|200643|171549|171552|1283313|671218;2|1224|29547|213849|72294|194|199;2|32066|203490|203491|1129771|32067|104608;2|1239|909932|909929|1843491|970|2053611;2|1239|186801|186802;2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171552|838|60133;2|201174|84998|84999|1643824|2767353|1382;2|1239|186801|186802|186803;2|976;2|1239|186801|186802|186803|1164882|979627;2|1239|526524|526525|128827|123375|102148;2|1239|909932|1843489|31977|29465|1926307;2|976|200643|171549|171552|838|76123,Complete,Shaimaa Elsafoury
Study 43,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H , Sawalha AH",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,Experiment 2,Turkey,Homo sapiens,oral gland,UBERON:0010047,Behcet's syndrome,EFO:0003780,non-immunosuppressent users among behcet's patients,immunosuppressant users,NA,19,12,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text,10 October 2019,Shaimaa Elsafoury,WikiWorks743,the association between the use of immunosuppressants in BD patients with gut microbiota,increased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas catoniae",2|976|117743|200644|2762318|59735;2|976|200643|171549|171552|838;2|976|200643|171549|171551|836|41976,Complete,Shaimaa Elsafoury
Study 43,case-control,27283393,10.1016/j.clim.2016.06.002,NA,"Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H , Sawalha AH",Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease,"Clinical immunology (Orlando, Fla.)",2016,Experiment 2,Turkey,Homo sapiens,oral gland,UBERON:0010047,Behcet's syndrome,EFO:0003780,non-immunosuppressent users among behcet's patients,immunosuppressant users,NA,19,12,6 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,text,10 October 2019,Shaimaa Elsafoury,WikiWorks743,the association between the use of immunosuppressants in BD patients with gut microbiota,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella baroniae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.",2|976|200643|171549|171552|838|305719;2|1239|186801|186802|186803|265975|1969407,Complete,Shaimaa Elsafoury
Study 44,case-control,27450202,10.1111/1462-2920.13463,NA,"Riva A, Borgo F, Lassandro C, Verduci E, Morace G, Borghi E , Berry D",Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations,Environmental microbiology,2017,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,pediatric obese,NA,36,42,6 months,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,Table 1 & Supplementary Table 5,15 December 2018,Marianthi Thomatos,WikiWorks743,Differential abundance in pediatric obesity  versus normal weight  controls,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
Study 44,case-control,27450202,10.1111/1462-2920.13463,NA,"Riva A, Borgo F, Lassandro C, Verduci E, Morace G, Borghi E , Berry D",Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations,Environmental microbiology,2017,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,pediatric obese,NA,36,42,6 months,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,Table 1 & Supplementary Table 5,15 December 2018,Marianthi Thomatos,WikiWorks743,Differential abundance in pediatric obesity  versus normal weight  controls,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris",2|976;2|976|200643;2|976|200643|171549;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|815|909656|821;2|976|200643|171549|815|816|46506,Complete,Shaimaa Elsafoury
Study 45,laboratory experiment,30466372,10.1080/1028415X.2018.1537169,NA,"Reichelt AC, Loughman A, Bernard A, Raipuria M, Abbott KN, Dachtler J, Van TTH , Moore RJ","An intermittent hypercaloric diet alters gut microbiota, prefrontal cortical gene expression and social behaviours in rats",Nutritional neuroscience,2018,Experiment 1,Australia,Rattus norvegicus,feces,UBERON:0001988,obesity,EFO:0001073,control rats,Rats fed  HFHS,NA,8,8,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3a & 3b,15 December 2018,Marianthi Thomatos,WikiWorks743,Relative abundance of rats fed high fat and high surgar diet (HFHS) VS. Controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum",2|1239|186801|186802|186803|572511;2|201174|1760|85004|31953|1678;2|1239|909932|1843488|909930|33024;2|1239|526524|526525|128827|174708,Complete,Shaimaa Elsafoury
Study 46,case-control,27007700,10.1089/chi.2015.0194,NA,"Borgo F, Verduci E, Riva A, Lassandro C, Riva E, Morace G , Borghi E",Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study,Childhood obesity (Print),2017,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,pediatric obese,NA,33,28,previous month,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, figure 2",16 December 2018,Marianthi Thomatos,"WikiWorks743,Fatima",Relative abundance of bacterial and fungal gut microbes in obese children vs. controls,decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces sp.,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|g__Candida|s__Candida sp. (in: Saccharomycetales)",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171552|838;2759|4751|4890|4891|4892|4893|4930|4935;2759|4751|4890|4891|4892|5475|1853550,Complete,Fatima
Study 47,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner CM, Maldonado J, Dente B, Krajmalnik-Brown R , Bruening M","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,high dietary fiber,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Text and figure 4,16 December 2018,Marianthi Thomatos,WikiWorks743,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|2005519;2|1224|28211;2|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
Study 47,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner CM, Maldonado J, Dente B, Krajmalnik-Brown R , Bruening M","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,high dietary fiber,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Text and figure 4,16 December 2018,Marianthi Thomatos,WikiWorks743,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,decreased,k__Bacteria|p__Tenericutes,2|544448,Complete,Shaimaa Elsafoury
Study 47,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner CM, Maldonado J, Dente B, Krajmalnik-Brown R , Bruening M","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,hight moderate to vigrous physical activity,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text and figure 4,15 October 2019,Shaimaa Elsafoury,WikiWorks743,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales",2|1224|1236|91347|543;2|1224|1236|91347,Complete,Shaimaa Elsafoury
Study 47,"cross-sectional observational, not case-control",30541450,10.1186/s12866-018-1362-x,NA,"Whisner CM, Maldonado J, Dente B, Krajmalnik-Brown R , Bruening M","Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study",BMC microbiology,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,hight moderate to vigrous physical activity,low,BMI ≥ 30.0 kg/m2 was considered obese,68,68,2-3 months,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text and figure 4,15 October 2019,Shaimaa Elsafoury,WikiWorks743,Relative abundance of fiber intake in a cohort of diverse cohort of first year college students living in university housing,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control adolescent,obese adolescent,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2 and Table 3,16 December 2018,Marianthi Thomatos,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552;2|1224|28216|80840|995019;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control adolescent,obese adolescent,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2 and Table 3,16 December 2018,Marianthi Thomatos,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|976|200643|171549|815;2|976|200643|171549|171550;2|1239|186801|186802|541000;2|976|200643|171549|815|816;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|459786,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low BMI zscores,high BMI zscore,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,9 March 2019,Marianthi Thomatos,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low BMI zscores,high BMI zscore,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,9 March 2019,Marianthi Thomatos,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|815|816;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low triglycerides,high triglycerides,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,15 October 2019,Shaimaa Elsafoury,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low triglycerides,high triglycerides,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,15 October 2019,Shaimaa Elsafoury,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 4,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low total cholesterol,high total cholesterol,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,15 October 2019,Shaimaa Elsafoury,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 5,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low HDL-C,high HDL-C,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,15 October 2019,Shaimaa Elsafoury,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 6,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low sensetive C reactive protein,high senstive C reactive protein,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 4,15 October 2019,Shaimaa Elsafoury,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 48,case-control,26230509,10.1371/journal.pone.0134333,NA,"Hu HJ, Park SG, Jang HB, Choi MK, Choi MG, Park KH, Kang JH, Park SI, Lee HJ , Cho SH",Obesity Alters the Microbial Community Profile in Korean Adolescents,PloS one,2015,Experiment 6,South Korea,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low sensetive C reactive protein,high senstive C reactive protein,"body mass index BMI >= 30 kg/m2, or >= 99th BMI percentile",67,67,1 month,16S,123,Roche454,Spearman Correlation,0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 4,15 October 2019,Shaimaa Elsafoury,WikiWorks743,Relative microbial abundance in obese Korean adolescents (13-16 year old),decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|976|200643|171549|815|816;2|1239|186801|186802|216572|459786,Complete,Shaimaa Elsafoury
Study 49,case-control,29576948,10.7717/peerj.4458,NA,"Wu Y, Chi X, Zhang Q, Chen F , Deng X",Characterization of the salivary microbiome in people with obesity,PeerJ,2018,Experiment 1,China,Homo sapiens,oral gland,UBERON:0010047,obesity,EFO:0001073,controls,Obesity group,obesity group (BMI ≥30),29,33,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 2,17 December 2018,Rimsha Azhar,"WikiWorks743,Lwaldron",Differentially abundant taxa between people with obesity and normal weight control,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|976|200643|171549;2|976|200643;2|1224|1236|135615|868;2|1239|91061|186826|186828;2|1239|186801|186802|186803|43996;2|1224|28216|80840|80864;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|91061|186826|186828|117563;2|1239|186801|186802|543314|86331;2|1239|186801|186802|186807;2|1239|186801|186802|186804|1257;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|526524|526525|128827|123375;2|1224|28211|356|335928;2|1239|186801|186802|186804,Complete,Shaimaa Elsafoury
Study 49,case-control,29576948,10.7717/peerj.4458,NA,"Wu Y, Chi X, Zhang Q, Chen F , Deng X",Characterization of the salivary microbiome in people with obesity,PeerJ,2018,Experiment 1,China,Homo sapiens,oral gland,UBERON:0010047,obesity,EFO:0001073,controls,Obesity group,obesity group (BMI ≥30),29,33,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 2,17 December 2018,Rimsha Azhar,WikiWorks743,Differentially abundant taxa between people with obesity and normal weight control,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas",2|1224|1236;2|976|117743;2|1224|1236|135625;2|1224|28216|80840;2|976|117743|200644;2|201174|1760|85007;2|1224|1236|135615;2|1224|1236|135614;2|1224|1236|135625|712;2|1224|28216|80840|119060;2|976|117743|200644|49546;2|201174|1760|85007|1653;2|1224|1236|135625|712|724;2|1224|1236|135615|868|2717;2|1239|91061|1385|90964;2|976|117743|200644|49546|1016;2|1224|28216|80840|119060|47670;2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279;2|1224|1236|135614|32033|40323,Complete,Shaimaa Elsafoury
Study 50,case-control,21850056,10.1038/ismej.2011.109,NA,"Wang T, Cai G, Qiu Y, Fei N, Zhang M, Pang X, Jia W, Cai S , Zhao L",Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers,The ISME journal,2012,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy controls,Colrectal cancer patients,All patients were categorized according to histopathological features by TNM classification of malignant tumors after surgery,56,46,3 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks743,List of genera that were significantly different between Healthy controls and Colorectal cancer patients,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|976|200643|171549|171551|836;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186804|1257,Complete,Shaimaa Elsafoury
Study 50,case-control,21850056,10.1038/ismej.2011.109,NA,"Wang T, Cai G, Qiu Y, Fei N, Zhang M, Pang X, Jia W, Cai S , Zhao L",Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers,The ISME journal,2012,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy controls,Colrectal cancer patients,All patients were categorized according to histopathological features by TNM classification of malignant tumors after surgery,56,46,3 months,16S,3,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,table 2,10 January 2021,Shaimaa Elsafoury,WikiWorks743,List of genera that were significantly different between Healthy controls and Colorectal cancer patients,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella",2|976|200643|171549|815|816;2|1239|186801|186802|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|186806|1730;2|1224|28216|80840|995019|577310,Complete,Shaimaa Elsafoury
Study 51,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R , Wei Y",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,postoperation patients,Carcinoma patients,The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,47,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Supplemental Figure 5 and Table S2,8 January 2019,Rimsha Azhar,WikiWorks743,The relative abundance of genus in carcinoma and postoperative patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|150022;2|1224|28216|80840|119060|48736;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|404402;2|976|200643|171549|171552|1283313;2|201174|1760|85007|1653|1716;2|1239|526524|526525|2810280|135858;2|1239|526524|526525|128827|1573535;2|1239|1737404|1737405|1570339|543311;2|1224|1236|72274|135621|286;2|1239|91061|1385|1378;2|1239|186801|186802|186804|1257;2|976|200643|171549|171551|836;2|1239|91061|186826|33958|46255;2|1239|91061|186826|186828|117563;2|201174|1760|2037|2049|1654,Complete,Shaimaa Elsafoury
Study 51,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R , Wei Y",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,postoperation patients,Carcinoma patients,The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,47,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Supplemental Figure 5 and Table S2,8 January 2019,Rimsha Azhar,WikiWorks743,The relative abundance of genus in carcinoma and postoperative patients,decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus",2|32066|203490|203491|1129771|32067;2|201174|1760|85004|31953|196082;2|201174|1760|85004|31953|1678;2|201174|1760|85006|85023|33882;2|201174|1760|85007|2805586|1847725;2|1239|526524|526525|128827|1573534;2|1224|28216|80840|995019|40544;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|1506577;2|1224|1236|91347|543|570;2|1239|186801|186802|186803|2316020|33038,Complete,Shaimaa Elsafoury
Study 51,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R , Wei Y",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,CIT(cleain intestine),NDA(new dev. adenoma),The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,26,21,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2.5,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 4 and Table B,8 January 2019,Rimsha Azhar,WikiWorks743,LEfSe identified differene in abundace between NDA and CIT,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",2|1239|91061|186826|186827|46123;2|201174|84998|84999|1643824|1380;2|1224|1236|91347|1903414|581;2|976|200643|171549|171552|838;2|1239|526524|526525|128827|123375,Complete,Shaimaa Elsafoury
Study 51,case-control,30548192,10.1111/1462-2920.14498,NA,"Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R , Wei Y",Gut microbiota in patients after surgical treatment for colorectal cancer,Environmental microbiology,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,CIT(cleain intestine),NDA(new dev. adenoma),The adenoma and carcinoma patients were diagnosed by colonoscopic examination and histopathological review of biopsies. Postoperative patients were classified as having NDA or CIT by follow-up surveillance colonoscopy and biopsies,26,21,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2.5,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 4 and Table B,8 January 2019,Rimsha Azhar,WikiWorks743,LEfSe identified differene in abundace between NDA and CIT,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",2|976|200643|171549|1853231|574697;2|1239|186801|186802|216572|1263;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803|33042;2|1239|1737404|1737405|1570339|150022;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186803|437755;2|1239|186801|186802|216572|459786;2|1224|28221|213115|194924|872;2|1239|186801|186802|216572|244127,Complete,Shaimaa Elsafoury
Study 52,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y, Xie Z, Wang H, Shen Z, Guo Y, Gao Y, Chen X, Wu Q, Li X , Wang K",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,substance-related disorder,MONDO:0002494,Healthy controls,Substance use disorder patients,NA,45,48,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,increased,Signature 1,Figure 4,9 January 2019,Fatima Zohra,WikiWorks743,Differential abundance in community compositions between SUD and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera",2|976|200643|171549|171552;2|1224|28211|204455|31989;2|1224|28216|206389|75787;2|1224|28211;2|976|200643|171549|171552|838;2|1224|28211|204455|31989|265;2|1239|186801|186802|31979|1485;2|1224|28216|206389|2008794|33057,Complete,Shaimaa Elsafoury
Study 52,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y, Xie Z, Wang H, Shen Z, Guo Y, Gao Y, Chen X, Wu Q, Li X , Wang K",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,substance-related disorder,MONDO:0002494,Healthy controls,Substance use disorder patients,NA,45,48,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,unchanged,NA,NA,increased,Signature 2,Figure 4,9 January 2019,Fatima Zohra,WikiWorks743,Differential abundance in community compositions between SUD and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|976|200643|171549|815;2|976|200643|171549|171550;2|1224|1236|91347|543;2|1239|526524|526525|128827;2|1224|28221|213115|194924;2|1239|91061;2|1239|526524;2|1224|28221;2|1224|28221|213115|194924|35832;2|1239|186801|186802|186803|189330;2|976|200643|171549|2005525|375288;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|207244;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803|1407607;2|976|200643|171549|171550|239759;2|1239|186801|186802|204475;2|976|200643|171549|815|816;2|1239|526524|526525;2|1239|91061|186826;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300,Complete,Shaimaa Elsafoury
Study 52,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y, Xie Z, Wang H, Shen Z, Guo Y, Gao Y, Chen X, Wu Q, Li X , Wang K",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,substance-related disorder,MONDO:0002494,adjusted Healthy controls,Substance use disorder patients,NA,28,29,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 5B,9 January 2019,Fatima Zohra,WikiWorks743,Significantly different microbial composition between SUD and age matched healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206389|2008794|33057;2|1224|28211|204455|31989|265;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 52,case-control,28620208,10.1038/s41598-017-03706-9,NA,"Xu Y, Xie Z, Wang H, Shen Z, Guo Y, Gao Y, Chen X, Wu Q, Li X , Wang K",Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing,Scientific reports,2017,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,substance-related disorder,MONDO:0002494,adjusted Healthy controls,Substance use disorder patients,NA,28,29,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 5B,9 January 2019,Fatima Zohra,WikiWorks743,Significantly different microbial composition between SUD and age matched healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter",2|1239|186801|186802|186803|207244;2|976|200643|171549|2005525|375288;2|1239|186801|186802|204475;2|1224|28221|213115|194924|35832;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803|1407607,Complete,Shaimaa Elsafoury
Study 53,case-control,26683192,10.1371/journal.pone.0145453,NA,"Shukla SK, Cook D, Meyer J, Vernon SD, Le T, Clevidence D, Robertson CE, Schrodi SJ, Yale S , Frank DN",Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS),PloS one,2015,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,chronic fatigue syndrome,EFO:0004540,healthy controls,chronic fatigue syndrome patients,patients met the ME/CFS case definition criteria established by Fukuda et al in 1994,10,10,current use,16S,NA,Roche454,Kolmogorov-Smirnov Test,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,10 January 2019,Shaimaa Elsafoury,WikiWorks743,Relative Abundance of Bacterial Phyla in Blood and Stool Samples from ME/CFS Patients and Health Controls.,decreased,k__Bacteria|p__Acidobacteria,2|57723,Complete,Shaimaa Elsafoury
Study 54,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado MC, Rautava S, Aakko J, Isolauri E , Salminen S",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,Experiment 1,Finland,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,placenta,meconium,NA,15,15,prior to or during c-section,16S,123,Roche454,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,decreased,NA,NA,unchanged,Signature 1,Figure 4B,16 January 2019,Rimsha Azhar,WikiWorks743,Differentially abundant bacteria in placenta and meconium samples from LEfSe analysis,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae",2|1239|91061|186826|1300;2|1239|91061|1385|186817,Complete,Shaimaa Elsafoury
Study 54,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado MC, Rautava S, Aakko J, Isolauri E , Salminen S",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,Experiment 1,Finland,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,placenta,meconium,NA,15,15,prior to or during c-section,16S,123,Roche454,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,decreased,NA,NA,unchanged,Signature 2,Figure 4B,16 January 2019,Rimsha Azhar,WikiWorks743,Differentially abundant bacteria in placenta and meconium samples from LEfSe analysis,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Shaimaa Elsafoury
Study 54,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado MC, Rautava S, Aakko J, Isolauri E , Salminen S",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,Experiment 2,Finland,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,placenta,colostrum,NA,15,15,prior to or during c-section,16S,123,Roche454,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,Figure 4D,16 January 2019,Rimsha Azhar,WikiWorks743,Differentially abundant bacteria in placenta and colostrum samples from LEfSe analysis,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|91061|1385|186817;2|1239|91061|186826|1300,Complete,Shaimaa Elsafoury
Study 54,time series / longitudinal observational,27001291,10.1038/srep23129,NA,"Collado MC, Rautava S, Aakko J, Isolauri E , Salminen S",Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid,Scientific reports,2016,Experiment 2,Finland,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,placenta,colostrum,NA,15,15,prior to or during c-section,16S,123,Roche454,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,Figure 4D,16 January 2019,Rimsha Azhar,WikiWorks743,Differentially abundant bacteria in placenta and colostrum samples from LEfSe analysis,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,Shaimaa Elsafoury
Study 55,laboratory experiment,23056268,10.1371/journal.pone.0046231,NA,"Bangsgaard Bendtsen KM, Krych L, Sørensen DB, Pang W, Nielsen DS, Josefsen K, Hansen LH, Sørensen SJ , Hansen AK",Gut microbiota composition is correlated to grid floor induced stress and behavior in the BALB/c mouse,PloS one,2012,Experiment 1,Denmark,Mus musculus,caecum,UBERON:0001153,stimulus or stress design,EFO:0001762,control,grid floor induced stress,cases were exposed to a stress factor which is a grid floor exposure for two weeks. this implies that the use of grid floor is a sufficient stressor for inducing a depression-like behavioral state in the TST.,14,14,NA,16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,23 January 2019,Fatima Zohra,WikiWorks743,Significantly different taxa between control mice and grid floor housed mice,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|1853231|283168;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
Study 56,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H , Peter I",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,Experiment 1,United States of America,Homo sapiens,meconium,UBERON:0007109,type II diabetes mellitus,MONDO:0005148,adult stool,Healthy baby meconium,NA,9,13,9 months,16S,34,PacBio RS,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 2,23 January 2019,Rimsha Azhar,WikiWorks743,Bacterial Composition of the Meconium and Comparison to the healthy Adult and healthy Infant Microbiome,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1224;2|1224|28216|80840|80864;2|1224|1236|91347|543;2|1224|28216|80840|80864|283;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570;2|1224|1236|91347|1903414|583;2|1224|1236|91347|543|620,Complete,Shaimaa Elsafoury
Study 56,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H , Peter I",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,Experiment 1,United States of America,Homo sapiens,meconium,UBERON:0007109,type II diabetes mellitus,MONDO:0005148,adult stool,Healthy baby meconium,NA,9,13,9 months,16S,34,PacBio RS,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text + Figure 2,23 January 2019,Rimsha Azhar,WikiWorks743,Bacterial Composition of the Meconium and Comparison to the healthy Adult and healthy Infant Microbiome,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976;2|1239;2|74201;2|976|200643|171549|815;2|1239|186801|186802|186803;2|1239|186801|186802|541000;2|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
Study 56,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H , Peter I",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,Experiment 2,United States of America,Homo sapiens,meconium,UBERON:0007109,gestational diabetes,EFO:0004593,Healthy baby meconium,Baby meconium with GDM mothers,NA,13,5,9 months,16S,34,PacBio RS,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 4,28 March 2019,Rimsha Azhar,WikiWorks743,Significant difference between neonates from mothers with different diabetes states,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas",2|1224|28216;2|1224|28211|356|118882;2|1224|28216|80840|506;2|1224|28216|80840|80864;2|1224|28211|356|335928;2|1224|28216|80840|506|507;2|1224|28216|80840|119060|106589;2|1224|28216|80840|80864|283;2|1224|28216|80840|80864|80865;2|1224|1236|135614|32033|40323,Complete,Shaimaa Elsafoury
Study 56,"cross-sectional observational, not case-control",24223144,10.1371/journal.pone.0078257,NA,"Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H , Peter I",Diversified microbiota of meconium is affected by maternal diabetes status,PloS one,2013,Experiment 3,United States of America,Homo sapiens,meconium,UBERON:0007109,type II diabetes mellitus,MONDO:0005148,Healthy baby meconium,Baby meconium with DM mothers,NA,13,5,9 months,16S,34,PacBio RS,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text + Figure 4,28 March 2019,Rimsha Azhar,"WikiWorks743,Lwaldron",Significant difference between neonates from mothers with different diabetes states,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Intrasporangiaceae|g__Arsenicicoccus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Planomicrobium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|28211|204441|433;2|1239|909932|1843488|909930|904;2|201174|1760|85006|85021|267408;2|201174|84998|84999|1643824|1380;2|976|200643|171549|815;2|976;2|976|200643;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|976|200643|171549|1853231|574697;2|1239|526524|526525|2810280|135858;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186803|33042;2|201174|84998|84999|84107;2|201174|1760|85006|85020;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|189330;2|976|200643|171549|2005520|156973;2|1239|526524|526525|128827;2|1239|526524;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|91061|1385|1378;2|201174|1760|85007|85026|2053;2|1239|526524|526525|128827|61170;2|201174|1760|85006|1268|57493;2|1239|186801|186802|186803;2|201174|1760|85006|85023|33882;2|201174|1760|1643682|85030|88138;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|1224|28211|356|69277;2|1239|91061|1385|186818|162291;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|186801|186802|186803|841;2|1224|28211|204441|433|125216;2|1239|186801|186802|216572|1263;2|1239|526524|526525|2810281|191303;2|1239|909932|1843489|31977,Complete,Fatima
Study 57,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG , Henderson WA",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,Experiment 1,United States of America,Homo sapiens,buccal mucosa,UBERON:0006956,inflammatory bowel disease,EFO:0003767,control,irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,9,NA,16S,NA,PhyloChip,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,6 June 2019,Rimsha Azhar,WikiWorks743,OTUs showed significant differential abundance between healthy controls and IBS participants,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulfosporosinus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|976|200643|171549|171552|838;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186807|79206;2|1239|186801|186802|186804|1257;2|1224|28216|80840|506|507;2|1224|28216|80840|119060|32008;2|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
Study 57,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG , Henderson WA",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,Experiment 1,United States of America,Homo sapiens,buccal mucosa,UBERON:0006956,inflammatory bowel disease,EFO:0003767,control,irritable bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,9,NA,16S,NA,PhyloChip,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,6 June 2019,Rimsha Azhar,WikiWorks743,OTUs showed significant differential abundance between healthy controls and IBS participants,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1743;2|1239|91061|186826|1300|1301;2|1224|28211|204457|41297|13687;2|1224|1236|72274|135621|286,Complete,Shaimaa Elsafoury
Study 57,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG , Henderson WA",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,Experiment 2,United States of America,Homo sapiens,buccal mucosa,UBERON:0006956,inflammatory bowel disease,EFO:0003767,control,overweight irritabe bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,11,NA,16S,NA,PhyloChip,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,6 June 2019,Rimsha Azhar,WikiWorks743,OTUs showed significant differential abundance between healthy controls and IBS participants,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Planomicrobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85007|1653|1716;2|201174|1760|85004|31953|1678;2|201174|84998|84999|1643824|1380;2|201174|84998|84999|1643824|133925;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186818|162291;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186806|113286;2|1239|186801|186802|186803|265975;2|1239|186801|186802|186803|177971;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|970;2|1224|28216|80840|92793;2|1224|28216|80840|80864|80865;2|1224|29547|213849|72294|194;2|1224|1236|72274|135621|286;2|203691|203692|136|2845253|157;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
Study 57,case-control,26963804,10.1080/19490976.2016.1162363,NA,"Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG , Henderson WA",The microbiome of the oral mucosa in irritable bowel syndrome,Gut microbes,2016,Experiment 2,United States of America,Homo sapiens,buccal mucosa,UBERON:0006956,inflammatory bowel disease,EFO:0003767,control,overweight irritabe bowel syndrome,IBS are who suffered from chronic visceral pain and altered bowel habits for more than 6 months for which no organic cause had been identified,20,11,NA,16S,NA,PhyloChip,Welch's T-Test,0.05,FALSE,NA,"age,body weight,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,6 June 2019,Rimsha Azhar,WikiWorks743,OTUs showed significant differential abundance between healthy controls and IBS participants,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Aestuariimicrobium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Haloanella,k__Bacteria|p__Chloroflexi|c__Dehalococcoidia|g__Dehalogenimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85009|31957|396388;2|976|117743|200644|2762318|59732;2|976|117743|200644|49546|109244;2|200795|301297|670486;2|1239|91061|1385|1378;2|1239|91061|186826|1300|1301;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
Study 58,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M , Aagaard KM",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,Experiment 1,United States of America,Homo sapiens,meconium,UBERON:0007109,high fat diet,EFO:0002757,nebowrns of maternal control,newborns of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",13,13,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,29 January 2019,Rimsha Azhar,WikiWorks743,Neonaatal meconium identified by  LEfSe betwen maternal high-fat or maternal control diet during pregnancy,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|91061|186826|1300|1357;2|1239|91061|186826|186828|117563;2|1239|91061|186826|81852|1350,Complete,Shaimaa Elsafoury
Study 58,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M , Aagaard KM",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,Experiment 1,United States of America,Homo sapiens,meconium,UBERON:0007109,high fat diet,EFO:0002757,nebowrns of maternal control,newborns of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",13,13,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,29 January 2019,Rimsha Azhar,WikiWorks743,Neonaatal meconium identified by  LEfSe betwen maternal high-fat or maternal control diet during pregnancy,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas",2|1224|28216|80840|995019|40544;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|816;2|1224|28216|80840|80864|283,Complete,Shaimaa Elsafoury
Study 58,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M , Aagaard KM",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,high fat diet,EFO:0002757,6 months babies control,6 months babies of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",75,75,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5 + Supplemental Figure 3,29 January 2019,Rimsha Azhar,WikiWorks743,The impact of maternal gestational diet persists to 6 weeks of age,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|561,Complete,Shaimaa Elsafoury
Study 58,prospective cohort,27503374,10.1186/s13073-016-0330-z,NA,"Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M , Aagaard KM",The early infant gut microbiome varies in association with a maternal high-fat diet,Genome medicine,2016,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,high fat diet,EFO:0002757,6 months babies control,6 months babies of maternal high-fat diet,"To determine maternal dietary intake during pregnancy, each mother was asked by trained personnel at each sample collection time point to answer the Dietary Screener Questionnaire (DSQ), which was developed and validated by the National Health and Examination Survey (NHANES) program (2009–2010)",75,75,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5 + Supplemental Figure 3,29 January 2019,Rimsha Azhar,WikiWorks743,The impact of maternal gestational diet persists to 6 weeks of age,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 59,time series / longitudinal observational,30656437,10.1186/s11671-018-2834-5,NA,"Mao Z, Li Y, Dong T, Zhang L, Zhang Y, Li S, Hu H, Sun C , Xia Y",Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota and Increased Blood Glucose of Rat,Nanoscale research letters,2019,Experiment 1,China,Rattus norvegicus,feces,UBERON:0001988,titanium dioxide nanoparticle,CHEBI:51050,control pregnant rats at gestational day 10,pregnant rats exposed to titanium dioxide nanoparticles,The female rats were daily gavage administrated with 5 mg/kg bw/day of TiO2 NPs from the 5th to 18th day after pregnancy.,4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,30 January 2019,Yaseen Javaid,WikiWorks743,Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota of preganat rats,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Shaimaa Elsafoury
Study 59,time series / longitudinal observational,30656437,10.1186/s11671-018-2834-5,NA,"Mao Z, Li Y, Dong T, Zhang L, Zhang Y, Li S, Hu H, Sun C , Xia Y",Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota and Increased Blood Glucose of Rat,Nanoscale research letters,2019,Experiment 1,China,Rattus norvegicus,feces,UBERON:0001988,titanium dioxide nanoparticle,CHEBI:51050,control pregnant rats at gestational day 10,pregnant rats exposed to titanium dioxide nanoparticles,The female rats were daily gavage administrated with 5 mg/kg bw/day of TiO2 NPs from the 5th to 18th day after pregnancy.,4,4,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,30 January 2019,Yaseen Javaid,"WikiWorks743,Fatima",Exposure to Titanium Dioxide Nanoparticles During Pregnancy Changed Maternal Gut Microbiota of preganat rats,decreased,k__Bacteria|p__Acidobacteria|c__Acidobacteriia|o__Acidobacteriales|f__Acidobacteriaceae|s__bacterium Ellin6075,2|57723|204432|204433|204434|234266,Complete,Fatima
Study 60,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J, Zhou H, Jing Y , Dong C",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,Experiment 1,China,Homo sapiens,blood,UBERON:0000178,type II diabetes mellitus,MONDO:0005148,controls,Type-2 DM cases,NA,100,50,2 months,16S,56,Illumina,T-Test,0.05,FALSE,NA,"age,sex","blood pressure,body mass index,smoking behavior,total cholesterol measurement",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 5,6 February 2019,Yaseen Javaid,WikiWorks743,Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study. (all the bacteria either have zero mean or not detectable in both groups except Aquabacterium),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Cellulomonadaceae|g__Actinotalea,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter",2|201174|1760|85006|85016|458839;2|1224|1236|135622|72275|111142;2|976|1853228|1853229|563835|504481;2|201174|1760|85006|85023|255204,Complete,Shaimaa Elsafoury
Study 60,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J, Zhou H, Jing Y , Dong C",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,Experiment 1,China,Homo sapiens,blood,UBERON:0000178,type II diabetes mellitus,MONDO:0005148,controls,Type-2 DM cases,NA,100,50,2 months,16S,56,Illumina,T-Test,0.05,FALSE,NA,"age,sex","blood pressure,body mass index,smoking behavior,total cholesterol measurement",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 5,6 February 2019,Yaseen Javaid,WikiWorks743,Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study. (all the bacteria either have zero mean or not detectable in both groups except Aquabacterium),decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Xanthomonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia",2|1224|28216|80840|92793;2|1224|1236|135614|32033|338;2|201174|1760|85010|2070|1847,Complete,Shaimaa Elsafoury
Study 60,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J, Zhou H, Jing Y , Dong C",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,Experiment 2,China,Homo sapiens,blood,UBERON:0000178,type II diabetes mellitus,MONDO:0005148,carier of pathogens controls,Type-2 DM cariers of pathogens,The non-carrier meant that the individual did not have sequence read for the specific pathogen.,NA,NA,2 months,16S,56,Illumina,T-Test,0.05,FALSE,NA,"age,sex","blood pressure,body mass index,smoking behavior,total cholesterol measurement",NA,NA,NA,NA,NA,NA,Signature 1,Table 6,4 November 2019,Shaimaa Elsafoury,WikiWorks743,Associations between blood microbiome and the subsequent risk of Type-2 diabetes mellitus,increased,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,2|976|1853228|1853229|563835|504481,Complete,Shaimaa Elsafoury
Study 60,case-control,30714640,10.1002/jcla.22842,NA,"Qiu J, Zhou H, Jing Y , Dong C",Association between blood microbiome and type 2 diabetes mellitus: A nested case-control study,Journal of clinical laboratory analysis,2019,Experiment 2,China,Homo sapiens,blood,UBERON:0000178,type II diabetes mellitus,MONDO:0005148,carier of pathogens controls,Type-2 DM cariers of pathogens,The non-carrier meant that the individual did not have sequence read for the specific pathogen.,NA,NA,2 months,16S,56,Illumina,T-Test,0.05,FALSE,NA,"age,sex","blood pressure,body mass index,smoking behavior,total cholesterol measurement",NA,NA,NA,NA,NA,NA,Signature 2,Table 6,4 November 2019,Shaimaa Elsafoury,WikiWorks743,Associations between blood microbiome and the subsequent risk of Type-2 diabetes mellitus,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 61,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado MC, Isolauri E, Laitinen K , Salminen S","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,infants of normal weight mother at age 1 month,infants of overweight mothers,mothers whose prepregnancy body mass index (BMI; in kg/m2) was >25,26,16,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Tale 4,13 February 2019,Rimsha Azhar,WikiWorks743,Mirobial groups in feacal samples at 1 and 6 months of age according to maternal weight gain during pregnancy and BMI,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|816;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 61,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado MC, Isolauri E, Laitinen K , Salminen S","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,infants of normal weight mother at age 6 month,infants of overweight mothers,mothers whose prepregnancy body mass index (BMI; in kg/m2) was >25,26,16,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Tale 4,5 November 2019,Shaimaa Elsafoury,WikiWorks743,Mirobial groups in feacal samples at 1 and 6 months of age according to maternal weight gain during pregnancy and BMI,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hathewaya|s__Hathewaya histolytica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum",2|1239|186801|186802|31979|1769729|1498;2|201174|1760|85004|31953|1678|1686,Complete,Shaimaa Elsafoury
Study 61,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado MC, Isolauri E, Laitinen K , Salminen S","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,Experiment 3,Finland,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,infants of normal maternal weight gain mothers at age 1 month,infants of excessive maternal weight gain mothers,Weight gain >16.0 kg in women with BMI (in kg/m2) <25 and >11.5 kg in women with BMI >25 was considered excessive,20,22,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,5 November 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial counts in infant fecal samples at 1 and 6 months of age according to maternal weight gain during pregnancy,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|815|816;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 61,time series / longitudinal observational,20844065,10.3945/ajcn.2010.29877,NA,"Collado MC, Isolauri E, Laitinen K , Salminen S","Effect of mother's weight on infant's microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy",The American journal of clinical nutrition,2010,Experiment 4,Finland,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,infants of normal maternal weight gain mothers at age 6 months,infants of excessive maternal weight gain mothers,Weight gain >16.0 kg in women with BMI (in kg/m2) <25 and >11.5 kg in women with BMI >25 was considered excessive,20,22,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,5 November 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial counts in infant fecal samples at 1 and 6 months of age according to maternal weight gain during pregnancy,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hathewaya|s__Hathewaya histolytica,2|1239|186801|186802|31979|1769729|1498,Complete,Shaimaa Elsafoury
Study 62,"cross-sectional observational, not case-control",28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R, Tsuji H, Takahashi T, Kawashima K, Nagata S, Nomoto K , Yamashiro Y",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,Experiment 1,Japan,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,NA,134,17,No information about pre-delivey duration. 3 Vaginally-delivered infants have been exposed to antibiotics (birth to sampling),16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Figure 2,5 April 2019,Shaimaa Elsafoury,WikiWorks743,Count and detection rate of bacterial groups in meconium of vaginally and ceasarean born babies,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|1596,Complete,Shaimaa Elsafoury
Study 63,time series / longitudinal observational,28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R, Tsuji H, Takahashi T, Kawashima K, Nagata S, Nomoto K , Yamashiro Y",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery after 7 days of delivery,C-section delivery,NA,134,17,No information about pre-delivey duration. 3 Vaginally-delivered infants have been exposed to antibiotics (birth to sampling),16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,4 November 2019,Shaimaa Elsafoury,WikiWorks743,"Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,2|1239|91061|186826|33958|1578|1596,Complete,Shaimaa Elsafoury
Study 63,time series / longitudinal observational,28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R, Tsuji H, Takahashi T, Kawashima K, Nagata S, Nomoto K , Yamashiro Y",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,Experiment 2,Japan,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery after 3 months of delivery,C-section delivery,NA,134,17,No information about pre-delivey duration. 3 Vaginally-delivered infants have been exposed to antibiotics (birth to sampling),16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,5 April 2019,Shaimaa Elsafoury,WikiWorks743,"Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
Study 63,time series / longitudinal observational,28018325,10.3389/fmicb.2016.01997,NA,"Nagpal R, Tsuji H, Takahashi T, Kawashima K, Nagata S, Nomoto K , Yamashiro Y",Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section,Frontiers in microbiology,2016,Experiment 3,Japan,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery after 6 months of delivery,C-section delivery,NA,134,17,No information about pre-delivey duration. 3 Vaginally-delivered infants have been exposed to antibiotics (birth to sampling),16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,5 April 2019,Shaimaa Elsafoury,WikiWorks743,"Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,2|1239|91061|186826|33958|2742598|1598,Complete,Shaimaa Elsafoury
Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,Experiment 1,China,Homo sapiens,oral gland,UBERON:0010047,periodontitis,EFO:0000649,No Periodontitis within negative diabetic background only,periodnotitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,6,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,7 March 2019,Yaseen Javaid,WikiWorks743,sognatures of Health-associated and periodontitis-associated OTUs,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii",2|1239|909932|909929|1843491|970|69823;2|976|200643|171549|171552;2|1239|91061|186826|1300|1301|1302,Complete,Shaimaa Elsafoury
Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,Experiment 1,China,Homo sapiens,oral gland,UBERON:0010047,periodontitis,EFO:0000649,No Periodontitis within negative diabetic background only,periodnotitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,6,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,7 March 2019,Yaseen Javaid,"WikiWorks743,Fatima",sognatures of Health-associated and periodontitis-associated OTUs,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella loescheii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.",2|1224|1236|135625|712|416916;2|976|117743|200644|49546|1016|1019;2|1224|1236|135615|868|2717|2718;2|1224|1236|135615|868|2717|194702;2|201174|1760|85007|1653|1716|43768;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1224|28216|206351|481|482|484;2|976|200643|171549|171552|838|840;2|201174|1760|85009|31957;2|1239|909932|909929|1843491|970|135083;2|976|200643|171549|171551|836|1924944,Complete,Fatima
Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,Experiment 2,China,Homo sapiens,oral gland,UBERON:0010047,type II diabetes mellitus,MONDO:0005148,Non-diabetic within negative  periodnotitis,Diabetic,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,8,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,7 March 2019,Yaseen Javaid,WikiWorks743,Signature OTUs associated with diabetic and non-diabetic samples.,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales",2|1224|28216|206351;2|201174|1760|2037;2|976|200643|171549|2005525|195950|28112;2|1224|28216|80840,Complete,Shaimaa Elsafoury
Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,Experiment 2,China,Homo sapiens,oral gland,UBERON:0010047,type II diabetes mellitus,MONDO:0005148,Non-diabetic within negative  periodnotitis,Diabetic,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",5,8,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,7 March 2019,Yaseen Javaid,WikiWorks743,Signature OTUs associated with diabetic and non-diabetic samples.,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella loescheii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea",2|201174|1760|85007|1653|1716|43768;2|976|200643|171549|171552|838|840;2|1224|1236|135615|868|2717|194702;2|1224|28216|206351|481|482|484;2|976|117743|200644|49546|1016|1018,Complete,Shaimaa Elsafoury
Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,Experiment 3,China,Homo sapiens,oral gland,UBERON:0010047,type II diabetes mellitus,MONDO:0005148,Non-diabetic within positive  periodnotitis,Diabetic,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",6,12,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,5 November 2019,Shaimaa Elsafoury,WikiWorks743,Signature OTUs associated with diabetic and non-diabetic samples.,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena",2|201174|1760|85009|31957;2|976|117743|200644|49546|1016|1019,Complete,Shaimaa Elsafoury
Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,Experiment 4,China,Homo sapiens,oral gland,UBERON:0010047,periodontitis,EFO:0000649,No Periodontitis within positive diabetic background only,periodnotitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",8,12,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,5 November 2019,Shaimaa Elsafoury,WikiWorks743,sognatures of Health-associated and periodontitis-associated OTUs,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor|s__Filifactor alocis",2|976|200643|171549|171551|836|837;2|32066|203490|203491|1129771|32067;2|203691|203692|136|2845253|157|58231;2|976|200643|171549;2|976|200643|171549|2005525|195950|28112;2|508458|649775|649776|649777;2|976|200643|171549|171551|836|28124;2|1239|186801|186802|186804|44259|143361,Complete,Shaimaa Elsafoury
Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,Experiment 4,China,Homo sapiens,oral gland,UBERON:0010047,periodontitis,EFO:0000649,No Periodontitis within positive diabetic background only,periodnotitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",8,12,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,5 November 2019,Shaimaa Elsafoury,WikiWorks743,sognatures of Health-associated and periodontitis-associated OTUs,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1224|28216|206351|481|482|495;2|201174|1760|85006|1268|32207|2047;2|1239|909932|1843489|31977|29465;2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,Experiment 5,China,Homo sapiens,oral gland,UBERON:0010047,periodontitis,EFO:0000649,No Periodontitis within both positive and negative diabetic background,periodnotitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",13,18,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,5 November 2019,Shaimaa Elsafoury,WikiWorks743,sognatures of Health-associated and periodontitis-associated OTUs,increased,"k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|203691|203692|136|2845253|157|158;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552,Complete,Shaimaa Elsafoury
Study 64,case-control,23613868,10.1371/journal.pone.0061516,NA,"Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q , Dong Q",Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing,PloS one,2013,Experiment 5,China,Homo sapiens,oral gland,UBERON:0010047,periodontitis,EFO:0000649,No Periodontitis within both positive and negative diabetic background,periodnotitis,"Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L",13,18,3 months,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,5 November 2019,Shaimaa Elsafoury,WikiWorks743,sognatures of Health-associated and periodontitis-associated OTUs,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii",2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|1302;2|201174|1760|2037|2049|1654|1655,Complete,Shaimaa Elsafoury
Study 65,case-control,22762355,10.1111/j.1600-0765.2012.01498.x,NA,"Casarin RC, Barbagallo A, Meulman T, Santos VR, Sallum EA, Nociti FH, Duarte PM, Casati MZ , Gonçalves RB",Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis,Journal of periodontal research,2013,Experiment 1,Brazil,Homo sapiens,oral gland,UBERON:0010047,type II diabetes mellitus,MONDO:0005148,Non-diabetic,Diabetic,"chronic periodontitis, according to the criteria of the 1999 International Classification; the presence of at least 15 teeth; >= 30% of the sites and at least nine teeth pre-senting a probing pocket depth of >= 5 mm with bleeding on probing (with two or more of these teeth having a probing pocket depth of >= 7 mm); uncontrolled type-2 DM, determined by a glycated hemoglobin (HbA1c) concentration of > 8%",11,12,3 months,16S,NA,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Table 3 & text,13 March 2019,Yaseen Javaid,WikiWorks743,Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis.,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Deferribacteres,k__Bacteria|p__Firmicutes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|201174;2|200930;2|1239;2|32066;2|1224;2|1239|91061|186826|1300|1301|28037;2|32066|203490|203491|203492|848|851;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|39778;2|1224|28216|206351|481|538|539;2|1224|1236|135625|712|416916;2|1224|28216|206351|481|482;2|1239|91061|1385|1378;2|1224|28216|206351|481|538;2|201174|1760|2037|2049|1654;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|1239|909932|909929|1843491|970,Complete,Shaimaa Elsafoury
Study 65,case-control,22762355,10.1111/j.1600-0765.2012.01498.x,NA,"Casarin RC, Barbagallo A, Meulman T, Santos VR, Sallum EA, Nociti FH, Duarte PM, Casati MZ , Gonçalves RB",Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis,Journal of periodontal research,2013,Experiment 1,Brazil,Homo sapiens,oral gland,UBERON:0010047,type II diabetes mellitus,MONDO:0005148,Non-diabetic,Diabetic,"chronic periodontitis, according to the criteria of the 1999 International Classification; the presence of at least 15 teeth; >= 30% of the sites and at least nine teeth pre-senting a probing pocket depth of >= 5 mm with bleeding on probing (with two or more of these teeth having a probing pocket depth of >= 7 mm); uncontrolled type-2 DM, determined by a glycated hemoglobin (HbA1c) concentration of > 8%",11,12,3 months,16S,NA,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2 & Table 3 & text,13 March 2019,Yaseen Javaid,WikiWorks743,Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis.,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Synergistetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976;2|203691;2|508458;2|1239|186801|186802|186804|44259|143361;2|976|200643|171549|171551|836|837;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186804|44259;2|976|200643|171549|171551|836;2|1239|186801|186802|186804;2|976|200643|171549|2005525|195950|28112;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,Shaimaa Elsafoury
Study 66,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T, Chen T, White RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H , Xia Y",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,Experiment 1,China,Homo sapiens,meconium,UBERON:0007109,neonatal jaundice,EFO:1000739,control,cesarean infants with jaundice,NA,160,141,"among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.",16S,3,Illumina,LEfSe,0.05,FALSE,2.5,NA,"birth weight,gestational age,maternal age,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,19 February 2019,Rimsha Azhar,WikiWorks743,LDA Score (log10) between control and case groups in cesarean infants with jaundice,increased,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,2|1224|28216|80840|119060|106589,Complete,Shaimaa Elsafoury
Study 66,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T, Chen T, White RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H , Xia Y",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,Experiment 1,China,Homo sapiens,meconium,UBERON:0007109,neonatal jaundice,EFO:1000739,control,cesarean infants with jaundice,NA,160,141,"among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.",16S,3,Illumina,LEfSe,0.05,FALSE,2.5,NA,"birth weight,gestational age,maternal age,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,19 February 2019,Rimsha Azhar,WikiWorks743,LDA Score (log10) between control and case groups in cesarean infants with jaundice,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum|s__Bifidobacterium pseudolongum subsp. globosum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales",2|1239|186801|186802|31979;2|1224|1236|135625|712;2|201174|1760|85004|31953|1678|1694|1690;2|1224|1236|135625,Complete,Shaimaa Elsafoury
Study 66,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T, Chen T, White RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H , Xia Y",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,Experiment 2,China,Homo sapiens,meconium,UBERON:0007109,neonatal jaundice,EFO:1000739,control,infants with jaundice,NA,160,141,"among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.",16S,3,Illumina,LEfSe,0.05,FALSE,2.5,NA,"birth weight,gestational age,maternal age,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Figure 2,19 February 2019,Rimsha Azhar,WikiWorks743,LDA Score (log10) between control and case groups in all infants,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,2|1239|186801|186802|31979|1485|1502,Complete,Shaimaa Elsafoury
Study 66,case-control,30237489,10.1038/s41424-018-0048-x,NA,"Dong T, Chen T, White RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H , Xia Y",Meconium microbiome associates with the development of neonatal jaundice,Clinical and translational gastroenterology,2018,Experiment 2,China,Homo sapiens,meconium,UBERON:0007109,neonatal jaundice,EFO:1000739,control,infants with jaundice,NA,160,141,"among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.",16S,3,Illumina,LEfSe,0.05,FALSE,2.5,NA,"birth weight,gestational age,maternal age,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Figure 2,19 February 2019,Rimsha Azhar,WikiWorks743,LDA Score (log10) between control and case groups in all infants,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,neurotypical,autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",40,40,3 months,16S,345,Roche454,Welch's T-Test,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,21 February 2019,Fatima Zohra,WikiWorks743,Mean relative abundance in autistic (AD) and neurotypical (NT) subjects,decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Shaimaa Elsafoury
Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,neurotypical,autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",40,40,3 months,16S,345,Roche454,LEfSe,0.01,FALSE,2,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,21 February 2019,Fatima Zohra,WikiWorks743,Differences in the bacterial taxa between autistic (AD) and neurotypical (NT) subjects,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia",2|1239|91061|186826|33958|1578;2|201174|84998|84999|84107|102106;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653;2|1239|186801|186802|186803|189330;2|976|200643,Complete,Shaimaa Elsafoury
Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,neurotypical,autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",40,40,3 months,16S,345,Roche454,LEfSe,0.01,FALSE,2,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,21 February 2019,Fatima Zohra,WikiWorks743,Differences in the bacterial taxa between autistic (AD) and neurotypical (NT) subjects,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|171550|239759;2|1239|909932|1843489|31977;2|1239|909932|909929;2|1239|909932;2|1239|909932|1843489|31977|39948;2|976|200643|171549|2005525|375288;2|1239|909932|1843489|31977|29465;2|1224|28221|213115|194924|35832;2|976|200643|171549,Complete,Shaimaa Elsafoury
Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,Experiment 3,Italy,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,non constipated autistic,constipated autistic,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",29,5,3 months,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,8 November 2019,Shaimaa Elsafoury,WikiWorks743,Differences in the bacterial taxa between constipated and non-constipated autistic (AD) patients,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|186801|186802|31979|1485,Complete,Shaimaa Elsafoury
Study 67,case-control,28222761,10.1186/s40168-017-0242-1,NA,"Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A , De Filippo C",New evidences on the altered gut microbiota in autism spectrum disorders,Microbiome,2017,Experiment 4,Italy,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,non constipated neurotypical,constipated neurotypical,"cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.",29,11,3 months,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,8 November 2019,Shaimaa Elsafoury,WikiWorks743,Differences in the bacterial taxa between constipated and non-constipated neurotypical (NT) subjects,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,2|1239|186801|186802|204475,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,142,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,decreased,Signature 1,Supplemental Table 4,25 February 2019,Marianthi Thomatos,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|201174|1760|2037;2|201174|1760|2037|2049;2|976|200643|171549|815|816|28116;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|140625;2|1239|186801|186802|216572|1263;2|1239|909932|1843489|31977;2|1239|526524|526525|128827|2749846|31971;2|1224;2|1224|28221|213115|194924|35832;2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|186801|186802;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803;2|1239|186801|186802|186803|33042;2|1239|186801|186802|541000,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,142,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,decreased,Signature 2,Supplemental Table 4,25 February 2019,Marianthi Thomatos,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|2005525|375288;2|976|200643|171549|171550;2|1239|186801|186802|990719;2|1239|186801|186802|186807|51514;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|119852;2|1239|526524|526525|128827;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|186802|31979;2|1239|186801|186802;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803;2|1239|186801|186802|186803|33042;2|1239|186801|186802|541000,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,overweight,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,246,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table 4,11 December 2019,Shaimaa Elsafoury,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|976|200643|171549|815|816;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|140625;2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|1263;2|1224|28221|213115|194924|35832,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,overweight,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",211,246,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Table 4,11 December 2019,Shaimaa Elsafoury,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|2005525|375288;2|1239|186801|186802;2|1239|186801|186802|990719;2|1239|186801|186802|31979;2|1239|186801|186802|186807|51514;2|1239|186801|186802|541000;2|1239|186801|186802|216572|119852;2|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight men,obese men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",80,70,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,25 February 2019,Marianthi Thomatos,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria",2|976|200643|171549|2005525|375288|823;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|572511;2|1239|186801|186802|541000;2|1239|909932|1843489|31977;2|1224;2|1224|1236,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight men,obese men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2",80,70,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,25 February 2019,Marianthi Thomatos,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|186801|186802|31979;2|1239|186801|186802|186807|51514;2|1239|1737404|1737405|1737406;2|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight men,overweight men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m3",80,171,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,13 December 2019,Shaimaa Elsafoury,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium",2|976|200643|171549|815|816;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|140625,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight men,overweight men,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m3",80,171,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,13 December 2019,Shaimaa Elsafoury,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Synergistetes|c__Synergistia",2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1239|1737404|1737405|1737406;2|1239|1737404|1737405|1570339|150022;2|1239|186801|186802|990719;2|1239|186801|186802|31979;2|1239|186801|186802|186807|51514;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|2316020|33038;2|1239|909932|1843489|31977|906;2|1224|28216|80840;2|1224|1236|91347;2|1224|1236|91347|543;2|508458|649775,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 5,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight women,obese women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m5",131,72,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,25 February 2019,Marianthi Thomatos,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186803|140625;2|1224;2|1224|28216|80840;2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|1737404|1737405|1737406;2|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 5,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight women,obese women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m5",131,72,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,25 February 2019,Marianthi Thomatos,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium",2|1239|186801|186802|990719;2|1239|186801|186802|31979;2|1239|186801|186802|186807|51514,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 6,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight women,overweight women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m7",131,75,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 5,13 December 2019,Shaimaa Elsafoury,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|140625;2|1224;2|1224|28216|80840;2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543,Complete,Shaimaa Elsafoury
Study 68,"cross-sectional observational, not case-control",29950689,10.1038/s41598-018-28126-1,NA,"Peters BA, Shapiro JA, Church TR, Miller G, Trinh-Shevrin C, Yuen E, Friedlander C, Hayes RB , Ahn J",A taxonomic signature of obesity in a large study of American adults,Scientific reports,2018,Experiment 6,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight women,overweight women,"Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m7",131,75,long term use in NYU study. NA for CDC study,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,polyp,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table 5,13 December 2019,Shaimaa Elsafoury,WikiWorks743,Taxonomic sginature of obesity in a large study of American adults,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,Shaimaa Elsafoury
Study 69,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X, Zhang M, Xue J, Huang J, Zhuang R, Zhou X, Zhang H, Fu Q , Hao Y",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,sex design,EFO:0001752,male,female,NA,259,292,2 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,unchanged,unchanged,increased,Signature 1,supplementry figure S2,9 March 2019,Marianthi Thomatos,WikiWorks743,Differences in body mass index  and gut microbiota by Gender,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,2|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
Study 69,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X, Zhang M, Xue J, Huang J, Zhuang R, Zhou X, Zhang H, Fu Q , Hao Y",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,female normal weight,female obese,NA,168,20,2 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,unchanged,increased,Signature 1,Text + fig 2B,25 February 2019,Marianthi Thomatos,WikiWorks743,Differences in body mass index and gut microbiota by Gender,decreased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,2|1239|909932|1843488|909930|33024,Complete,Shaimaa Elsafoury
Study 69,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X, Zhang M, Xue J, Huang J, Zhuang R, Zhou X, Zhang H, Fu Q , Hao Y",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,male normal weight,male obese,NA,93,38,2 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,Text + fig 2B,25 February 2019,Marianthi Thomatos,WikiWorks743,Differences in body mass index and gut microbiota by Gender,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|976|200643|171549|1853231|574697;2|32066|203490|203491|203492|848,Complete,Shaimaa Elsafoury
Study 69,"cross-sectional observational, not case-control",29988340,10.3389/fmicb.2018.01250,NA,"Gao X, Zhang M, Xue J, Huang J, Zhuang R, Zhou X, Zhang H, Fu Q , Hao Y",Body Mass Index Differences in the Gut Microbiota Are Gender Specific,Frontiers in microbiology,2018,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,NA,261,58,2 months,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,unchanged,unchanged,Signature 1,Text + fig 2B,25 February 2019,Marianthi Thomatos,WikiWorks743,Differences in body mass index and gut microbiota by Gender,increased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|32066;2|32066|203490|203491|203492|848,Complete,Shaimaa Elsafoury
Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,pediatric normal weight,pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",67,71,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table S6,9 March 2019,Marianthi Thomatos,WikiWorks743,Composition of gut microbiota in obese and normal-weight mexican school-age children,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides acidifaciens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|85831;2|976|200643|171549|815|816|28116;2|1239|909932|1843489|31977|39948;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|165179;2|1239|186801|186802|186803,Complete,Shaimaa Elsafoury
Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,pediatric normal weight,pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",67,71,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table S6,9 March 2019,Marianthi Thomatos,WikiWorks743,Composition of gut microbiota in obese and normal-weight mexican school-age children,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella stercorea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|990719;2|976|200643|171549|815|909656|310297;2|1224|1236|91347|543;2|976|200643|171549|171550;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803;2|976|200643|171549|171552|838|363265;2|976|200643|171549|171552|838|165179;2|1224|28216|80840|995019|40544;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,Experiment 2,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,female pediatric normal weight,female pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",29,29,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,25 February 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in obese and normal weight mexican school-age children,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,2|976|200643|171549|815|816|28111,Complete,Shaimaa Elsafoury
Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,Experiment 2,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,female pediatric normal weight,female pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",29,29,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,25 February 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in obese and normal weight mexican school-age children,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,2|976|200643|171549|1853231|283168,Complete,Shaimaa Elsafoury
Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,Experiment 3,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,male pediatric normal weight,male pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",38,42,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,25 February 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in obese and normal weight mexican school-age children,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,2|976|200643|171549|815|816|28111,Complete,Shaimaa Elsafoury
Study 70,case-control,29388394,10.1111/ijpo.12262,NA,"López-Contreras BE, Morán-Ramos S, Villarruel-Vázquez R, Macías-Kauffer L, Villamil-Ramírez H, León-Mimila P, Vega-Badillo J, Sánchez-Muñoz F, Llanos-Moreno LE, Canizalez-Román A, Del Río-Navarro B, Ibarra-González I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA , Canizales-Quinteros S",Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits,Pediatric obesity,2018,Experiment 3,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,male pediatric normal weight,male pediatric obese,"Obesity was defined as body mass index (BMI) ≥95th percentile, whereas NW was de- fined as BMI between the 15th and 75th percentiles for age and gender based on Centers for Disease Control and Prevention (CDC) reference data",38,42,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,25 February 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in obese and normal weight mexican school-age children,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,2|976|200643|171549|815|909656|310297,Complete,Shaimaa Elsafoury
Study 71,"cross-sectional observational, not case-control",24614698,10.1371/journal.pone.0090784,NA,"Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW , Neu J",Meconium microbiome analysis identifies bacteria correlated with premature birth,PloS one,2014,Experiment 1,United States of America,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks,19,33,NA,16S,4,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"birth weight,chorioamnionitis,sex",NA,increased,increased,NA,NA,NA,Signature 1,Table S6 in File S1,26 February 2019,Rimsha Azhar,WikiWorks743,Meconium microbiome related to mode of delivery in premature infants,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio",2|1239|91061|186826|33958|1243;2|1239|909932|1843489|31977|909928;2|1239|91061|186826|81852|2737;2|1239|186801|186802|186803|830,Complete,Shaimaa Elsafoury
Study 71,"cross-sectional observational, not case-control",24614698,10.1371/journal.pone.0090784,NA,"Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW , Neu J",Meconium microbiome analysis identifies bacteria correlated with premature birth,PloS one,2014,Experiment 2,United States of America,Homo sapiens,meconium,UBERON:0007109,premature birth,EFO:0003917,>/=33 weeks,infants <33 weeks gestational age,the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks,17,35,NA,16S,4,Ion Torrent,Spearman Correlation,0.05,FALSE,NA,NA,"birth weight,chorioamnionitis,sex",NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 1,1 March 2019,Rimsha Azhar,WikiWorks743,"Phyla, family, and genera taxonomy significantly correlated with gestational age",increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Photorhabdus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Actinobacteria",2|1239;2|1239|91061|1385|186817;2|1239|91061|1385|90964;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|1239|91061|186826|81850;2|1239|186801|186802|31979;2|1239|186801|186802|186804;2|1239|909932|1843489|31977;2|1239|526524|526525|128827;2|201174|1760|85004|31953;2|1224|1236|91347|543;2|1239|91061|1385|186817|1386;2|1239|91061|1385|90964|1279;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|2737;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1243;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|909928;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|547;2|1224|1236|91347|543|544;2|1224|1236|91347|1903409|551;2|1224|1236|91347|543|570;2|1224|1236|91347|543|160674;2|1224|1236|91347|1903409|53335;2|1224|1236|91347|1903414|29487;2|976|200643|171549|2005525|195950;2|201174,Complete,Shaimaa Elsafoury
Study 71,"cross-sectional observational, not case-control",24614698,10.1371/journal.pone.0090784,NA,"Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW , Neu J",Meconium microbiome analysis identifies bacteria correlated with premature birth,PloS one,2014,Experiment 2,United States of America,Homo sapiens,meconium,UBERON:0007109,premature birth,EFO:0003917,>/=33 weeks,infants <33 weeks gestational age,the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks,17,35,NA,16S,4,Ion Torrent,Spearman Correlation,0.05,FALSE,NA,NA,"birth weight,chorioamnionitis,sex",NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 1,1 March 2019,Rimsha Azhar,WikiWorks743,"Phyla, family, and genera taxonomy significantly correlated with gestational age",decreased,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalicibacterium,2|1224|28216|80840|75682|223927,Complete,Shaimaa Elsafoury
Study 72,case-control,30228282,10.1038/s41598-018-32219-2,NA,"Zhang M, Ma W, Zhang J, He Y , Wang J",Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China,Scientific reports,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,typically developing controls,autism,diagnosed with autistic spectrum disorder according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders-5th Edition),6,35,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,28 February 2019,Fatima Zohra,WikiWorks743,The bacterial abundance at the level of phylum and genus in autistic and typically developing children with significant difference,increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Shaimaa Elsafoury
Study 72,case-control,30228282,10.1038/s41598-018-32219-2,NA,"Zhang M, Ma W, Zhang J, He Y , Wang J",Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China,Scientific reports,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,typically developing controls,autism,diagnosed with autistic spectrum disorder according to DSM-5 (Diagnostic and Statistical Manual of Mental Disorders-5th Edition),6,35,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,28 February 2019,Fatima Zohra,WikiWorks743,The bacterial abundance at the level of phylum and genus in autistic and typically developing children with significant difference,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1239;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1224|1236|91347|543|561;2|201174|1760|2037|2049|1654;2|1239|1737404|1737405|1570339|543311;2|1239|526524|526525|128827|118747;2|1239|1737404|1737405|1570339|162289,Complete,Shaimaa Elsafoury
Study 73,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A, Nirmalkar K, Pérez-Lizaur A, Hernández-Quiroz F, Ramírez-Del-Alto S, García-Mena J , Hernández-Guerrero C",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,17,3 months,16S,3,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Text + figure 1 + Table S1 + Table S2  Table S7,28 February 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|33042,Complete,Shaimaa Elsafoury
Study 73,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A, Nirmalkar K, Pérez-Lizaur A, Hernández-Quiroz F, Ramírez-Del-Alto S, García-Mena J , Hernández-Guerrero C",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,17,3 months,16S,3,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,Text + figure 1 + Table S1 + Table S2  Table S7,28 February 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|815|816;2|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
Study 73,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A, Nirmalkar K, Pérez-Lizaur A, Hernández-Quiroz F, Ramírez-Del-Alto S, García-Mena J , Hernández-Guerrero C",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,Experiment 2,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese + metabolic syndrome,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,25,3 months,16S,3,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Text + figure 1 + Table S1 + Table S2  Table S7,28 February 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|33042,Complete,Shaimaa Elsafoury
Study 73,"cross-sectional observational, not case-control",30669548,10.3390/ijms20020438,NA,"Chávez-Carbajal A, Nirmalkar K, Pérez-Lizaur A, Hernández-Quiroz F, Ramírez-Del-Alto S, García-Mena J , Hernández-Guerrero C",Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,International journal of molecular sciences,2019,Experiment 2,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese + metabolic syndrome,"the guidelines from the American Heart Association was used to diagnose metabolic syndrome, which must adhere to at least three of the five following parameters; 1. Elevated waist circumference: waist circumference of ≥80, 2. Elevated Triglycerides ≥150 mg/dL, 3. Reduced HDL- Cholesterol <50 mg/dL, 4. Elevated Blood pressure; systolic ≥130 mm Hg and/or diastolic ≥85 mm Hg and 5. Elevated Fasting blood glucose ≥100 mg/dL. On the other hand, the women with just OB were identified using body mass index (BMI) as follows: normal rank was considered 18.5–24.99 kg/m2, the rank for obese class I was 30–34.99 kg/m2, obese class II 35–39.99 kg/m2, and obese class III greater than or equal to 40 kg/m2.",25,25,3 months,16S,3,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,Text + figure 1 + Table S1 + Table S2  Table S7,28 February 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in a sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|815|816;2|1239|526524|526525|128827,Complete,Shaimaa Elsafoury
Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,Experiment 1,Netherlands,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-obese,obese,obesity: BMI 30.5-60.3 kg/m2,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,1 March 2019,Marianthi Thomatos,WikiWorks743,Association of intestinal microbiota with local and systemic inflammation in obesity,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans",2|1239|186801|186802|216572|100175|100176;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|189330|39486,Complete,Shaimaa Elsafoury
Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,Experiment 1,Netherlands,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-obese,obese,obesity: BMI 30.5-60.3 kg/m2,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,1 March 2019,Marianthi Thomatos,WikiWorks743,Association of intestinal microbiota with local and systemic inflammation in obesity,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oralis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella ruminicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|820;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|171552|838|28134;2|976|200643|171549|171552|838|839;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|2005525|195950,Complete,Shaimaa Elsafoury
Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,Experiment 2,Netherlands,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,Nonobese microbiota cluster,obese,obesity: BMI 30.5-60.3 kg/m3,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Table 2,19 December 2019,Shaimaa Elsafoury,WikiWorks743,Association of intestinal microbiota with local and systemic inflammation in obesity,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|1506577|36835;2|1239|186801|186802|186803|2569097|39488,Complete,Shaimaa Elsafoury
Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,Experiment 2,Netherlands,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,Nonobese microbiota cluster,obese,obesity: BMI 30.5-60.3 kg/m3,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,Table 2,19 December 2019,Shaimaa Elsafoury,WikiWorks743,Association of intestinal microbiota with local and systemic inflammation in obesity,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|1853231|283168|28118;2|1239|186801|186802|216572|119852|119853,Complete,Shaimaa Elsafoury
Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,Experiment 3,Netherlands,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low BMI,high BMI,obesity: BMI 30.5-60.3 kg/m4,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,4 March 2019,Marianthi Thomatos,WikiWorks743,Association of intestinal microbiota with local and systemic inflammation in obesity,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia",2|1239|91061|1385|186822|55079;2|1239|186801|186802|186803|1506577|36835;2|1239|186801|186802|216572|100175|100176;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|841|166486;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186806|1730|1736;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|570|548;2|1224|1236|91347|543|570|573;2|1224|1236|135623|641|662;2|1224|1236|91347|1903411|629,Complete,Shaimaa Elsafoury
Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,Experiment 3,Netherlands,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low BMI,high BMI,obesity: BMI 30.5-60.3 kg/m4,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,4 March 2019,Marianthi Thomatos,WikiWorks743,Association of intestinal microbiota with local and systemic inflammation in obesity,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oralis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella ruminicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes|s__Alcaligenes faecalis",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|909656|310297;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|815|816|820;2|976|200643|171549|815|909656|821;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|171552|838|28134;2|976|200643|171549|171552|838|839;2|976|200643|171549|2005525|195950;2|1239|186801|186802|216572|216851|853;2|1239|526524|526525|2810280|100883|100884;2|1224|28216|80840|506|507|511,Complete,Shaimaa Elsafoury
Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,Experiment 4,Netherlands,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low C-Reactive Protein,high C-Reactive Protein,obesity: BMI 30.5-60.3 kg/m5,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,19 December 2019,Shaimaa Elsafoury,WikiWorks743,Association of intestinal microbiota with local and systemic inflammation in obesity,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides",2|1239|186801|186802|216572|100175|100176;2|1239|91061|1385|186822|55079;2|1239|186801|186802|216572|292632|214851;2|1239|186801|186802|186803|841|166486;2|1239|186801|186802|186803|2719231|29370,Complete,Shaimaa Elsafoury
Study 74,case-control,23526699,10.1002/oby.20466,NA,"Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM , Rensen SS",Human intestinal microbiota composition is associated with local and systemic inflammation in obesity,"Obesity (Silver Spring, Md.)",2013,Experiment 4,Netherlands,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low C-Reactive Protein,high C-Reactive Protein,obesity: BMI 30.5-60.3 kg/m5,13,15,6 months,16S,NA,Human Intestinal Tract Chip,Spearman Correlation,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,19 December 2019,Shaimaa Elsafoury,WikiWorks743,Association of intestinal microbiota with local and systemic inflammation in obesity,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|909656|310297;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|815|909656|821;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|2005525|195950,Complete,Shaimaa Elsafoury
Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,smoking behavior,EFO:0004318,right oropharynx of nonsmokers,right oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S3,6 March 2019,Rimsha Azhar,WikiWorks743,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|976|117743|200644|49546|1016;2|1239|186801|186802|186804|1257;2|32066|203490|203491|203492|848;2|1224|28216|80840|80864|12916;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,smoking behavior,EFO:0004318,right oropharynx of nonsmokers,right oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S4,23 December 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|52228;2|1239|91061|186826|1300|1301;2|1239|186801|186802|541000,Complete,Shaimaa Elsafoury
Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,Experiment 2,United States of America,Homo sapiens,oral gland,UBERON:0010047,smoking behavior,EFO:0004318,left oropharynx of nonsmokers,left oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S5,6 March 2019,Rimsha Azhar,WikiWorks743,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482;2|1224|1236|135625|712|416916,Complete,Shaimaa Elsafoury
Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,Experiment 2,United States of America,Homo sapiens,oral gland,UBERON:0010047,smoking behavior,EFO:0004318,left oropharynx of nonsmokers,left oropharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S6,23 December 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|84111;2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|1129771|34104,Complete,Shaimaa Elsafoury
Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,Experiment 3,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,smoking behavior,EFO:0004318,right nasopharynx of nonsmokers,right nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S7,11 March 2019,Rimsha Azhar,WikiWorks743,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Aquitalea,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Zoogloea",2|201174|1760|2037|2049|1654;2|1239|91061|186826|33958|1243;2|1224|1236|2887326|468|469;2|1224|28216|206351|1499392|407217;2|1224|1236|91347|543|620;2|1224|28216|206389|2008794|349,Complete,Shaimaa Elsafoury
Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,Experiment 3,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,smoking behavior,EFO:0004318,right nasopharynx of nonsmokers,right nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S8,11 March 2019,Rimsha Azhar,WikiWorks743,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum",2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186806|1730;2|1239|91061|186826|186827|46123;2|1239|526524|526525|128827|174708;2|1239|186801|186802|543314|109326;2|1239|186801|186802|186803|33042;2|1239|526524|526525|128827;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|1378;2|1239|186801|186802|186803;2|1239|186801|186802|186804;2|1239|186801|186802|541000;2|1239|186801|186802|186803|84036;2|1239|186801|186802|216572|52784,Complete,Shaimaa Elsafoury
Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,Experiment 4,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,smoking behavior,EFO:0004318,left nasopharynx of nonsmokers,left nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table3 + Table S9,23 December 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,increased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|117743|200644|49546|237;2|1239|526524|526525|128827|1647;2|1239|91061|1385|1378;2|1224|1236|91347|543|620;2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
Study 75,case-control,21188149,10.1371/journal.pone.0015216,NA,"Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD , Collman RG",Disordered microbial communities in the upper respiratory tract of cigarette smokers,PloS one,2010,Experiment 4,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,smoking behavior,EFO:0004318,left nasopharynx of nonsmokers,left nasopharynx of smokers,"Smokers were defined as current smoking of .2 cigarettes daily for more than 6 months, and nonsmokers were defined as less than 100 cigarettes lifetime.",33,29,3 months,16S,12,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table3 + Table S10,23 December 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial taxa that distinguish airway microbial communities of smokers from nonsmokers,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas",2|201174|84998|1643822|1643826|84111;2|976|200643|171549|171551|836;2|1239|91061|186826|186827|46123;2|1239|186801|186802|216572|52784;2|1239|186801|186802|543314|109326;2|1239|186801|186802|186803|189330;2|1239|526524|526525|128827;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186803;2|1239|186801|186802|186803|841;2|1239|186801|186802|541000;2|1239|186801|186802|186803|84036;2|1224|29547|213849|72294|194;2|1224|1236|135625|712|724;2|1224|1236|135614|32033|40323,Complete,Shaimaa Elsafoury
Study 76,case-control,27231166,10.4103/0366-6999.182841,NA,"Qi CJ, Zhang Q, Yu M, Xu JP, Zheng J, Wang T , Xiao XH",Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,Chinese medical journal,2016,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,controls,type I diabetes mellitus children,type 1 diabetes mellitus,15,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,Table 3 +  Figure 3,20 March 2019,Yaseen Javaid,WikiWorks743,Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",2|1239|186801|186802|186803|572511;2|1239|909932|1843488|909930|904,Complete,Rimsha Azhar
Study 76,case-control,27231166,10.4103/0366-6999.182841,NA,"Qi CJ, Zhang Q, Yu M, Xu JP, Zheng J, Wang T , Xiao XH",Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,Chinese medical journal,2016,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,controls,type I diabetes mellitus children,type 1 diabetes mellitus,15,15,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,unchanged,decreased,NA,NA,decreased,Signature 2,Table 3 +  Figure 3,20 March 2019,Yaseen Javaid,WikiWorks743,Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Defluviitaleaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas",2|1239|909932|1843489|31977|39948;2|1224|1236|135625;2|1224|1236|135625|712;2|1239|186801|186802|186803;2|1224|1236|135625|712|724;2|1239|186801|186802|1185407;2|1239|186801|186802|543314;2|201174|1760|85006;2|1224|28211|204458;2|1239|186801|186802|1392389,Complete,Rimsha Azhar
Study 77,"cross-sectional observational, not case-control",28035686,10.1002/phar.1890,NA,"Flowers SA, Evans SJ, Ward KM, McInnis MG , Ellingrod VL",Interaction Between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort,Pharmacotherapy,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,non users,atypical antipsychotic users,Medication group was defined by the use of an Atypical Antipsychotics at the time of fecal sample collection,68,49,NA,16S,4,Illumina,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,decreased,NA,Signature 1,Figure3,21 March 2019,Fatima Zohra,WikiWorks743,Differentially abundant members of gut microbiota in bipolar disorder (BD) patients treated with atypical antipsychotics (AAP),increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,2|1239|186801|186802|186803,Complete,Shaimaa Elsafoury
Study 77,"cross-sectional observational, not case-control",28035686,10.1002/phar.1890,NA,"Flowers SA, Evans SJ, Ward KM, McInnis MG , Ellingrod VL",Interaction Between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort,Pharmacotherapy,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,non users,atypical antipsychotic users,Medication group was defined by the use of an Atypical Antipsychotics at the time of fecal sample collection,68,49,NA,16S,4,Illumina,Linear Regression,0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,decreased,NA,Signature 2,Figure3,21 March 2019,Fatima Zohra,WikiWorks743,Differentially abundant members of gut microbiota in bipolar disorder (BD) patients treated with atypical antipsychotics (AAP),decreased,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,2|74201|203494|48461|1647988|239934,Complete,Shaimaa Elsafoury
Study 78,laboratory experiment,27829577,10.5056/jnm16105,NA,"Moussaoui N, Jacobs JP, Larauche M, Biraud M, Million M, Mayer E , Taché Y","Chronic Early-life Stress in Rat Pups Alters Basal Corticosterone, Intestinal Permeability, and Fecal Microbiota at Weaning: Influence of Sex",Journal of neurogastroenterology and motility,2017,Experiment 1,United States of America,Rattus norvegicus,feces,UBERON:0001988,stimulus or stress design,EFO:0001762,controls,limited nesting stress,NA,23,23,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,decreased,NA,NA,NA,Signature 1,Fig3C + text,28 March 2019,Fatima Zohra,WikiWorks743,Genera with differentially abundance in the LNS ( limited nesting stress) group compared to control,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera",2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186807|2740;2|1239|91061|186826|186827|1375;2|1239|91061|1385|90964|227979;2|1239|91061|186826|186827|66831;2|1239|186801|186802|31979|1485;2|201174|1760|85007|1653|1716;2|1224|28221|213115|194924|872;2|1239|91061|186826|186828|117563;2|201174|1760|85006|1268|32207;2|1224|1236|91347|1903414|583;2|1239|186801|186802|31979;2|1239|526524|526525|2810280|100883;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300;2|1239|91061|186826|81852;2|1239|526524|526525|2810281|191303;2157|28890|183925|2158|2159|2316,Complete,NA
Study 78,laboratory experiment,27829577,10.5056/jnm16105,NA,"Moussaoui N, Jacobs JP, Larauche M, Biraud M, Million M, Mayer E , Taché Y","Chronic Early-life Stress in Rat Pups Alters Basal Corticosterone, Intestinal Permeability, and Fecal Microbiota at Weaning: Influence of Sex",Journal of neurogastroenterology and motility,2017,Experiment 1,United States of America,Rattus norvegicus,feces,UBERON:0001988,stimulus or stress design,EFO:0001762,controls,limited nesting stress,NA,23,23,NA,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,decreased,NA,NA,NA,Signature 2,Fig3C + text,28 March 2019,Fatima Zohra,WikiWorks743,Genera with differentially abundance in the LNS ( limited nesting stress) group compared to control,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium dolichum CAG:375,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Mucispirillum|s__Mucispirillum schaedleri,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186806|1730|1263076;2|74201|203494|48461|1647988|239934|239935;2|200930|68337|191393|191394|248038|248039;2|1239|526524|526525|128827|1573535;2|1239|186801|186802|541000;2|976|200643|171549|2005519;2|1239|91061|1385|90964|1279;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186807;2|1239|526524|526525|128827;2|1239|186801|186802;2|1239|186801|186802|186803|28050;2|1239|186801|186802|216572|244127;2|1224|1236|135625|712|724;2|976|200643|171549|1853231|283168,Complete,NA
Study 79,time series / longitudinal observational,25710027,10.1155/2015/806248,NA,"Damms-Machado A, Mitra S, Schollenberger AE, Kramer KM, Meile T, Königsrainer A, Huson DH , Bischoff SC",Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption,BioMed research international,2015,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,Laparoscopic sleeve gastrectomy after 3 months and 6 Months combined,Laparoscopic sleeve gastrectomy baseline,NA,3,3,3 months,WMS,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1A,28 March 2019,Marianthi Thomatos,WikiWorks743,Effects of laparoscopic sleeve gastrectomy (LSG) and very low calorie diet (VLCD) for obesity on gut microbiota composition,increased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. 3_1_40A,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. L2-50,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus obeum CAG:39,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena",2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|541000;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|1263;2|976|200643|171549|815|816|469593;2|1239|186801|186802|31979|1485|411489;2|1239|186801|186802|216572|1263|1263107;2|1239|186801|186802|186803|189330|88431,Complete,Shaimaa Elsafoury
Study 79,time series / longitudinal observational,25710027,10.1155/2015/806248,NA,"Damms-Machado A, Mitra S, Schollenberger AE, Kramer KM, Meile T, Königsrainer A, Huson DH , Bischoff SC",Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption,BioMed research international,2015,Experiment 2,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,very low calorie diet after 3 months and 6 months,Very low calorie diet baseline,NA,3,3,3 months,WMS,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S1B,28 March 2019,Marianthi Thomatos,"WikiWorks743,Fatima",Effects of laparoscopic sleeve gastrectomy (LSG) and very low calorie diet (VLCD) for obesity on gut microbiota composition,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. D5,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. M62/1,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis",2|1239|91061;2|1239|186801|186802|186803|572511|53443;2|1239|186801|186802|31979|1485|556261;2|1239|186801|186802|31979|1485|411486;2|1239|526524|526525|2810280|100883;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|1350|1352;2|1239|186801|186802|186806|1730|1736;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|1239|526524|526525|128827|61170;2|1239|186801|186802|186803|2719231|84030;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|265975;2|1239|186801|186802|541000;2|1239|186801|186802|186804;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|1506553|1512;2|1239|526524|526525|2810280|100883|100884,Complete,Fatima
Study 80,"cross-sectional observational, not case-control",24448554,10.1038/srep03814,NA,"Mejía-León ME, Petrosino JF, Ajami NJ, Domínguez-Bello MG , de la Barca AM",Fecal microbiota imbalance in Mexican children with type 1 diabetes,Scientific reports,2014,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,controls,Type I diabetic children at onset,"T1D diagnose as established according to the American Diabetes Association criteria1, a positive anti-GAD and/or anti-IA-2 auto- antibodies result, HbA1C levels , 8%",8,8,3 months,16S,4,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,text,28 March 2019,Yaseen Javaid,WikiWorks743,Fecal microbiota imbalance in Mexican children with type 1 diabetes,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 80,"cross-sectional observational, not case-control",24448554,10.1038/srep03814,NA,"Mejía-León ME, Petrosino JF, Ajami NJ, Domínguez-Bello MG , de la Barca AM",Fecal microbiota imbalance in Mexican children with type 1 diabetes,Scientific reports,2014,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,controls,Type I diabetic children at onset,"T1D diagnose as established according to the American Diabetes Association criteria1, a positive anti-GAD and/or anti-IA-2 auto- antibodies result, HbA1C levels , 8%",8,8,3 months,16S,4,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,text,28 March 2019,Yaseen Javaid,WikiWorks743,Fecal microbiota imbalance in Mexican children with type 1 diabetes,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|976|200643|171549|171552|838;2|1239|909932|1843488|909930|904;2|1239|909932|909929|1843491|158846,Complete,Shaimaa Elsafoury
Study 81,time series / longitudinal observational,27306058,10.1186/s13073-016-0312-1,NA,"Palleja A, Kashani A, Allin KH, Nielsen T, Zhang C, Li Y, Brach T, Liang S, Feng Q, Jørgensen NB, Bojsen-Møller KN, Dirksen C, Burgdorf KS, Holst JJ, Madsbad S, Wang J, Pedersen O, Hansen T , Arumugam M",Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota,Genome medicine,2016,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,baseline,3 Months after Roux-en-Y gastric bypass surgery,NA,13,12,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 3 & Table S3,28 March 2019,Marianthi Thomatos,WikiWorks743,Roux-en-Y gastric bypass surgery and changes of gut microbiota in morbidly obese,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria",2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|573;2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|1300|1301|1343;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465|39778;2|1239|91061|186826|1300|1301|1313;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|113107;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|31979|1485|1502;2|1239|91061|186826|1300|1301|68892;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|1328;2|1239|186801|186802|186803|2316020|46228;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|1853231|283168|28118;2|201174|1760|85004|31953|1678|1689;2|1239|91061|186826|81852|1350|1351;2|1239|909932|1843489|31977|906|187326;2|1239|186801|186802|216572|244127|169435;2|32066;2|1224,Complete,Shaimaa Elsafoury
Study 81,time series / longitudinal observational,27306058,10.1186/s13073-016-0312-1,NA,"Palleja A, Kashani A, Allin KH, Nielsen T, Zhang C, Li Y, Brach T, Liang S, Feng Q, Jørgensen NB, Bojsen-Møller KN, Dirksen C, Burgdorf KS, Holst JJ, Madsbad S, Wang J, Pedersen O, Hansen T , Arumugam M",Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota,Genome medicine,2016,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,baseline,3 Months after Roux-en-Y gastric bypass surgery,NA,13,12,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 3 & Table S3,28 March 2019,Marianthi Thomatos,WikiWorks743,Roux-en-Y gastric bypass surgery and changes of gut microbiota in morbidly obese,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
Study 81,time series / longitudinal observational,27306058,10.1186/s13073-016-0312-1,NA,"Palleja A, Kashani A, Allin KH, Nielsen T, Zhang C, Li Y, Brach T, Liang S, Feng Q, Jørgensen NB, Bojsen-Møller KN, Dirksen C, Burgdorf KS, Holst JJ, Madsbad S, Wang J, Pedersen O, Hansen T , Arumugam M",Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota,Genome medicine,2016,Experiment 2,Denmark,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,baseline,one year after Roux-en-Y gastric bypass surgery,NA,13,8,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 3 & Table S3,18 February 2020,Shaimaa Elsafoury,WikiWorks743,Roux-en-Y gastric bypass surgery and changes of gut microbiota in morbidly obese,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Fusobacteria",2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|561|562;2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|1300|1301|1343;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465|39778;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|68892;2|976|200643|171549|171550|239759|328814;2|1239|91061|186826|186828|117563|46124;2|201174|1760|2037|2049|2529408|1660;2|1224;2|32066,Complete,Shaimaa Elsafoury
Study 82,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean controls,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,28 March 2019,Marianthi Thomatos,WikiWorks743,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,Shaimaa Elsafoury
Study 82,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean controls,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,28 March 2019,Marianthi Thomatos,WikiWorks743,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] spiroforme,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira hyodysenteriae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum",2|1239|526524|526525|128827|1505663|29348;2|203691|203692|1643686|143786|29521|159;2|32066|203490|203491|203492|848|860,Complete,Shaimaa Elsafoury
Study 83,time series / longitudinal observational,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,after surgery,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,6,3 weeks,WMS,NA,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 &Table 3,28 March 2019,Marianthi Thomatos,"WikiWorks743,Fatima",gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira hyodysenteriae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Fibrobacteres|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter|s__Fibrobacter succinogenes,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Leptospirales|f__Leptospiraceae|g__Leptospira|s__Leptospira interrogans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium|s__Mycobacterium kansasii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Nakamurellales|f__Nakamurellaceae|g__Nakamurella|s__Nakamurella multipartita,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas mendocina,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Chloroflexi|c__Thermomicrobia|o__Thermomicrobiales|f__Thermomicrobiaceae|g__Thermomicrobium|s__Thermomicrobium roseum,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema pallidum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] spiroforme,k__Eukaryota|p__Evosea|c__Eumycetozoa|o__Dictyosteliales|f__Dictyosteliaceae|g__Dictyostelium,k__Eukaryota|p__Ciliophora|c__Litostomatea|o__Entodiniomorphida|f__Ophryoscolecidae|g__Epidinium",2|1224|1236|2887326|468|469|40214;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|207244|105841;2|203691|203692|1643686|143786|29521|159;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|65842|204430|218872|204431|832|833;2|32066|203490|203491|203492|848|860;2|1224|29547|213849|72293|209;2|1239|91061|186826|33958|1578|1579;2|203691|203692|1643688|170|171|173;2|1239|91061|186826|33958|2742598|1598;2|201174|1760|85007|1762|1763|1768;2|201174|1760|1643684|85031|53460|53461;2|1224|1236|72274|135621|286|300;2|1239|91061|1385|90964|1279|1282;2|200795|189775|189776|189777|499|500;2|203691|203692|136|2845253|157|160;2|1239|526524|526525|128827|1505663|29348;2759|2605435|142796|2058949|2058185|5782;2759|5878|5988|40634|47890|40637,Complete,Fatima
Study 83,time series / longitudinal observational,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,after surgery,before surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,6,3 weeks,WMS,NA,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2 &Table 3,28 March 2019,Marianthi Thomatos,"WikiWorks743,Fatima",gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora",2|1224|1236|91347|543|544;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|69218;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|28901;2|1224|1236|91347|543|620|621;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|29466;2759|4751|4890|147550|5139|5148|5140,Complete,Fatima
Study 84,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean controls,after surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,5 December 2019,Shaimaa Elsafoury,WikiWorks743,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii",2|1224|1236|91347|543|547|69218;2|1239|909932|1843489|31977|29465|29466;2|1224|1236|91347|543|620|621,Complete,Shaimaa Elsafoury
Study 84,case-control,23032991,10.1038/tpj.2012.43,NA,"Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T , Bornstein SR",Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters,The pharmacogenomics journal,2013,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean controls,after surgery,Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity,6,NA,3 weeks,WMS,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,5 December 2019,Shaimaa Elsafoury,WikiWorks743,gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes,decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] spiroforme,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira hyodysenteriae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Chloroflexi|c__Thermomicrobia|o__Thermomicrobiales|f__Thermomicrobiaceae|g__Thermomicrobium|s__Thermomicrobium roseum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Fibrobacteres|c__Fibrobacteria|o__Fibrobacterales|f__Fibrobacteraceae|g__Fibrobacter|s__Fibrobacter succinogenes",2|1239|526524|526525|128827|1505663|29348;2|203691|203692|1643686|143786|29521|159;2|1239|91061|186826|33958|2742598|1598;2|1239|186801|186802|186803|207244|105841;2|32066|203490|203491|203492|848|860;2|200795|189775|189776|189777|499|500;2|1239|91061|1385|90964|1279|1282;2|65842|204430|218872|204431|832|833,Complete,Shaimaa Elsafoury
Study 85,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L, Elguero E, Koumavor CK, Renaud N, Prugnolle F, Thomas F, Ategbo S, Engoba M, Obengui EM, Leroy P, Durand F, Renaud P , Becquart",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,Experiment 1,Gabon,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,two-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,30 March 2019,Shaimaa Elsafoury,WikiWorks743,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",2|1224|1236|91347|543|570;2|1239|186801|186802|31979|1266,Complete,Shaimaa Elsafoury
Study 85,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L, Elguero E, Koumavor CK, Renaud N, Prugnolle F, Thomas F, Ategbo S, Engoba M, Obengui EM, Leroy P, Durand F, Renaud P , Becquart",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,Experiment 2,Congo,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,two-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,30 March 2019,Shaimaa Elsafoury,WikiWorks743,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 85,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L, Elguero E, Koumavor CK, Renaud N, Prugnolle F, Thomas F, Ategbo S, Engoba M, Obengui EM, Leroy P, Durand F, Renaud P , Becquart",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,Experiment 3,Gabon,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery,seven-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,5 December 2019,Shaimaa Elsafoury,WikiWorks743,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina",2|1224|1236|91347|543|570;2|1239|186801|186802|31979|1266,Complete,Shaimaa Elsafoury
Study 85,"cross-sectional observational, not case-control",28968427,10.1371/journal.pone.0185569,NA,"Brazier L, Elguero E, Koumavor CK, Renaud N, Prugnolle F, Thomas F, Ategbo S, Engoba M, Obengui EM, Leroy P, Durand F, Renaud P , Becquart",Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life,PloS one,2017,Experiment 4,Congo,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery,seven-day aged babies c-section,NA,7,8,NA,16S,3,Roche454,Linear Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 4 &text,5 December 2019,Shaimaa Elsafoury,WikiWorks743,"Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|976|200643|171549|815|816;2|201174|84998|84999|84107|102106,Complete,Shaimaa Elsafoury
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 1,Luxembourg,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery at day 3,c-section,meconium samples were collected at day 1 after delivery,6,3,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,increased,NA,NA,increased,Signature 1,Figure 7 and Fig. S4,31 March 2019,Shaimaa Elsafoury,WikiWorks743,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 2,Luxembourg,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery at day 5,c-section,meconium samples were collected at day 1 after delivery,7,5,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 6S,31 March 2019,Shaimaa Elsafoury,WikiWorks743,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,increased,k__Bacteria|p__Firmicutes,2|1239,Complete,Shaimaa Elsafoury
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 2,Luxembourg,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery at day 5,c-section,meconium samples were collected at day 1 after delivery,7,5,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 6S,31 March 2019,Shaimaa Elsafoury,WikiWorks743,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Shaimaa Elsafoury
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 3,Luxembourg,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery at day 28,c-section,meconium samples were collected at day 1 after delivery,7,6,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,decreased,NA,NA,unchanged,Signature 1,Figure 6S and Fig. S4,31 March 2019,Shaimaa Elsafoury,WikiWorks743,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 4,Luxembourg,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery at day 150,c-section,meconium samples were collected at day 1 after delivery,6,4,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 6S,31 March 2019,Shaimaa Elsafoury,WikiWorks743,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 5,Luxembourg,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery at day 365,c-section,meconium samples were collected at day 1 after delivery,5,5,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 6S,31 March 2019,Shaimaa Elsafoury,WikiWorks743,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Shaimaa Elsafoury
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 6,Luxembourg,Homo sapiens,feces,UBERON:0001988,premature birth,EFO:0003917,full-term delivery >39 weeks at day 3,late preterm 34-36 weeks,meconium samples were collected at day 1 after delivery,4,5,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Kruskall-Wallis,0.01,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text pg11 and figure 7s,31 March 2019,Shaimaa Elsafoury,WikiWorks743,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Shaimaa Elsafoury
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 7,Luxembourg,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery,overall time point infants samples of c-section,meconium samples were collected at day 1 after delivery,8,7,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplemantry file 9,1 April 2019,Shaimaa Elsafoury,"WikiWorks743,Fatima",qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|186803|207244;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|946234;2|1239|91061|1385|1378;2|1224|1236|135625|712|724;2|1239|91061|186826|33958|1578;2|201174|1760|85009|31957|1743;2|201174|1760|85006|1268|32207;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803,Complete,Fatima
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 7,Luxembourg,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal delivery,overall time point infants samples of c-section,meconium samples were collected at day 1 after delivery,8,7,11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supplemantry file 9,1 April 2019,Shaimaa Elsafoury,WikiWorks743,qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|2005525|375288;2|976|200643|171549|815|816;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
Study 86,time series / longitudinal observational,28512451,10.3389/fmicb.2017.00738,NA,"Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P","Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life",Frontiers in microbiology,2017,Experiment 8,Luxembourg,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,NA,4,6,"11 mothers (6 controls and 5 cases) used antibiotics 12 hours before and after delivery, 3 VD mothers were positive group B Streptococcus screening.",16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 87,case-control,30224347,10.2337/dc18-0253,NA,"Leiva-Gea I, Sánchez-Alcoholado L, Martín-Tejedor B, Castellano-Castillo D, Moreno-Indias I, Urda-Cardona A, Tinahones FJ, Fernández-García JC , Queipo-Ortuño MI",Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study,Diabetes care,2018,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,maturity-onset diabetes of the young 2 (MODY2) and healthy Controls,Type I Diabetics,"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",28,15,3 months,16S,23,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,3 April 2019,Yaseen Javaid,WikiWorks743,"differentially abundant taxa of the fecal microbiota in type 1 diabetes, MODY2, and healthy controls",increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976;2|976|200643|171549|815;2|976|200643|171549|171550;2|1224|1236|91347|543;2|1239|186801|186802|186803|572511;2|1239|186801|186802|541000;2|1239|909932|1843489|31977;2|1239|91061|186826|1300;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|547;2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
Study 87,case-control,30224347,10.2337/dc18-0253,NA,"Leiva-Gea I, Sánchez-Alcoholado L, Martín-Tejedor B, Castellano-Castillo D, Moreno-Indias I, Urda-Cardona A, Tinahones FJ, Fernández-García JC , Queipo-Ortuño MI",Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study,Diabetes care,2018,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,maturity-onset diabetes of the young 2 (MODY2) and healthy Controls,Type I Diabetics,"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",28,15,3 months,16S,23,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,3 April 2019,Yaseen Javaid,WikiWorks743,"differentially abundant taxa of the fecal microbiota in type 1 diabetes, MODY2, and healthy controls",decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria",2|1239;2|201174,Complete,Shaimaa Elsafoury
Study 87,case-control,30224347,10.2337/dc18-0253,NA,"Leiva-Gea I, Sánchez-Alcoholado L, Martín-Tejedor B, Castellano-Castillo D, Moreno-Indias I, Urda-Cardona A, Tinahones FJ, Fernández-García JC , Queipo-Ortuño MI",Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes and MODY2 and Healthy Control Subjects: A Case-Control Study,Diabetes care,2018,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,healthy Controls,Type I Diabetics and maturity-onset diabetes of the young 2 (MODY2),"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",13,30,3 months,16S,23,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,delivery procedure,race,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,2 March 2020,Shaimaa Elsafoury,WikiWorks743,"differentially abundant taxa of the fecal microbiota in type 1 diabetes, MODY2, and healthy controls",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|207244;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
Study 88,"cross-sectional observational, not case-control",30268819,10.1016/j.schres.2018.09.014,NA,"Nguyen TT, Kosciolek T, Maldonado Y, Daly RE, Martin AS, McDonald D, Knight R , Jeste DV",Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects,Schizophrenia research,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,non-psychiatric controls,schizophrenia,"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",25,25,NA,16S,4,Illumina,Kruskall-Wallis,0.01,TRUE,NA,demographics,"age,antimicrobial agent,body mass index,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2+ Supplemental Table S2,4 April 2019,Fatima Zohra,WikiWorks743,Differentially abundant genera in schizophrenia and non-psychiatric controls,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia",2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977|906;2|1239|186801|186802;2|1239|186801|186802|186803|572511,Complete,NA
Study 88,"cross-sectional observational, not case-control",30268819,10.1016/j.schres.2018.09.014,NA,"Nguyen TT, Kosciolek T, Maldonado Y, Daly RE, Martin AS, McDonald D, Knight R , Jeste DV",Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects,Schizophrenia research,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,non-psychiatric controls,schizophrenia,"type 1 diabetes was diagnosed according to the criteria of the American Diabetes Association and the positivity of at least two persistent, confirmed anti-islet autoantibodies (anti-insulin autoantibodies, GAD autoantibodies, or tyrosine phosphatase autoantibodies). MODY2 children were diagnosed by suggestive clinical history, negative anti-islet autoantibodies, and positive genetic testing. Healthy control subjects were children with negative anti-islet autoantibodies,",25,25,NA,16S,4,Illumina,Kruskall-Wallis,0.01,TRUE,NA,demographics,"age,antimicrobial agent,body mass index,race,sex",NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2+ Supplemental Table S2,4 April 2019,Fatima Zohra,WikiWorks743,Differentially abundant genera in schizophrenia and non-psychiatric controls,decreased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|1224;2|1224|1236|135625|712|724;2|1224|28216|80840|995019|40544;2|1239|186801|186802|31979|1485;2|1224|1236|135625|712|724|729,Complete,NA
Study 89,"cross-sectional observational, not case-control",29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,Experiment 1,Brazil,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery in transitional stools,C-section delivery,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,10,40,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 3,4 April 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485;2|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
Study 89,"cross-sectional observational, not case-control",29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,Experiment 2,Brazil,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,NA,13,46,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 90,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,Experiment 1,Brazil,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,mecomium in vaginal delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,10,10,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure S2,4 April 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,increased,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,2|1224|29547|213849|72293|209,Complete,Shaimaa Elsafoury
Study 90,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,Experiment 1,Brazil,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,mecomium in vaginal delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,10,10,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure S2,4 April 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia",2|1224|1236|2887326|468|469;2|1224|2008785|119069|206349|70774;2|1239|91061|186826|1300|1301;2|1224|28211|204457|41297|13687;2|201174|1760|85007|1653|1716;2|201174|84995|84996|84997|42255;2|1224|28211|204457|41297|165695;2|1239|91061|1385|186817|129337;2|1224|28216|206351|481|482;2|1239|1737404|1737405|1570339|165779;2|1224|28211|356|119045|407;2|1239|909932|1843489|31977|29465;2|201174|1760|85006|1268|1269;2|1239|91061|186826|1300|1357;2|1224|28211|356|82115|357;2|1224|28211|356|212791;2|1224|28216|80840|75682|29580;2|1224|28216|80840|80864|80865,Complete,Shaimaa Elsafoury
Study 90,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,Experiment 2,Brazil,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,mecomium in C-section delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,40,40,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure S2,4 April 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|81852|1350,Complete,Shaimaa Elsafoury
Study 90,time series / longitudinal observational,29207565,10.3390/genes8120364,NA,"Mueller NT, Shin H, Pizoni A, Werlang IC, Matte U, Goldani MZ, Goldani HAS , Dominguez-Bello MG","Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function",Genes,2017,Experiment 2,Brazil,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,mecomium in C-section delivery,transitional stool,cases are delivery or an elective C-section delivery between 38 and 42 weeks of gestation (confirmed by an ultrasound taken before the 20th week of pregnancy).,40,40,oral antibiotics in the third trimester of pregnancy,16S,4,Illumina,LEfSe,NA,FALSE,3,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure S2,4 April 2019,Shaimaa Elsafoury,WikiWorks743,Bacterial taxa comparisons in meconium and transitional stool by delivery mode.,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium",2|1224|1236|72274|135621|286;2|1239|91061|1385|186817|400634;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|1224|28216|80840|119060|106589;2|32066|203490|203491|1129771|32067;2|201174|1760|2037|2049|1654;2|32066|203490|203491|203492|848;2|1224|28211|204457|41297|13687;2|201174|84995|84996|84997|42255;2|1224|1236|135619|28256|2745;2|203691|203692|136|2845253|157;2|1224|1236|135625|712|724;2|1224|28211|204458|76892|41275;2|1224|1236|135615|868|2717;2|1224|28211|204457|41297|165695,Complete,Shaimaa Elsafoury
Study 91,"cross-sectional observational, not case-control",29459704,10.1038/s41598-018-21657-7,NA,"Shi YC, Guo H, Chen J, Sun G, Ren RR, Guo MZ, Peng LH , Yang YS",Initial meconium microbiome in Chinese neonates delivered naturally or by cesarean section,Scientific reports,2018,Experiment 1,China,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,the first-pass meconium stools from within 24 h of delivery,8,10,None of VD mothers received antibiotics during delivery. CSD mothers recieved prophylactic antibiotics after delivery.,WMS,NA,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,5 April 2019,Shaimaa Elsafoury,"WikiWorks743,Fatima",Comparison of the microbiome of vaginally delivered and C-section-delivered newborns,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas|s__Aeromonas veronii,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus amyloliquefaciens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Deinococcus-Thermus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|1224|1236|135624|84642|642|654;2|1224|28211;2|1239|91061|1385|186817;2|1239|91061|1385;2|1239|91061;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186817|1386|1390;2|1239|91061|1385|186817|1386|1402;2|1297|188787|118964|183710;2|1297|188787|118964;2|1297|188787;2|1297|188787|118964|183710|1298;2|1297;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239;2|976|200643|171549|815|909656|821;2|1224|1236|135614|32033|40323;2|1224|1236|135614|32033;2|1224|1236|135614;2|1239|186801|186802|186803|39491,Complete,Fatima
Study 91,"cross-sectional observational, not case-control",29459704,10.1038/s41598-018-21657-7,NA,"Shi YC, Guo H, Chen J, Sun G, Ren RR, Guo MZ, Peng LH , Yang YS",Initial meconium microbiome in Chinese neonates delivered naturally or by cesarean section,Scientific reports,2018,Experiment 1,China,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,the first-pass meconium stools from within 24 h of delivery,8,10,None of VD mothers received antibiotics during delivery. CSD mothers recieved prophylactic antibiotics after delivery.,WMS,NA,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,5 April 2019,Shaimaa Elsafoury,WikiWorks743,ComparisonofthemicrobiomesofvaginallydeliveredandC-section-deliverednewborns,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|201174|1760;2|201174;2|201174|1760|2037;2|201174|1760|85009|31957;2|1224|1236;2|201174|1760|85009|31957|1912216|1747;2|201174|1760|85009|31957|1743;2|1224|1236|72274;2|201174|1760|85010|2070;2|1224|28216|80840;2|1224|28216;2|1224|28216|80840|80864|283;2|1224|28216|80840|80864;2|1224|28216|80840|80864|283|285;2|1224|1236|72274|135621|286,Complete,Shaimaa Elsafoury
Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,healthy controls,obese without non-alcoholic fatty liver disease,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,11,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,6 April 2019,Marianthi Thomatos,WikiWorks743,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Actinobacteria",2|1224|1236;2|201174,Complete,Shaimaa Elsafoury
Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,healthy controls,obese without non-alcoholic fatty liver disease,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,11,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,6 April 2019,Marianthi Thomatos,WikiWorks743,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease,decreased,k__Bacteria|p__Firmicutes|c__Clostridia,2|1239|186801,Complete,Shaimaa Elsafoury
Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,healthy controls,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,13,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,6 April 2019,Marianthi Thomatos,WikiWorks743,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria",2|201174|1760;2|976|200643|171549|171552|838;2|32066|203490;2|1224|29547;2|1224|1236,Complete,Shaimaa Elsafoury
Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,healthy controls,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,26,13,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,6 April 2019,Marianthi Thomatos,WikiWorks743,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria",2|1239|526524;2|1224|28211,Complete,Shaimaa Elsafoury
Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,obese without non-alcoholic fatty liver disease,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,11,13,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,11 March 2020,Shaimaa Elsafoury,WikiWorks743,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria",2|201174|1760;2|976|200643|171549|171552|838;2|32066|203490;2|1224|29547,Complete,Shaimaa Elsafoury
Study 92,case-control,25764541,10.1093/femsec/fiu002,NA,"Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B , Reo NV",Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease,FEMS microbiology ecology,2015,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,obese without non-alcoholic fatty liver disease,non-alcoholic fatty liver disease patients,clinical diagnosis of NAFLD based on ultrasound findings and elevated transaminases.  BMI for obese children with and without clinical NAFLD were greater than the 95% for age,11,13,6 months,16S,NA,Ion Torrent,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,11 March 2020,Shaimaa Elsafoury,WikiWorks743,Altered gut microbial energy and metabolism in children withi non-alcoholic fatty liver disease (NAFLD),decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria",2|1239|526524;2|1224|28211;2|1224|1236,Complete,Shaimaa Elsafoury
Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,Experiment 1,Finland,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,NA,172,40,"newborns administerated antibiotics during delivery: Cefuroxime (n= 31), penicillin (n= 28), piperacillin-tazobactam (n=2)",16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,6 April 2019,Shaimaa Elsafoury,WikiWorks743,Effects of delivery mode on the microbiome of the first stool.,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,Shaimaa Elsafoury
Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,Experiment 2,Finland,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,no,Antimicrobials use during delivery yes,NA,151,61,"newborns administerated antibiotics during delivery: Cefuroxime (n= 31), penicillin (n= 28), piperacillin-tazobactam (n=2)",16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,6 April 2019,Shaimaa Elsafoury,WikiWorks743,Effect of antimicrobial use on the microbioome of the first stool,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,Experiment 3,Finland,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,no,Maternal consumption of probiotics yes,NA,151,61,"newborns administerated antibiotics during delivery: Cefuroxime (n= 31), penicillin (n= 28), piperacillin-tazobactam (n=2)",16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,6 April 2019,Shaimaa Elsafoury,WikiWorks743,Effect of probiotics during pregnancy on the microbioome of the first stool,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,Experiment 4,Finland,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,no,Furry pets at home yes,NA,108,104,"newborns administerated antibiotics during delivery: Cefuroxime (n= 31), penicillin (n= 28), piperacillin-tazobactam (n=2)",16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"antimicrobial agent during labor,delivery procedure,probiotics during pregnancy",NA,increased,NA,NA,NA,NA,Signature 1,Table 4,6 April 2019,Shaimaa Elsafoury,WikiWorks743,mulivariate analysis adjusting for furry pets at home,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
Study 93,"cross-sectional observational, not case-control",29538354,10.1038/pr.2018.29,NA,"Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M , Renko M",Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium,Pediatric research,2018,Experiment 4,Finland,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,no,Furry pets at home yes,NA,108,104,"newborns administerated antibiotics during delivery: Cefuroxime (n= 31), penicillin (n= 28), piperacillin-tazobactam (n=2)",16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"antimicrobial agent during labor,delivery procedure,probiotics during pregnancy",NA,increased,NA,NA,NA,NA,Signature 2,Table 4,6 April 2019,Shaimaa Elsafoury,WikiWorks743,mulivariate analysis adjusting for furry pets at home,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes",2|1239|91061|1385|90964|1279;2|1239,Complete,Shaimaa Elsafoury
Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,baseline participants,3 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,6 April 2019,Marianthi Thomatos,"WikiWorks743,Fatima",Gut microbial community of obese patients following weight-loss intervention,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum|s__Anaerobiospirillum succiniciproducens,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum variabile,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47",2|1224|1236|135624|83763|13334|13335;2|201174|84998|84999|84107|102106|74426;2|1224|28216|80840|995019|577310|487175;2|1239|186801|186802|186803|841|166486;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|216572|292632|214851;2|1224|28216|80840|469610,Complete,Fatima
Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,baseline participants,3 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,6 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbial community of obese patients following weight-loss intervention,decreased,"k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema brennaborense,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter heparinus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__Dysgonomonas gadei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulfitobacterium|s__Desulfitobacterium hafniense,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Desulforamulus|s__Desulforamulus ruminis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens|s__Ethanoligenens harbinense,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Weizmannia|s__Weizmannia coagulans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus mucilaginosus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia|s__Marvinbryantia formatexigens,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfuromonadales|f__Geobacteraceae|g__Geobacter|s__Geobacter sp. M18,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas stutzeri,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces coelicolor,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia heliotrinireducens,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Thermanaerovibrio|s__Thermanaerovibrio acidaminovorans,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Fretibacterium|s__Fretibacterium fastidiosum",2|203691|203692|136|2845253|157|81028;2|976|117747|200666|84566|84567|984;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|2005520|156973|156974;2|1239|186801|186802|186807|36853|49338;2|1239|186801|186802|186807|2916693|1564;2|1239|909932|909929|1843491|970|69823;2|1239|186801|186802|216572|244127|169435;2|1239|186801|186802|216572|253238|253239;2|1239|186801|186802|216572|459786|351091;2|1239|186801|186802|216572|1017280|106588;2|1239|526524|526525|128827|61170|61171;2|1239|91061|1385|186817|2817139|1398;2|1239|91061|186826|81852|1350|1351;2|1239|91061|186826|81852|1350|1352;2|1239|91061|1385|186822|44249|61624;2|1239|186801|186802|186804|1870884|1496;2|1239|186801|186802|186803|2719313|333367;2|1239|186801|186802|186803|248744|168384;2|1224|28221|69541|213422|28231|443143;2|1224|1236|91347|543|561|562;2|1224|1236|72274|135621|286|316;2|201174|1760|85011|2062|1883|1902;2|201174|84998|1643822|1643826|84108|84110;2|201174|84998|1643822|1643826|84111|84112;2|74201|203494|48461|1647988|239934|239935;2|508458|649775|649776|649777|81461|81462;2|508458|649775|649776|649777|1434006|651822,Complete,Shaimaa Elsafoury
Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,Experiment 2,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,3 months participants,6 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,6 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbial community of obese patients following weight-loss intervention,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__Dysgonomonas gadei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Thermanaerovibrio|s__Thermanaerovibrio acidaminovorans",2|976|200643|171549|171550|239759|214856;2|976|200643|171549|2005520|156973|156974;2|1239|186801|186802|186803|2719313|333367;2|1239|186801|186802|186803|2719231|84030;2|1224|28221|213115|194924|872|876;2|1224|1236|91347|543|561|562;2|201174|84998|1643822|1643826|84111|84112;2|201174|84998|1643822|1643826|644652|471189;2|508458|649775|649776|649777|81461|81462,Complete,Shaimaa Elsafoury
Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,Experiment 2,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,3 months participants,6 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,6 April 2019,Marianthi Thomatos,"WikiWorks743,Fatima",Gut microbial community of obese patients following weight-loss intervention,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Anaerobiospirillum|s__Anaerobiospirillum succiniciproducens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|g__Micavibrio|s__Micavibrio aeruginosavorus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47",2|1224|1236|135624|83763|13334|13335;2|1239|91061|186826|1300|1357|1358;2|1224|28211|213485|349221;2|1224|28216|80840|995019|577310|487175;2|1239|186801|186802|186803|841|360807;2|1239|91061|186826|1300|1301|1308;2|1239|909932|1843489|31977|29465|29466;2|1224|28216|80840|469610,Complete,Fatima
Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,Experiment 3,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,6 months participants,24 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,6 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbial community of obese patients following weight-loss intervention,increased,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter heparinus,2|976|117747|200666|84566|84567|984,Complete,Shaimaa Elsafoury
Study 94,time series / longitudinal observational,26919743,10.1371/journal.pone.0149564,NA,"Louis S, Tappu RM, Damms-Machado A, Huson DH , Bischoff SC",Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing,PloS one,2016,Experiment 3,Germany,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,6 months participants,24 months,A threshold of 10% weight loss and maintenance of it over one year has been proposed as definition for successful weight loss maintenance,16,16,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,6 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbial community of obese patients following weight-loss intervention,decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens",2|74201|203494|48461|1647988|239934|239935;2|1224|1236|91347|543|561|562;2|201174|84998|84999|84107|102106|74426,Complete,Shaimaa Elsafoury
Study 95,"cross-sectional observational, not case-control",30568265,NA,NA,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control babies at the age of 3,overweight/obese babies,NA,356,146,7 days,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,education level,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 3 & 4,9 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in overweight 3 year old children,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|841,Complete,Shaimaa Elsafoury
Study 95,"cross-sectional observational, not case-control",30568265,NA,NA,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control babies at the age of 3,overweight/obese babies,NA,356,146,7 days,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,education level,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 3 & 4,9 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in overweight 3 year old children,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
Study 96,case-control,27499582,10.3164/jcbn.15-152,NA,"Andoh A, Nishida A, Takahashi K, Inatomi O, Imaeda H, Bamba S, Kito K, Sugimoto M , Kobayashi T",Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population,Journal of clinical biochemistry and nutrition,2016,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,obese,NA,10,10,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, 3, 4",9 April 2019,Marianthi Thomatos,"WikiWorks743,Fatima",Gut microbial community comparison between obese and lean Japanese population,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus",2|1239|909932|1843488|909930|904|187327;2|976|200643|171549|171550|239759;2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|186803|33042;2|32066|203490|203491|203492|848;2|1239|91061|1385|1378|1379;2|1239|91061|186826|186828|117563|46124;2|1224|1236|91347|543|570|573;2|201174|84998|84999|1643824|2767353|1382;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186804|1257|341694;2|976|200643|171549|815|909656|821;2|1239|186801|186802|186803|841|301302;2|201174|1760|85006|1268|32207|43675;2|201174|1760|2037|2049|2529408|52773;2|1239|186801|186802|186803|207244|649756,Complete,Fatima
Study 96,case-control,27499582,10.3164/jcbn.15-152,NA,"Andoh A, Nishida A, Takahashi K, Inatomi O, Imaeda H, Bamba S, Kito K, Sugimoto M , Kobayashi T",Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population,Journal of clinical biochemistry and nutrition,2016,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,obese,NA,10,10,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Table 2, 3, 4",9 April 2019,Marianthi Thomatos,"WikiWorks743,Fatima",Gut microbial community comparison between obese and lean Japanese population,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania filiformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__Erysipelatoclostridium ramosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena fissicatena",2|976|200643|171549|815|816;2|1224|28221|213115|194924|872;2|1239|186801|186802|186803|2719313|358743;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|1737404|1737405|1570339|150022;2|1239|526524|526525|128827|61170|61171;2|1239|186801|186802|186803|1164882;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|216572|292632;2|1239|526524|526525|128827|1505663|1547;2|1239|186801|186802|216572|2048137|39484;2|1239|186801|186802|186803|2005359|290055,Complete,Fatima
Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,healthy controls,obese patients prior to Sleeve gastrectomy SG0,obese patients had a body mass index (BMI) of >28 kg/m2.,20,19,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,9 April 2019,Marianthi Thomatos,WikiWorks743,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving sleeve gastrectomy,increased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|541000;2|32066|203490|203491|203492|848|850;2|1239|186801|186802|186804,Complete,Shaimaa Elsafoury
Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,healthy controls,Roux-en-Y gastric bypass (RYGB),obese patients had a body mass index (BMI) of >28 kg/m2.,20,7,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,4 March 2020,Shaimaa Elsafoury,WikiWorks743,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving Roux-en-Y gastric bypass,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186804;2|1239|909932|1843489|31977|906,Complete,Shaimaa Elsafoury
Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,obese patients prior to Sleeve gastrectomy SG0,obese patients three months after Sleeve gastrectomy SG3,obese patients had a body mass index (BMI) of >28 kg/m2.,19,8,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 3,4 March 2020,Shaimaa Elsafoury,WikiWorks743,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving sleeve gastrectomy,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1308;2|976|200643|171549|171551;2|976|200643|171549|171550|239759|214856,Complete,Shaimaa Elsafoury
Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,patients prior to Roux-en-Y gastric bypass RYGB0,obese patients 3 moths after Roux-en-Y gastric bypass RYGB3,obese patients had a body mass index (BMI) of >28 kg/m2.,7,3,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,4 March 2020,Shaimaa Elsafoury,WikiWorks743,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving Roux-en-Y gastric bypass,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|909932;2|1239|909932|909929;2|1239|186801|186802|216572|216851,Complete,Shaimaa Elsafoury
Study 97,case-control,30867711,10.3892/etm.2019.7200,NA,"Wang FG, Bai RX, Yan WM, Yan M, Dong LY , Song MM","Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients",Experimental and therapeutic medicine,2019,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,patients prior to Roux-en-Y gastric bypass RYGB0,obese patients 3 moths after Roux-en-Y gastric bypass RYGB3,obese patients had a body mass index (BMI) of >28 kg/m2.,7,3,3 months,16S,4,Ion Torrent,Kruskall-Wallis,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 3,9 April 2019,Shaimaa Elsafoury,WikiWorks743,Differential composition of gut microbiota among healthy volunteers and morbidly obese patients before recieving Roux-en-Y gastric bypass,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1308,Complete,Shaimaa Elsafoury
Study 98,"cross-sectional observational, not case-control",30962186,10.2215/CJN.12161018,NA,"Shah NB, Allegretti AS, Nigwekar SU, Kalim S, Zhao S, Lelouvier B, Servant F, Serena G, Thadhani RI, Raj DS , Fasano A",Blood Microbiome Profile in CKD : A Pilot Study,Clinical journal of the American Society of Nephrology : CJASN,2019,Experiment 1,United States of America,Homo sapiens,blood,UBERON:0000178,chronic kidney disease,EFO:0003884,controls,CKD,NA,20,20,current use,16S,34,Illumina,LEfSe,0.05,TRUE,NA,age,"age,body mass index,hyperlipidemia,hypertension,leukocyte",NA,NA,decreased,NA,NA,NA,Signature 1,Figure 3 and Table 2,15 April 2019,Rimsha Azhar,"WikiWorks743,Lwaldron",Linear discriminant analysis Effect Size (LEfSe) showing microbiome differences between groups at various taxonomic levels.,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Hyphomicrobium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Spirosomaceae|g__Pseudarcicella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia intermedia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales",2|1224|28211|204441|433;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|351;2|1239|91061|1385|186817|1386;2|976|1853228|1853229|563835;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|1224|28211|356|45401;2|1224|28211|356|45401|81;2|1224|1236|118969|444|445;2|1224|1236|118969|444;2|1224|1236|118969;2|1224|1236|135614|32033|68;2|1239|186801|186802|186804;2|1224;2|976|768503|768507|2896860|1664383;2|1224|1236|72274|135621|286;2|976|1853228|1853229|563835|504481;2|1224|1236|91347|1903411|613;2|1224|1236|91347|1903411|629;2|1224|1236|91347|1903411|629|631;2|1224|28211|204441,Complete,Shaimaa Elsafoury
Study 98,"cross-sectional observational, not case-control",30962186,10.2215/CJN.12161018,NA,"Shah NB, Allegretti AS, Nigwekar SU, Kalim S, Zhao S, Lelouvier B, Servant F, Serena G, Thadhani RI, Raj DS , Fasano A",Blood Microbiome Profile in CKD : A Pilot Study,Clinical journal of the American Society of Nephrology : CJASN,2019,Experiment 1,United States of America,Homo sapiens,blood,UBERON:0000178,chronic kidney disease,EFO:0003884,controls,CKD,NA,20,20,current use,16S,34,Illumina,LEfSe,0.05,TRUE,NA,age,"age,body mass index,hyperlipidemia,hypertension,leukocyte",NA,NA,decreased,NA,NA,NA,Signature 2,Figure 3 and Table 2,15 April 2019,Rimsha Azhar,"WikiWorks743,Fatima,Lwaldron",Linear discriminant analysis Effect Size (LEfSe) showing microbiome differences between groups at various taxonomic levels.,decreased,"k__Bacteria|p__Actinobacteria|c__Acidimicrobiia|o__Acidimicrobiales|f__Acidimicrobiaceae,k__Bacteria|p__Actinobacteria|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacteria|p__Acidobacteria|c__Acidobacteriia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Aurantimicrobium,k__Bacteria|p__Acidobacteria|c__Acidobacteriia|o__Bryobacterales|f__Bryobacteraceae|g__Bryobacter,k__Bacteria|p__Acidobacteria|c__Acidobacteriia|o__Bryobacterales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobulbaceae,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Grylloblattodea|f__Grylloblattidae|g__Galloisiana|s__Galloisiana yuasai,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Microscillaceae,k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Fulvivirgaceae|g__Ohtaekwangia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella",2|201174|84992|84993|84994;2|201174|84992|84993;2|57723|204432;2|201174|1760|85006|85023|1705353;2|57723|204432|332160|1962910|911113;2|57723|204432|332160;2|201174|1760|85007|1653|1716;2|1224|28221|213118|213121;2759|33208|6656|50557|58557|244939|73579|378494;2|1239|186801|186802|186803;2|976|768503|768507|1937962;2|976|768503|768507|2762286|1210119;2|1224|28211|204455|31989|265;2|1224|28211|204457|41297|13687;2|1224|1236|135614|32033|40323;2|1239|186801|186802|186803|1506577,Complete,Shaimaa Elsafoury
Study 99,case-control,28628112,10.1038/nm.4358,NA,"Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, Shi J, Zhao S, Liu W, Wang X, Xia H, Liu Z, Cui B, Liang P, Xi L, Jin J, Ying X, Wang X, Zhao X, Li W, Jia H, Lan Z, Li F, Wang R, Sun Y, Yang M, Shen Y, Jie Z, Li J, Chen X, Zhong H, Xie H, Zhang Y, Gu W, Deng X, Shen B, Xu X, Yang H, Xu G, Bi Y, Lai S, Wang J, Qi L, Madsen L, Wang J, Ning G, Kristiansen K , Wang W",Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention,Nature medicine,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,obese,NA,79,72,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 1,16 April 2019,Marianthi Thomatos,"WikiWorks743,Fatima",Gut microbiome alterations in obesity among cohort of lean vs obese Chinese,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",2|1239|186801|186802|186803|572511|40520;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|189330|88431;2|32066|203490|203491|203492|848|861;2|32066|203490|203491|203492|848|856;2|1239|186801|186802|186803;2|1239|909932|1843489|31977|906|907;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186803|2316020|33039;2|1239|186801|186802|186803|2569097|39488,Complete,Fatima
Study 99,case-control,28628112,10.1038/nm.4358,NA,"Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, Shi J, Zhao S, Liu W, Wang X, Xia H, Liu Z, Cui B, Liang P, Xi L, Jin J, Ying X, Wang X, Zhao X, Li W, Jia H, Lan Z, Li F, Wang R, Sun Y, Yang M, Shen Y, Jie Z, Li J, Chen X, Zhong H, Xie H, Zhang Y, Gu W, Deng X, Shen B, Xu X, Yang H, Xu G, Bi Y, Lai S, Wang J, Qi L, Madsen L, Wang J, Ning G, Kristiansen K , Wang W",Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention,Nature medicine,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,obese,NA,79,72,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 1,16 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbiome alterations in obesity among cohort of lean vs obese Chinese,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|371601;2|976|200643|171549|815|816|820;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|329854;2|976|200643|171549|171550|239759|328814;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|815|816|28111;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|571;2|1224|1236|135625|712|724|729;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|815|816;2|976|200643|171549|171550|239759,Complete,NA
Study 100,"cross-sectional observational, not case-control",30257444,10.3390/microorganisms6040098,NA,"Kashtanova DA, Tkacheva ON, Doudinskaya EN, Strazhesko ID, Kotovskaya YV, Popenko AS, Tyakht AV , Alexeev DG",Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study,Microorganisms,2018,Experiment 1,Russian Federation,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,low BMI,High BMI,NA,69,23,3 months,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,16 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in patients with obesity,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|91347|1903411|613;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 100,"cross-sectional observational, not case-control",30257444,10.3390/microorganisms6040098,NA,"Kashtanova DA, Tkacheva ON, Doudinskaya EN, Strazhesko ID, Kotovskaya YV, Popenko AS, Tyakht AV , Alexeev DG",Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study,Microorganisms,2018,Experiment 2,Russian Federation,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-abdominal obesity,Abdominal obesity,NA,39,53,3 months,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,16 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in patients with obesity,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|91347|1903411|613;2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 100,"cross-sectional observational, not case-control",30257444,10.3390/microorganisms6040098,NA,"Kashtanova DA, Tkacheva ON, Doudinskaya EN, Strazhesko ID, Kotovskaya YV, Popenko AS, Tyakht AV , Alexeev DG",Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study,Microorganisms,2018,Experiment 2,Russian Federation,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-abdominal obesity,Abdominal obesity,NA,39,53,3 months,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,16 April 2019,Marianthi Thomatos,WikiWorks743,Gut microbiota in patients with obesity,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,2|1239|186801|186802|216572|119852,Complete,Shaimaa Elsafoury
Study 101,case-control,21829158,10.1038/ijo.2011.153,NA,"Million M, Maraninchi M, Henry M, Armougom F, Richet H, Carrieri P, Valero R, Raccah D, Vialettes B , Raoult D",Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii,International journal of obesity (2005),2012,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean controls,obese,"Obese patients, as defined by a BMI>=30 kg/m2",47,68,less than one month before stool collection,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,"Text & Tables 2, 3, 4 & 5",25 November 2018,Marianthi Thomatos,WikiWorks743,Gut alterations of Lactobacillus or bifidobacterium species between obese and controls,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
Study 101,case-control,21829158,10.1038/ijo.2011.153,NA,"Million M, Maraninchi M, Henry M, Armougom F, Richet H, Carrieri P, Valero R, Raccah D, Vialettes B , Raoult D",Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii,International journal of obesity (2005),2012,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean controls,obese,"Obese patients, as defined by a BMI>=30 kg/m2",47,68,less than one month before stool collection,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,"Text & Tables 2, 3, 4 & 5",25 November 2018,Marianthi Thomatos,WikiWorks743,Gut alterations of Lactobacillus or bifidobacterium species between obese and controls,decreased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium animalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum",2157|28890|183925|2158|2159|2172|2173;2|201174|1760|85004|31953|1678|28025;2|1239|91061|186826|33958|2759736|1597;2|1239|91061|186826|33958|2767842|1590,Complete,Shaimaa Elsafoury
Study 102,"cross-sectional observational, not case-control",26279179,10.1038/srep13212,NA,"Fugmann M, Breier M, Rottenkolber M, Banning F, Ferrari U, Sacco V, Grallert H, Parhofer KG, Seissler J, Clavel T , Lechner A","The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes",Scientific reports,2015,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,normoglycemic controls,Women with gestational DM,Gestational Diabetes Mellitus  was diagnosed by a standardized oral glucose tolerance test (OGTT) after the 23rd week of the preceding pregnecy,35,42,14 days,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Text and Figure 2,18 April 2019,Yaseen Javaid,WikiWorks743,Comparison of relative sequence abundances at the different bacterial taxonomic ranks between pGDM and controls.,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|909932|1843489|31977;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1263,Complete,Shaimaa Elsafoury
Study 102,"cross-sectional observational, not case-control",26279179,10.1038/srep13212,NA,"Fugmann M, Breier M, Rottenkolber M, Banning F, Ferrari U, Sacco V, Grallert H, Parhofer KG, Seissler J, Clavel T , Lechner A","The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes",Scientific reports,2015,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,normoglycemic controls,Women with gestational DM,Gestational Diabetes Mellitus  was diagnosed by a standardized oral glucose tolerance test (OGTT) after the 23rd week of the preceding pregnecy,35,42,14 days,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Text and Figure 2,18 April 2019,Yaseen Javaid,WikiWorks743,Comparison of relative sequence abundances at the different bacterial taxonomic ranks between pGDM and controls.,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239;2|1239|186801;2|1239|186801|186802;2|976|200643|171549|171550;2|1239|186801|186802|186803|572511;2|976|200643|171549|171550|239759,Complete,Shaimaa Elsafoury
Study 103,case-control,29520144,10.2147/NDT.S159322,NA,"Chen JJ, Zheng P, Liu YY, Zhong XG, Wang HY, Guo YJ , Xie P",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,Healthy Controls,depressed female,NA,24,24,yes,16S,345,Roche454,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,26 April 2019,Fatima Zohra,WikiWorks743,Sex differences in gut microbiota in female patients with major depressive disorder,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|1239|186801|186802|186803|572511;2|201174;2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|1678;2|201174|84998|1643822|1643826|553372;2|201174|84998|84999|1643824|1380;2|201174|84998|1643822|1643826|84111;2|201174|84998|1643822|1643826|644652;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|216851;2|1224|28221|213115|194924|872;2|201174|84998|84999;2|1239|186801|186802|186803;2|201174|1760|85004|31953;2|201174|1760|85004;2|1224|1236|135625;2|1224|1236|135625|712;2|1239|186801|186802|186806;2|201174|84998|84999|84107,Complete,Shaimaa Elsafoury
Study 103,case-control,29520144,10.2147/NDT.S159322,NA,"Chen JJ, Zheng P, Liu YY, Zhong XG, Wang HY, Guo YJ , Xie P",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,Healthy Controls,depressed female,NA,24,24,yes,16S,345,Roche454,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,26 April 2019,Fatima Zohra,WikiWorks743,Sex differences in gut microbiota in female patients with major depressive disorder,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter",2|1239|186801|186802|404402;2|1224|28216|80840|995019|40544;2|508458|649775|649776|649777|638847,Complete,Shaimaa Elsafoury
Study 103,case-control,29520144,10.2147/NDT.S159322,NA,"Chen JJ, Zheng P, Liu YY, Zhong XG, Wang HY, Guo YJ , Xie P",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,Healthy Controls,depressed male,NA,20,20,yes,16S,345,Roche454,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,26 April 2019,Fatima Zohra,"WikiWorks743,Fatima",Sex differences in gut microbiota in male patients with major depressive disorder,increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|201174|84998|84999|1643824|1380;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643;2|1239|909932|1843489|31977|29465;2|1239|526524|526525|128827,Complete,Fatima
Study 103,case-control,29520144,10.2147/NDT.S159322,NA,"Chen JJ, Zheng P, Liu YY, Zhong XG, Wang HY, Guo YJ , Xie P",Sex differences in gut microbiota in patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,Healthy Controls,depressed male,NA,20,20,yes,16S,345,Roche454,LEfSe,0.05,FALSE,NA,demographics,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6,26 April 2019,Fatima Zohra,WikiWorks743,Sex differences in gut microbiota in male patients with major depressive disorder,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter",2|201174|84998|84999|84107;2|1239|186801;2|201174|84998|1643822|1643826|644652;2|1239|186801|186802|543314|109326;2|508458|649775|649776|649777|638847,Complete,Shaimaa Elsafoury
Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,healthy controls,major depressive disoreder (visit 1),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2 and table 3,26 April 2019,Fatima Zohra,WikiWorks743,Major bacterial organism in subjects of MDD and control groups,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239;2|976|200643|171549|171552|838;2|1224|1236|91347|543|570;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,healthy controls,major depressive disoreder (visit 1),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,table 2 and table 3,26 April 2019,Fatima Zohra,WikiWorks743,Major bacterial organism in subjects of MDD and control groups,decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Shaimaa Elsafoury
Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,healthy controls,major depressive disoreder (visit 2),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2 and table 3,4 June 2020,Shaimaa Elsafoury,WikiWorks743,Major bacterial organism in subjects of MDD and control groups,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,healthy controls,major depressive disoreder (visit 2),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,table 2 and table 3,4 June 2020,Shaimaa Elsafoury,WikiWorks743,Major bacterial organism in subjects of MDD and control groups,decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Shaimaa Elsafoury
Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,healthy controls,major depressive disoreder (visit 3),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2 and table 3,4 June 2020,Shaimaa Elsafoury,"WikiWorks743,Fatima",Major bacterial organism in subjects of MDD and control groups,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|1239;2|1239|186801|186802|186804,Complete,Fatima
Study 104,case-control,27741466,10.1016/j.jad.2016.09.051,NA,"Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y , Li Q",Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder,Journal of affective disorders,2017,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,healthy controls,major depressive disoreder (visit 3),"The patients were assessed with the major depressive disorder criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV- TR) and 17-items HAM-D scales ≥23.Three visits occurred on day 1, day 15 and day 29.",10,10,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,table 2 and table 3,4 June 2020,Shaimaa Elsafoury,WikiWorks743,Major bacterial organism in subjects of MDD and control groups,decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Shaimaa Elsafoury
Study 105,case-control,27988330,10.1016/j.jpsychires.2016.12.007,NA,"Evans SJ, Bassis CM, Hein R, Assari S, Flowers SA, Kelly MB, Young VB, Ellingrod VE , McInnis MG",The gut microbiome composition associates with bipolar disorder and illness severity,Journal of psychiatric research,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,healthy controls,bipolar,NA,64,115,NA,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,table 2,26 April 2019,Fatima Zohra,WikiWorks743,the gut microbiome composition associates with bipolar disorder and illness severity,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,NA
Study 106,"cross-sectional observational, not case-control",30261302,10.1016/j.bbi.2018.09.026,NA,"Coello K, Hansen TH, Sørensen N, Munkholm K, Kessing LV, Pedersen O , Vinberg M",Gut microbiota composition in patients with newly diagnosed bipolar disorder and their unaffected first-degree relatives,"Brain, behavior, and immunity",2019,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,healthy controls,bipolar,NA,116,113,NA,16S,34,Illumina,Fisher's Exact Test,0.05,TRUE,NA,NA,"age,physical activity,sex,smoking behavior,waist circumference",NA,unchanged,NA,NA,NA,NA,Signature 1,"tabl2, figure3",26 April 2019,Fatima Zohra,WikiWorks743,gut microbiota composition in patients with newly diagnosed bipolar and unaffected first-degree relatives,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,2|1239|186801|186802|216572|946234,Complete,NA
Study 107,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman SC, Watson HJ, Bulik-Sullivan EC, Huh EY, Tarantino LM, Bulik CM , Carroll IM","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,healthy controls,anorexia,NA,12,16,2 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,NA,Signature 1,table 2,26 April 2019,Fatima Zohra,WikiWorks743,differences in microbial taxa among anorexia patients at hospital admission and healthy controls,increased,k__Bacteria|p__Firmicutes|c__Bacilli,2|1239|91061,Complete,NA
Study 107,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman SC, Watson HJ, Bulik-Sullivan EC, Huh EY, Tarantino LM, Bulik CM , Carroll IM","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,healthy controls,anorexia,NA,12,16,2 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,NA,Signature 2,table 2,26 April 2019,Fatima Zohra,WikiWorks743,differences in microbial taxa among anorexia patients at hospital admission and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186803|207244;2|1239|186801|186802|216572|216851,Complete,NA
Study 107,case-control,26428446,10.1097/PSY.0000000000000247,NA,"Kleiman SC, Watson HJ, Bulik-Sullivan EC, Huh EY, Tarantino LM, Bulik CM , Carroll IM","The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology",Psychosomatic medicine,2015,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,healthy controls,anorexia,NA,12,10,2 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,sex",NA,NA,NA,decreased,NA,NA,NA,Signature 1,table 3,26 April 2019,Fatima Zohra,WikiWorks743,differences in microbial taxa among anorexia patients at hospital discharge and healthy controls,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,NA
Study 108,case-control,26682545,10.1371/journal.pone.0145274,NA,"Morita C, Tsuji H, Hata T, Gondo M, Takakura S, Kawai K, Yoshihara K, Ogata K, Nomoto K, Miyazaki K , Sudo N",Gut Dysbiosis in Patients with Anorexia Nervosa,PloS one,2015,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,healthy controls,anorexia nervosa patients,NA,21,25,3 months,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.002,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,"table 3, table 5",26 April 2019,Fatima Zohra,WikiWorks743,gut microbiome dysbiosis in patients with anorexia nervosa versus healthy controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum",2|976|200643|171549|815|816|817;2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|2767842|1590,Complete,NA
Study 109,case-control,27229737,10.1038/srep26752,NA,"Mack I, Cuntz U, Grämer C, Niedermaier S, Pohl C, Schwiertz A, Zimmermann K, Zipfel S, Enck P , Penders J","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,normal weight participants,anorexia patients before weight gain,NA,55,55,8 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 1,figure 3,27 April 2019,Fatima Zohra,WikiWorks743,gut microbiota of anorexia patients before and after weight gain compared to healthy controls,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes",2|201174;2|74201;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|244127;2|1239|186801|186802|186803|207244,Complete,NA
Study 109,case-control,27229737,10.1038/srep26752,NA,"Mack I, Cuntz U, Grämer C, Niedermaier S, Pohl C, Schwiertz A, Zimmermann K, Zipfel S, Enck P , Penders J","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,normal weight participants,anorexia patients before weight gain,NA,55,55,8 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,Signature 2,figure 3,27 April 2019,Fatima Zohra,WikiWorks743,gut microbiota of anorexia patients before and after weight gain compared to healthy controls,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|976;2|1239|186801|186802|204475;2|1239|186801|186802|186803|841,Complete,NA
Study 109,case-control,27229737,10.1038/srep26752,NA,"Mack I, Cuntz U, Grämer C, Niedermaier S, Pohl C, Schwiertz A, Zimmermann K, Zipfel S, Enck P , Penders J","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,Experiment 2,Germany,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,HC,anorexia patients after weight gain,NA,55,44,8 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,figure 3,27 April 2019,Fatima Zohra,WikiWorks743,gut microbiota of anorexia patients before and after weight gain compared to healthy controls,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1239;2|201174;2|1239|186801|186802|186803|207244;2|1239|186801|186802|216572|44748;2|1239|186801|186802|216572|1263;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|1017280;2|1239|91061|186826|1300|1357,Complete,NA
Study 109,case-control,27229737,10.1038/srep26752,NA,"Mack I, Cuntz U, Grämer C, Niedermaier S, Pohl C, Schwiertz A, Zimmermann K, Zipfel S, Enck P , Penders J","Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints",Scientific reports,2016,Experiment 2,Germany,Homo sapiens,feces,UBERON:0001988,anorexia nervosa,EFO:0004215,HC,anorexia patients after weight gain,NA,55,44,8 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 2,figure 3,27 April 2019,Fatima Zohra,WikiWorks743,gut microbiota of anorexia patients before and after weight gain compared to healthy controls,decreased,"k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|74201;2|976|200643|171549|815|816,Complete,NA
Study 110,case-control,29859859,10.1016/j.schres.2018.05.017,NA,"Yuan X, Zhang P, Wang Y, Liu Y, Li X, Kumar BU, Hei G, Lv L, Huang XF, Fan X , Song X","Changes in metabolism and microbiota after 24-week risperidone treatment in drug naïve, normal weight patients with first episode schizophrenia",Schizophrenia research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,schizophrenia,NA,41,41,1 month,16S,NA,RT-qPCR,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,table 2,27 April 2019,Fatima Zohra,WikiWorks743,comparison of fecal bacteria between schizophrenic patients and controls,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|561|562;2|1239|91061|186826|33958|1578,Complete,NA
Study 111,"cross-sectional observational, not case-control",29580894,10.1016/j.bbr.2018.03.036,NA,"Jiang HY, Zhou YY, Zhou GL, Li YC, Yuan J, Li XH , Ruan B",Gut microbiota profiles in treatment-naïve children with attention deficit hyperactivity disorder,Behavioural brain research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,attention deficit hyperactivity disorder,EFO:0003888,healthy control,ADHD,NA,32,51,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,figure 1,27 April 2019,Fatima Zohra,WikiWorks743,Phylotypes significantly different between ADHD and healthy control groups,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae",2|1239|186801|186802|186804;2|1224|1236|135614|32033|40323;2|1224|1236|2887326|468|469;2|201174|84998|84999|84107|1473205;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|990719|990721;2|1239|526524|526525|128827|1573534;2|1239|186801|186802|186804|1505652;2|1239|186801|186802|186807,Complete,NA
Study 111,"cross-sectional observational, not case-control",29580894,10.1016/j.bbr.2018.03.036,NA,"Jiang HY, Zhou YY, Zhou GL, Li YC, Yuan J, Li XH , Ruan B",Gut microbiota profiles in treatment-naïve children with attention deficit hyperactivity disorder,Behavioural brain research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,attention deficit hyperactivity disorder,EFO:0003888,healthy control,ADHD,NA,32,51,2 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,figure1,27 April 2019,Fatima Zohra,WikiWorks743,Phylotypes significantly different between ADHD and healthy control groups,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|1224|28216|80840|506;2|1239|186801|186802|186803|1506553;2|1239|909932|1843489|31977|39948,Complete,NA
Study 112,case-control,30001426,10.1371/journal.pone.0200728,NA,"Prehn-Kristensen A, Zimmermann A, Tittmann L, Lieb W, Schreiber S, Baving L , Fischer A",Reduced microbiome alpha diversity in young patients with ADHD,PloS one,2018,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,attention deficit hyperactivity disorder,EFO:0003888,controls,ADHD males,NA,17,14,NA,16S,12,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,figure 3,27 April 2019,Fatima Zohra,WikiWorks743,Differential abundance of taxa in male ADHD and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|976|200643|171549|815|816,Complete,NA
Study 112,case-control,30001426,10.1371/journal.pone.0200728,NA,"Prehn-Kristensen A, Zimmermann A, Tittmann L, Lieb W, Schreiber S, Baving L , Fischer A",Reduced microbiome alpha diversity in young patients with ADHD,PloS one,2018,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,attention deficit hyperactivity disorder,EFO:0003888,controls,ADHD males,NA,17,14,NA,16S,12,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,figure 3,27 April 2019,Fatima Zohra,WikiWorks743,Differential abundance of taxa in male ADHD and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|171552;2|1239|186801|186802|424536;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|375288,Complete,NA
Study 113,"cross-sectional observational, not case-control",27288567,10.1016/j.jad.2016.05.038,NA,"Aizawa E, Tsuji H, Asahara T, Takahashi T, Teraishi T, Yoshida S, Ota M, Koga N, Hattori K , Kunugi H",Possible association of Bifidobacterium and Lactobacillus in the gut microbiota of patients with major depressive disorder,Journal of affective disorders,2016,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,controls,MDD,NA,57,43,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,27 April 2019,Fatima Zohra,WikiWorks743,Differential abundance of gut microbiota of patients with major depressive disorder,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Amylolactobacillus|s__Amylolactobacillus amylophilus",2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|2767876|1603,Complete,NA
Study 114,case-control,30584306,10.2147/NDT.S188340,NA,"Huang Y, Shi X, Li Z, Shen Y, Shi X, Wang L, Li G, Yuan Y, Wang J, Zhang Y, Zhao L, Zhang M, Kang Y , Liang Y",Possible association of Firmicutes in the gut microbiota of patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,controls,MDD,NA,27,27,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Fig 1, fig 3b, figure 4",27 April 2019,Fatima Zohra,WikiWorks743,Differential abundance of firmicutes in patients with major depressive disorder,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella",2|1224|28216|80840|75682|846;2|1239|1737404|1737405|1570339|543311;2|1239|526524|526525|128827|118747;2|1224|1236|72274|135621|286;2|1239|186801|186802|186804|1257;2|1239|91061|1385|1378,Complete,NA
Study 114,case-control,30584306,10.2147/NDT.S188340,NA,"Huang Y, Shi X, Li Z, Shen Y, Shi X, Wang L, Li G, Yuan Y, Wang J, Zhang Y, Zhao L, Zhang M, Kang Y , Liang Y",Possible association of Firmicutes in the gut microbiota of patients with major depressive disorder,Neuropsychiatric disease and treatment,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,controls,MDD,NA,27,27,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Fig 1, fig 3b, figure 4",27 April 2019,Fatima Zohra,WikiWorks743,Differential abundance of firmicutes in patients with major depressive disorder,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea",2|1239;2|1239|186801|186802|186803;2|1239|186801|186802|216572|216851;2|1239|186801|186802|541000;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|572511;2|1239|186801|186802|31979;2|1239|186801|186802|186803|189330,Complete,NA
Study 115,case-control,30927646,10.1016/j.jpsychires.2019.03.017,NA,"Rong H, Xie XH, Zhao J, Lai WT, Wang MB, Xu D, Liu YH, Guo YY, Xu SX, Deng WF, Yang QF, Xiao L, Zhang YL, He FS, Wang S , Liu TB","Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients",Journal of psychiatric research,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,controls,MDD,NA,30,31,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,unchanged,NA,Signature 1,"Figure 1, Table 2, figure 3",10 January 2021,Fatima Zohra,WikiWorks743,Comparison of bacterial abundance of major depressive disorder and healthy controls,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium",2|1239;2|201174;2|1239|186801|186802|31979|1485;2|201174|1760|85004|31953|1678;2|1239|186801|186802|216572|459786;2|1239|91061|186826|1300|1301;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|906;2|1239|909932|1843488|909930|904;2|1224|1236|91347|543;2|976|200643|171549|171552|838;2|1224|1236|91347|543|561|562;2|1239|909932|1843489|31977|906|907;2|1239|186801|186802|216572|459786|351091;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|171552|838|28132;2|201174|1760|85004|31953|1678|1689,Complete,NA
Study 115,case-control,30927646,10.1016/j.jpsychires.2019.03.017,NA,"Rong H, Xie XH, Zhao J, Lai WT, Wang MB, Xu D, Liu YH, Guo YY, Xu SX, Deng WF, Yang QF, Xiao L, Zhang YL, He FS, Wang S , Liu TB","Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients",Journal of psychiatric research,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,controls,MDD,NA,30,31,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,unchanged,NA,Signature 2,"Figure 1, Table 2, figure 3",10 January 2021,Fatima Zohra,WikiWorks743,Comparison of bacterial abundance of major depressive disorder and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|976;2|976|200643|171549|815|816;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|195950;2|1224|1236|135625|712|724|729,Complete,NA
Study 115,case-control,30927646,10.1016/j.jpsychires.2019.03.017,NA,"Rong H, Xie XH, Zhao J, Lai WT, Wang MB, Xu D, Liu YH, Guo YY, Xu SX, Deng WF, Yang QF, Xiao L, Zhang YL, He FS, Wang S , Liu TB","Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients",Journal of psychiatric research,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,bipolar disorder,EFO:0000289,healthy controls,bipolar,NA,30,30,1 month,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,Signature 1,"Figure 1, Table 2, figure 3",10 January 2021,Fatima Zohra,WikiWorks743,Comparison of bacterial abundance of bipolar disorder with major depressive disorder and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides helcogenes",2|976;2|976|200643|171549|815|816;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|195950;2|976|200643|171549|815|816|290053,Complete,NA
Study 116,case-control,23433344,10.1186/1741-7015-11-46,NA,"Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F , Queipo-Ortuño MI",Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study,BMC medicine,2013,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,healthy controls,children with type 1 diabetes,"Type 1 diabetes was diagnosed following the criteria of the American Diabetes Association and the appearance of at least two persistent, confirmed anti-islet autoantibodies (insulin autoantibodies, glutamic acid decarboxylase autoantibodies or tyrosine phosphatase autoantibodies)",16,16,3 months,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5 &6,5 September 2019,Yaseen Javaid,WikiWorks743,Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study.,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976;2|1239|186801|186802|31979|1485;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465,Complete,Shaimaa Elsafoury
Study 116,case-control,23433344,10.1186/1741-7015-11-46,NA,"Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F , Queipo-Ortuño MI",Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study,BMC medicine,2013,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,healthy controls,children with type 1 diabetes,"Type 1 diabetes was diagnosed following the criteria of the American Diabetes Association and the appearance of at least two persistent, confirmed anti-islet autoantibodies (insulin autoantibodies, glutamic acid decarboxylase autoantibodies or tyrosine phosphatase autoantibodies)",16,16,3 months,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,breastfeeding duration,delivery procedure,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 5 &6,5 September 2019,Yaseen Javaid,WikiWorks743,Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study.,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rectale CAG:36,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174;2|1239;2|976|200643|171549|171552|838;2|1239|186801|186802|186803|572511|1532;2|1239|186801|186802|186806|1730|1263079;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
Study 117,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA , Bogaert D",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,Experiment 1,Netherlands,Homo sapiens,oral gland,UBERON:0010047,pneumonia,EFO:0003106,elderly controls,elderly pneumonia patients,NA,91,100,3 months,16S,567,Roche454,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,increased,NA,NA,NA,decreased,Signature 1,Figure 2,5 September 2019,Rimsha Azhar,WikiWorks743,Patterns in relative abundance of frequently occurring OTUs in elderly and adult controls and pneumonia patients,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301|257758;2|1239|91061|186826|33958|1578,Complete,NA
Study 117,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA , Bogaert D",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,Experiment 1,Netherlands,Homo sapiens,oral gland,UBERON:0010047,pneumonia,EFO:0003106,elderly controls,elderly pneumonia patients,NA,91,100,3 months,16S,567,Roche454,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,increased,NA,NA,NA,decreased,Signature 2,Figure 2,5 September 2019,Rimsha Azhar,WikiWorks743,Patterns in relative abundance of frequently occurring OTUs in elderly and adult controls and pneumonia patients,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|29465|39778;2|201174|1760|85004|31953|196082;2|32066|203490|203491|1129771|32067,Complete,NA
Study 117,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA , Bogaert D",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,Experiment 2,Netherlands,Homo sapiens,oral gland,UBERON:0010047,pneumonia,EFO:0003106,adult controls,adult pneumonia patients,NA,187,27,3 months,16S,567,Roche454,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,16 September 2019,Rimsha Azhar,WikiWorks743,Patterns in relative abundance of frequently occurring OTUs in elderly and adult controls and pneumonia patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|186826|1300|1301|257758;2|201174|1760|85006|1268|32207;2|1239|91061|186826|33958|1578,Complete,NA
Study 117,case-control,26151645,10.1038/ismej.2015.99,NA,"de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA , Bogaert D",Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients,The ISME journal,2016,Experiment 2,Netherlands,Homo sapiens,oral gland,UBERON:0010047,pneumonia,EFO:0003106,adult controls,adult pneumonia patients,NA,187,27,3 months,16S,567,Roche454,T-Test,0.05,TRUE,NA,NA,"age,comorbidity,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,16 September 2019,Rimsha Azhar,WikiWorks743,Patterns in relative abundance of frequently occurring OTUs in elderly and adult controls and pneumonia patients,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1239|91061;2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|29465|39778;2|32066|203490|203491|1129771|32067;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482,Complete,NA
Study 118,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y, Qin S, Song Y, Feng Y, Lv N, Xue Y, Liu F, Wang S, Zhu B, Ma J , Yang H",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal born children,cesarean born,cesarean delivery,60,34,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1C and Text,14 May 2019,Yaseen Javaid,WikiWorks743,The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Amylolactobacillus|s__Amylolactobacillus amylophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|909932;2|1239|186801;2|1239|909932|909929;2|1224|1236|91347|543|570;2|1239|909932|1843489;2|1239|91061|186826|33958|2767876|1603;2|1239|186801|186802;2|1239;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958,Complete,Rimsha Azhar
Study 118,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y, Qin S, Song Y, Feng Y, Lv N, Xue Y, Liu F, Wang S, Zhu B, Ma J , Yang H",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginal born children,cesarean born,cesarean delivery,60,34,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1C and Text,14 May 2019,Yaseen Javaid,WikiWorks743,The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678,Complete,Rimsha Azhar
Study 118,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y, Qin S, Song Y, Feng Y, Lv N, Xue Y, Liu F, Wang S, Zhu B, Ma J , Yang H",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,cesarean born and breastfed,cesarean born and mixed-fed,cesarean delivery and mixed-fed,24,10,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3d and Text,1 March 2020,Rimsha Azhar,WikiWorks743,Enriched taxa of different level from cesarean born breastfed infants and from cesarean born mixed-fed infants,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|909932;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350,Complete,Rimsha Azhar
Study 118,"cross-sectional observational, not case-control",30972048,10.3389/fmicb.2019.00598,NA,"Liu Y, Qin S, Song Y, Feng Y, Lv N, Xue Y, Liu F, Wang S, Zhu B, Ma J , Yang H",The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding,Frontiers in microbiology,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,cesarean born and breastfed,cesarean born and mixed-fed,cesarean delivery and mixed-fed,24,10,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3d and Text,1 March 2020,Rimsha Azhar,WikiWorks743,Enriched taxa of different level from cesarean born breastfed infants and from cesarean born mixed-fed infants,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|186801|186802|186803|1506577;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552,Complete,Rimsha Azhar
Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid negative,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,21,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,14 May 2019,Yaseen Javaid,WikiWorks743,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid negative,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,21,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,14 May 2019,Yaseen Javaid,WikiWorks743,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,2|976|200643|171549|815|816|47678,Complete,Shaimaa Elsafoury
Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid positive,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",35,9,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,2 March 2020,Shaimaa Elsafoury,WikiWorks743,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Metaformin negative among Opoid positive,Metaformin positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",35,9,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,2 March 2020,Shaimaa Elsafoury,WikiWorks743,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,opoid negative among Metaformin negative,Opoid positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,35,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,2 March 2020,Shaimaa Elsafoury,WikiWorks743,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
Study 119,"cross-sectional observational, not case-control",29596446,10.1371/journal.pone.0194171,NA,"Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L , Chlipala G","Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease",PloS one,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,opoid negative among Metaformin negative,Opoid positive,"Opioid use was defined as “Yes” if during review of medical record two parameters were present: 1) the participant was under care of psychiatric care professional, and 2) psychiatric care professional established the diagnosis of opioid use disorder as official diagnosis in medical record",34,35,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,2 March 2020,Shaimaa Elsafoury,WikiWorks743,the interactive influence of metformin and opioids on gut microbiota in the subgroup with diabetes.,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,Shaimaa Elsafoury
Study 120,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F , Tinahones FJ",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,Experiment 1,Spain,Rattus norvegicus,feces,UBERON:0001988,physical activity,EFO:0003940,exercise group,Activity Based Anorexia group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,14 May 2019,Yaseen Javaid,WikiWorks743,Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1224;2|976|200643|171549|171552|838;2157|28890;2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350;2|976|200643|171549|815|816,Complete,Shaimaa Elsafoury
Study 120,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F , Tinahones FJ",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,Experiment 1,Spain,Rattus norvegicus,feces,UBERON:0001988,physical activity,EFO:0003940,exercise group,Activity Based Anorexia group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,14 May 2019,Yaseen Javaid,"WikiWorks743,Fatima",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|201174;2|976|200643|171549|815|816;2|976;2|201174|1760|85004|31953|1678;2|1239;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|39491,Complete,Fatima
Study 120,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F , Tinahones FJ",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,Experiment 2,Spain,Rattus norvegicus,feces,UBERON:0001988,physical activity,EFO:0003940,exercise group,Ad libitum group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,14 May 2019,Yaseen Javaid,WikiWorks743,Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|1239;2|1239|91061|186826|81852|1350;2|1239|186801|186802|31979|1485,Complete,Shaimaa Elsafoury
Study 120,laboratory experiment,23724144,10.1371/journal.pone.0065465,NA,"Queipo-Ortuño MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F , Tinahones FJ",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,PloS one,2013,Experiment 2,Spain,Rattus norvegicus,feces,UBERON:0001988,physical activity,EFO:0003940,exercise group,Ad libitum group,"(a) Activity based anorexia (ABA) group: rats starved by restricting food access to 23 hours per day and confined to running wheels except during a 60 min meal per day, (b) Control ABA group: rats submitted to the same food restriction schedule as ABA with no wheel access exercise, (c) Exercise group: rats feed ad libitum with free access to the activity wheel and (d) Ad libitum group: rats feed ad libitum but without access to the activity wheel.",10,10,NA,16S,23,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,body weight,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,14 May 2019,Yaseen Javaid,"WikiWorks743,Fatima",Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|201174;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|39491,Complete,Fatima
Study 121,case-control,28808698,10.3290/j.cjdr.a38769,NA,"Deng K, Ouyang XY, Chu Y , Zhang Q",Subgingival Microbiome of Gingivitis in Chinese Undergraduates,The Chinese journal of dental research : the official journal of the Scientific Section of the Chinese Stomatological Association (CSA),2017,Experiment 1,China,Homo sapiens,oral gland,UBERON:0010047,gingivitis,MONDO:0002508,healthy controls,gingivitis,NA,12,54,3 months,16S,34,Illumina,ANOSIM,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,figure 3 and text,22 May 2019,Marianthi Thomatos,"WikiWorks743,Lwaldron",Subgingival Microbiome of Gingivitis in Chinese undergraduates,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales genomosp. P1",2|976;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838|28131;2|203691;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157;2|976|200643|171549|241556,Complete,Shaimaa Elsafoury
Study 121,case-control,28808698,10.3290/j.cjdr.a38769,NA,"Deng K, Ouyang XY, Chu Y , Zhang Q",Subgingival Microbiome of Gingivitis in Chinese Undergraduates,The Chinese journal of dental research : the official journal of the Scientific Section of the Chinese Stomatological Association (CSA),2017,Experiment 1,China,Homo sapiens,oral gland,UBERON:0010047,gingivitis,MONDO:0002508,healthy controls,gingivitis,NA,12,54,3 months,16S,34,Illumina,ANOSIM,0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,figure 3 and text,22 May 2019,Marianthi Thomatos,WikiWorks743,Subgingival Microbiome of Gingivitis in Chinese undergraduates,decreased,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,2|976|117743|200644|49546|1016,Complete,Shaimaa Elsafoury
Study 122,case-control,24421902,10.1371/journal.pone.0083744,NA,"Xuan C, Shamonki JM, Chung A, Dinome ML, Chung M, Sieling PA , Lee DJ",Microbial dysbiosis is associated with human breast cancer,PloS one,2014,Experiment 1,United States of America,Homo sapiens,breast,UBERON:0000310,breast carcinoma,EFO:0000305,normal tissue,tumor tissue,NA,20,20,NA,16S,4,Illumina,T-Test,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,unchanged,Signature 1,Table S2 and Figure 1d,30 May 2019,Rimsha Azhar,WikiWorks743,OTUs enriched in paired normal or tumor tissue,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium radiotolerans,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium",2|1224|28211|356|119045|407|31998;2|976|117743|200644|49546|237;2|1224|28211|356|119045|407,Complete,NA
Study 122,case-control,24421902,10.1371/journal.pone.0083744,NA,"Xuan C, Shamonki JM, Chung A, Dinome ML, Chung M, Sieling PA , Lee DJ",Microbial dysbiosis is associated with human breast cancer,PloS one,2014,Experiment 1,United States of America,Homo sapiens,breast,UBERON:0000310,breast carcinoma,EFO:0000305,normal tissue,tumor tissue,NA,20,20,NA,16S,4,Illumina,T-Test,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,unchanged,Signature 2,Table S2 and Figure 1d,30 May 2019,Rimsha Azhar,WikiWorks743,OTUs enriched in paired normal or tumor tissue,decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae|g__Nitrosomonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium|s__Novosphingobium aromaticivorans,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae|g__Bradyrhizobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae",2|1224|28211|204457|41297|165695|13690;2|1224|28211|204457|41297|13687;2|1224|28216|32003|206379|914;2|1224|28211|204457|41297|165696|48935;2|1224|28211|356|41294|374;2|1239|91061|186826|1300|1301|257758,Complete,NA
Study 123,laboratory experiment,31141574,10.1371/journal.pone.0217553,NA,"Deshpande NG, Saxena J, Pesaresi TG, Carrell CD, Ashby GB, Liao MK , Freeman LR",High fat diet alters gut microbiota but not spatial working memory in early middle-aged Sprague Dawley rats,PloS one,2019,Experiment 1,United States of America,Rattus norvegicus,feces,UBERON:0001988,diet,EFO:0002755,low fat diet,high fat diet,"High fat diet rats were fed (20% protein, 35% carbohydrate, 45% fat by calories).  Controls or low fat diet were fed (20% protein, 70% carbohydrate, 10% fat by calories) for eight weeks.",6,6,NA,16S,NA,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,4 June 2019,Lora Kasselman,WikiWorks743,Mean relative abundances for gut genera and p-value for differences between high-fat and control animals are listed. Class and phylum are indicated as well,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|1239|91061|186826|1300|1357;2|1239|91061|186826|186828|117563;2|1239|186801|186802|216572|1486725;2|1239|186801|186802|543314|109326;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|100175;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|44748;2|1239|186801|186802|186803|1506577;2|1239|526524|526525|128827|1505663;2|1239|526524|526525|128827|61170;2|201174|1760|85006|1268|32207;2|201174|84998|1643822|1643826|447020;2|201174|84998|84999|84107|102106,Complete,Shaimaa Elsafoury
Study 123,laboratory experiment,31141574,10.1371/journal.pone.0217553,NA,"Deshpande NG, Saxena J, Pesaresi TG, Carrell CD, Ashby GB, Liao MK , Freeman LR",High fat diet alters gut microbiota but not spatial working memory in early middle-aged Sprague Dawley rats,PloS one,2019,Experiment 1,United States of America,Rattus norvegicus,feces,UBERON:0001988,diet,EFO:0002755,low fat diet,high fat diet,"High fat diet rats were fed (20% protein, 35% carbohydrate, 45% fat by calories).  Controls or low fat diet were fed (20% protein, 70% carbohydrate, 10% fat by calories) for eight weeks.",6,6,NA,16S,NA,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 1,23 July 2019,Lora Kasselman,WikiWorks743,Mean relative abundances for gut genera and p-value for differences between high-fat and control animals are listed. Class and phylum are indicated as well,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Robinsoniella",2|1224|1236|91347|543|544;2|976|200643|171549|2005519|397864;2|976|200643|171549|815|816;2|1239|186801|186802|186803|588605,Complete,Shaimaa Elsafoury
Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,distance runners (high carb),body builders (high protein),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,4 June 2019,Lora Kasselman,WikiWorks743,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae",2|1239|186801|186802|186803|572511|418240;2|1224|1236|91347|543|547|550,Complete,Shaimaa Elsafoury
Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,distance runners (high carb),body builders (high protein),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,4 June 2019,Lora Kasselman,WikiWorks743,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|201174|1760|85004|31953|1678|1680;2|1239|186801|186802|216572|1263|40519;2|976|200643|171549|815|816|47678;2|1224|1236|91347|543|561|562;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|561;2|1239|91061|186826|1300|1357,Complete,Shaimaa Elsafoury
Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,control,body builders (high protein),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,4 June 2019,Lora Kasselman,WikiWorks743,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella",2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572|216851;2|1239|186801|186802|31979|1485;2|1224|1236|135625|712|724;2|1239|186801|186802|186803|1432051,Complete,Shaimaa Elsafoury
Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,control,body builders (high protein),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,4 June 2019,Lora Kasselman,WikiWorks743,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus sakei,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",2|1239|186801|186802|186803|572511|418240;2|1239|186801|186802|186803|2569097|39488;2|976|200643|171549|815|816|46506;2|1239|186801|186802|216572|1263|40519;2|201174|1760|85004|31953|1678|216816|1679;2|1224|1236|91347|543|561|562;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|2767885|1599;2|1224|28216|80840|995019|577310;2|1239|91061|186826|33958|1243,Complete,Shaimaa Elsafoury
Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,control,distance runners (high carb),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3 and Text,4 June 2019,Lora Kasselman,WikiWorks743,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,increased,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
Study 124,"cross-sectional observational, not case-control",31053143,10.1186/s12970-019-0290-y,NA,"Jang LG, Choi G, Kim SW, Kim BY, Lee S , Park H",The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,Journal of the International Society of Sports Nutrition,2019,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,control,distance runners (high carb),NA,15,15,6 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3 and Text,4 June 2019,Lora Kasselman,WikiWorks743,The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] innocuum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",2|1224|1236|91347|543|547|550;2|1239|91061|186826|33958|46255|1583;2|1239|526524|526525|128827|1505663|1522;2|976|200643|171549|815|816|47678;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|572511|418240;2|1239|186801|186802|186803|572511;2|1224|1236|91347|543|547;2|1239|91061|186826|33958|46255;2|1239|91061|186826|33958|1243,Complete,Shaimaa Elsafoury
Study 125,case-control,31109865,10.1016/j.job.2019.03.003,NA,"Takahashi Y, Park J, Hosomi K, Yamada T, Kobayashi A, Yamaguchi Y, Iketani S, Kunisawa J, Mizuguchi K, Maeda N , Ohshima T",Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing,Journal of oral biosciences,2019,Experiment 1,Japan,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,noncancer individuals,Oral Squamous Cell Cancer patients,All diagnoses of oral squamous cell carcinoma were confirmed by biopsy and pathological findings.The control group was defined as individuals without any diagnosed mucosal diseases and other cancers and these individuals were over the age of 40.,80,60,28 days,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,"Fig 1,3 and Text",13 June 2019,Utsav Patel,WikiWorks743,Oral microbiota in japanese oral cancer patients vs. noncancer individuals: a case-control study,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|1239|186801|186802|186804|1257;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|1283313;2|976|117743|200644|49546|1016,Complete,Shaimaa Elsafoury
Study 125,case-control,31109865,10.1016/j.job.2019.03.003,NA,"Takahashi Y, Park J, Hosomi K, Yamada T, Kobayashi A, Yamaguchi Y, Iketani S, Kunisawa J, Mizuguchi K, Maeda N , Ohshima T",Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing,Journal of oral biosciences,2019,Experiment 1,Japan,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,noncancer individuals,Oral Squamous Cell Cancer patients,All diagnoses of oral squamous cell carcinoma were confirmed by biopsy and pathological findings.The control group was defined as individuals without any diagnosed mucosal diseases and other cancers and these individuals were over the age of 40.,80,60,28 days,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,"Fig 1,3 and Text",13 June 2019,Utsav Patel,WikiWorks743,Oral microbiota in japanese oral cancer patients vs. noncancer individuals: a case-control study,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|201174|1760|85006|1268|32207;2|1224|1236|135625|712|724,Complete,Shaimaa Elsafoury
Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Hu X, Zhang Q, Hua H , Chen F",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,healthy controls,Oral leukoplakia,NA,19,10,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 1,Fig 1 & 2,20 June 2019,Utsav Patel,WikiWorks743,Changes in oral microbiota in oral leukoplakia vs. healthy control: a case-control study,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",2|1224|1236|135625|712|724;2|1239|91061|1385|186817|1386,Complete,Shaimaa Elsafoury
Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Hu X, Zhang Q, Hua H , Chen F",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,healthy controls,Oral leukoplakia,NA,19,10,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,Signature 2,Fig 1 & 2,20 June 2019,Utsav Patel,WikiWorks743,Changes in oral microbiota in oral leukoplakia vs. healthy control: a case-control study,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1239|91061|186826|1300|1301;2|1239|91061|186826|186827|46123,Complete,Shaimaa Elsafoury
Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Hu X, Zhang Q, Hua H , Chen F",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,healthy controls,Oral Squamous Cell Cancer patients,NA,19,16,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Fig 1 & 2,20 June 2019,Utsav Patel,WikiWorks743,Changes in oral microbiota in OSCC vs. healthy control: a case-control study,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",2|1224|1236|135625|712|724;2|1239|91061|1385|186817|1386,Complete,Shaimaa Elsafoury
Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Hu X, Zhang Q, Hua H , Chen F",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,healthy controls,Oral Squamous Cell Cancer patients,NA,19,16,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Fig 1 & 2,20 June 2019,Utsav Patel,WikiWorks743,Changes in oral microbiota in OSCC vs. healthy control: a case-control study,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1239|91061|186826|1300|1301;2|1239|91061|186826|186827|46123,Complete,Shaimaa Elsafoury
Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Hu X, Zhang Q, Hua H , Chen F",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,Experiment 3,China,Homo sapiens,saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,Oral Squamous Cell Cancer patients,Oral leukoplakia,NA,16,10,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 1,Fig 1 & 2,20 June 2019,Utsav Patel,WikiWorks743,Changes in oral microbiota in oral leukoplakia vs. OSCC: a case-control study,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301,Complete,Shaimaa Elsafoury
Study 126,case-control,27026576,10.1016/j.oraloncology.2016.03.007,NA,"Hu X, Zhang Q, Hua H , Chen F",Changes in the salivary microbiota of oral leukoplakia and oral cancer,Oral oncology,2016,Experiment 3,China,Homo sapiens,saliva,UBERON:0001836,Oral leukoplakia,HP:0002745,Oral Squamous Cell Cancer patients,Oral leukoplakia,NA,16,10,NA,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,increased,NA,NA,Signature 2,Fig 1 & 2,20 June 2019,Utsav Patel,WikiWorks743,Changes in oral microbiota in oral leukoplakia vs. OSCC: a case-control study,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,2|1239|91061|1385|186817|1386,Complete,Shaimaa Elsafoury
Study 127,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW , Valeur J",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,Experiment 1,Norway,Homo sapiens,feces,UBERON:0001988,alcohol drinking,EFO:0004329,controls,alcohol overconsumers,NA,18,24,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, 3",20 July 2019,Fatima Zohra,WikiWorks743,Differential abundance of microbiota at phylum and genus level in patients with chornic alcohol consumption,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",2|1224;2|1224|28216|80840|995019|40544;2|1239|186801|186802|31979|1485;2|1239|526524|526525|128827|61170,Complete,NA
Study 127,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW , Valeur J",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,Experiment 1,Norway,Homo sapiens,feces,UBERON:0001988,alcohol drinking,EFO:0004329,controls,alcohol overconsumers,NA,18,24,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, 3",20 July 2019,Fatima Zohra,WikiWorks743,Differential abundance of microbiota at phylum and genus level in patients with chornic alcohol consumption,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,NA
Study 127,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW , Valeur J",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,Experiment 2,Norway,Homo sapiens,feces,UBERON:0001988,alcohol drinking,EFO:0004329,controls,alcohol overconsumers,NA,18,24,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,20 July 2019,Fatima Zohra,WikiWorks743,Taxa with statistical different relative levels between alcohol overconsumers and controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Epulopiscium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales",2|1239|186801|186802|186803;2|1224;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570;2|1239|186801|186802|31979|1485;2|1224|28216|80840|995019|40544;2|1224|28216|80840|506;2|1224|28221|213115;2|1239|909932|1843488|909930|904;2|1224|1236|91347|1903414|581;2|1239|526524|526525|128827|118747;2|201174|1760|85006|1268|32207;2|1239|186801|186802|186803|2383;2|1239|526524|526525|128827|61170;2|1239|909932|909929|1843491|158846;2|201174|1760|85006|1268;2|1239|1737404|1737405|1737406;2|201174|1760|2037,Complete,NA
Study 127,"cross-sectional observational, not case-control",30894059,10.1080/19490976.2019.1580097,NA,"Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW , Valeur J",Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption,Gut microbes,2019,Experiment 2,Norway,Homo sapiens,feces,UBERON:0001988,alcohol drinking,EFO:0004329,controls,alcohol overconsumers,NA,18,24,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,20 July 2019,Fatima Zohra,WikiWorks743,Taxa with statistical different relative levels between alcohol overconsumers and controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinatimonas,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia",2|976|200643|171549|1853231|283168;2|1239|909932|909929|1843491|52225;2|1239|186801|186802|186803|265975;2|1224|1236|135624|83763|674963;2|201174|84998|1643822|1643826|447020;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|201174|84998|84999|84107;2|976|200643|171549|171552|838;2|201174|84998|84999|84107|102106;2|201174|84998|84999;2|201174|84998;2|201174;2|976|200643|171549|171552;2|1239|186801|186802|216572|216851;2|1239|186801,Complete,NA
Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,intestinal metaplasia,gastric cancer,NA,37,17,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,helicobacter pylori,sex",NA,NA,decreased,NA,NA,decreased,Signature 1,Supplementary Figure 1,25 July 2019,Rimsha Azhar,"WikiWorks743,Fatima",The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|1283313;2|1239|186801|186802|186803|43996;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186806;2|32066|203490|203491|203492|848;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|437755;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186807|2740;2|1239|186801|186802|186804|1257;2|976|200643|171549|171552|838;2|201174|84998|1643822|1643826|84108;2|1239|91061|186826|1300|1301,Complete,NA
Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,intestinal metaplasia,gastric cancer,NA,37,17,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,helicobacter pylori,sex",NA,NA,decreased,NA,NA,decreased,Signature 2,Supplementary Figure 1,25 July 2019,Rimsha Azhar,WikiWorks743,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Portiera",2|1224|1236|2887326|468|469;2|1224|28216|206351|1499392|57739;2|1224|28216|32003|2008793|378210;2|1224|28221|213462|213465;2|1224|1236|135619|28256|235572,Complete,NA
Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,Experiment 2,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,atrophic gastric,gastric cancer,NA,37,74,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,helicobacter pylori,sex",NA,NA,unchanged,NA,NA,unchanged,Signature 1,Supplementary Figure 1,25 July 2019,Rimsha Azhar,WikiWorks743,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella",2|1239|91061|186826|1300|1301;2|1239|186801|186802|186804|1257;2|1239|91061|1385|1378;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186806|1730;2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|39948;2|201174|84998|1643822|1643826|84108;2|1239|186801|186802|186806;2|1239|186801|186802|186807|2740;2|1239|186801|186802|186803|43996;2|1239|186801|186802|186803|437755,Complete,NA
Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,Experiment 2,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,atrophic gastric,gastric cancer,NA,37,74,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,helicobacter pylori,sex",NA,NA,unchanged,NA,NA,unchanged,Signature 2,Supplementary Figure 1,25 July 2019,Rimsha Azhar,WikiWorks743,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Portiera",2|1224|28216|206351|1499392|57739;2|1224|1236|135619|28256|235572,Complete,NA
Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,Experiment 3,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,superficial gastric,gastric cancer,NA,37,77,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,helicobacter pylori,sex",NA,NA,decreased,NA,NA,decreased,Signature 1,Supplementary Figure 1,25 July 2019,Rimsha Azhar,WikiWorks743,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella",2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186804|1257;2|1239|91061|1385|1378;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|1283313;2|1239|186801|186802|186806|1730;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|39948;2|201174|84998|1643822|1643826|84108;2|1239|186801|186802|186806;2|1239|186801|186802|186807|2740;2|1239|186801|186802|186803|43996;2|1239|186801|186802|186803|437755,Complete,NA
Study 128,"cross-sectional observational, not case-control",28765474,10.1136/gutjnl-2017-314281,NA,"Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY , Yu J",Mucosal microbiome dysbiosis in gastric carcinogenesis,Gut,2018,Experiment 3,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,superficial gastric,gastric cancer,NA,37,77,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,helicobacter pylori,sex",NA,NA,decreased,NA,NA,decreased,Signature 2,Supplementary Figure 1,25 July 2019,Rimsha Azhar,WikiWorks743,The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Vogesella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Sterolibacteriaceae|g__Methyloversatilis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Candidatus Portiera",2|1224|28216|80840|80864;2|1224|28216|80840|80864|47420;2|1224|1236|2887326|468|469;2|1224|28216|206351|1499392|57739;2|1224|28216|32003|2008793|378210;2|1224|28221|213462|213465;2|1224|1236|135619|28256|235572,Complete,NA
Study 129,case-control,27346372,10.1038/srep28484,NA,"Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, Weinshenker BG, Rodriguez M, Kantarci OH, Nelson H, Murray JA , Mangalam AK",Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls,Scientific reports,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,healthy controls,multiple sclerosis,NA,36,31,current,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 3, Table 2",24 July 2019,Fatima Zohra,WikiWorks743,microbial signatures of the gut microbiota of MS patients,increased,"k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Mycoplana,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|976|117747|200666|84566;2|1239|186801|186802|186803;2|1224|28211|204458|76892;2|976|117743|200644|49546;2|1224|1236|72274|135621|351;2|976|117743|200644|49546|237;2|976|117747|200666|84566|84567;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|189330;2|1224|28211|356|118882|13159;2|1224|1236|72274|135621|286,Complete,NA
Study 129,case-control,27346372,10.1038/srep28484,NA,"Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, Weinshenker BG, Rodriguez M, Kantarci OH, Nelson H, Murray JA , Mangalam AK",Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls,Scientific reports,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,healthy controls,multiple sclerosis,NA,36,31,current,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 3, Table 2",24 July 2019,Fatima Zohra,WikiWorks743,microbial signatures of the gut microbiota of MS patients,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|201174;2|1224;2|201174|84998|84999|84107;2|976|200643|171549|171551;2|1239|526524|526525|128827;2|1239|91061|186826|33958;2|1239|909932|1843489|31977;2|1224|1236|91347|543;2|1224|1236|135625|712;2|201174|84998|84999|84107|102106;2|976|200643|171549|2005525|375288;2|1239|526524|526525|2810280|100883;2|1239|91061|186826|33958|1578;2|1224|1236|135625|712|724,Complete,NA
Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,low Southern European Atlantic Diet,high Southern European Atlantic Diet,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",3,7,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,23 July 2019,Lora Kasselman,WikiWorks743,"Bacterial groups quantified in human fecal samples in subjects with low, intermediate, and high adherence to Southern European Atlantic Diet (SEAD)",increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,low Southern European Atlantic Diet,intermediate Southern European Atlantic Diet,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",3,21,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,23 July 2019,Lora Kasselman,WikiWorks743,"Bacterial groups quantified in human fecal samples in subjects with low, intermediate, and high adherence to Southern European Atlantic Diet (SEAD)",increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,Experiment 3,Spain,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,<20 years participants,> 30 years participants,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,23 July 2019,Lora Kasselman,WikiWorks743,Gut microbiota composition in subjects of different age,increased,k__Bacteria|p__Proteobacteria,2|1224,Complete,Shaimaa Elsafoury
Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,Experiment 4,Spain,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,>20 years participants,20-30 years participants,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,15,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,30 April 2020,Shaimaa Elsafoury,WikiWorks743,Gut microbiota composition in subjects of different age,increased,k__Bacteria|p__Proteobacteria,2|1224,Complete,Shaimaa Elsafoury
Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,Experiment 5,Spain,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,20-30 years participants,> 30 years participants,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",15,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,30 April 2020,Shaimaa Elsafoury,WikiWorks743,Gut microbiota composition in subjects of different age,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Shaimaa Elsafoury
Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,Experiment 6,Spain,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,BMI < 20,BMI >25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,30 April 2020,Shaimaa Elsafoury,WikiWorks743,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Bacteroidetes",2|201174;2|976,Complete,Shaimaa Elsafoury
Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,Experiment 6,Spain,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,BMI < 20,BMI >25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,30 April 2020,Shaimaa Elsafoury,WikiWorks743,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,Experiment 7,Spain,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,BMI <20,BMI 20-25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",5,15,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,30 April 2020,Shaimaa Elsafoury,WikiWorks743,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,Shaimaa Elsafoury
Study 130,"cross-sectional observational, not case-control",28624933,10.1007/s13105-017-0570-4,NA,"Castro-Penalonga M, Roca-Saavedra P, Miranda JM, Porto-Arias JJ, Nebot C, Cardelle-Cobas A, Franco CM , Cepeda A",Influence of food consumption patterns and Galician lifestyle on human gut microbiota,Journal of physiology and biochemistry,2018,Experiment 8,Spain,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,BMI 20-25,BMI >25,"SEAD: Southern European Atlantic Diet. SEAD adherence was measured using an index of nine food components (fresh fish, cod, red meat and pork products, dairy products, legumes and vegetables, vegetable soup, po- tatoes, wholegrain bread and wine) that ranged from 0 (lowest adherence) to 9 (highest adherence).",15,11,6 months,16S,NA,RT-qPCR,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,30 April 2020,Shaimaa Elsafoury,WikiWorks743,Bacterial groups quantified in human fecal samples in subjects with different body mass index (BMI),increased,k__Bacteria|p__Actinobacteria,2|201174,Complete,Shaimaa Elsafoury
Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,Experiment 1,Brazil,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,Time 0 days controls,Time 7 days,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 1,"Table 1, Table 2, Table S2",23 July 2019,Lora Kasselman,WikiWorks743,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|1239|186801|186802|216572|119852;2|976|200643|171549|171551,Complete,Shaimaa Elsafoury
Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,Experiment 2,Brazil,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,Time 0 days Cara Cara,Time 7 days,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 1, Table 2, Table S3",23 July 2019,Lora Kasselman,WikiWorks743,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,2|1239|1737404|1737405|1737406,Complete,Shaimaa Elsafoury
Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,Experiment 2,Brazil,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,Time 0 days Cara Cara,Time 7 days,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Table 1, Table 2, Table S4",23 July 2019,Lora Kasselman,WikiWorks743,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,2|976|200643|171549|1853231|283168,Complete,Shaimaa Elsafoury
Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,Experiment 3,Brazil,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,Time 0 days Bahia,Time 7 days,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 1, Table 2, Table S5",23 July 2019,Lora Kasselman,WikiWorks743,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,2|1239|909932|1843489|31977,Complete,Shaimaa Elsafoury
Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,Experiment 4,Brazil,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,controls at time 7,Cara Cara,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, Table 2, Table S7",23 July 2019,Lora Kasselman,WikiWorks743,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium dolichum CAG:375,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",2|976|200643|171549|2005525|375288;2|976|200643|171549|2005519;2|1239|186801|186802|186806|1730|1263076;2|1239|186801|186802|31979;2|1239|186801|186802|186803|189330;2|1239|186801|186802|541000;2|1239|186801|186802|216572|244127;2|1224|1236|91347|543;2|976|200643|171549|1853231|574697,Complete,Shaimaa Elsafoury
Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,Experiment 4,Brazil,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,controls at time 7,Cara Cara,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 1, Table 2, Table S8",23 July 2019,Lora Kasselman,WikiWorks743,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,2|1239|186801|186802|990719,Complete,Shaimaa Elsafoury
Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,Experiment 5,Brazil,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,controls at time 7,Bahia,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, Table 2, Table S9",23 July 2019,Lora Kasselman,WikiWorks743,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",2|201174|84998|1643822|1643826|447020;2|1239|91061|186826|81852|1350;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802|541000;2|1239|186801|186802|216572|244127,Complete,Shaimaa Elsafoury
Study 131,randomized controlled trial,30644740,10.1021/acs.jafc.8b05408,NA,"Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L , Lajolo F",Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach,Journal of agricultural and food chemistry,2019,Experiment 6,Brazil,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,Bahia at time 7,Cara Cara,NA,21,21,current,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 1, Table 2, Table S11",23 July 2019,Lora Kasselman,WikiWorks743,"Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups",increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium dolichum CAG:375,2|1239|186801|186802|186806|1730|1263076,Complete,Shaimaa Elsafoury
Study 132,randomized controlled trial,30279332,10.3390/nu10101402,NA,"Hess J, Wang Q, Gould T , Slavin J",Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults,Nutrients,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,mushroom,Meat,NA,16,16,3 months,16S,123,Illumina,Linear Regression,0.004,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 9 and text,24 July 2019,Lora Kasselman,WikiWorks743,Percent abundance across 5 days of fecal collection for identified abundant bacterial taxa (mushroom diet vs meat diet),increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea",2|1239;2|1239|186801|186802|186803|189330,Complete,Shaimaa Elsafoury
Study 132,randomized controlled trial,30279332,10.3390/nu10101402,NA,"Hess J, Wang Q, Gould T , Slavin J",Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults,Nutrients,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,mushroom,Meat,NA,16,16,3 months,16S,123,Illumina,Linear Regression,0.004,TRUE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 9 and text,24 July 2019,Lora Kasselman,WikiWorks743,Percent abundance across 5 days of fecal collection for identified abundant bacterial taxa (mushroom diet vs meat diet),decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976;2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|207244;2|1224|28216|80840|995019|40544,Complete,Shaimaa Elsafoury
Study 133,"cross-sectional observational, not case-control",30188331,10.1097/GME.0000000000001202,NA,"Yoshikata R, Myint KZ, Ohta H , Ishigaki Y","Inter-relationship between diet, lifestyle habits, gut microflora, and the equol-producer phenotype: baseline findings from a placebo-controlled intervention trial","Menopause (New York, N.Y.)",2019,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,"Equol producer (""healhtier"" diet)","Equol NON producer (""unhealthier"" diet)",cross sectional,45,13,NA,16S,3,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, Table 3, and text",24 July 2019,Lora Kasselman,WikiWorks743,TABLE 2. Comparisons of microbial results between equol producers and nonproducers,increased,k__Bacteria|p__Proteobacteria,2|1224,Complete,NA
Study 133,"cross-sectional observational, not case-control",30188331,10.1097/GME.0000000000001202,NA,"Yoshikata R, Myint KZ, Ohta H , Ishigaki Y","Inter-relationship between diet, lifestyle habits, gut microflora, and the equol-producer phenotype: baseline findings from a placebo-controlled intervention trial","Menopause (New York, N.Y.)",2019,Experiment 2,Japan,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,"Equol producer (""healhtier"" diet)","Equol NON producer (""unhealthier"" diet)",cross sectional,45,13,NA,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Table 2, Table 3, and text",24 July 2019,Lora Kasselman,WikiWorks743,TABLE 2. Comparisons of microbial results between equol producers and nonproducers,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 134,randomized controlled trial,24296500,10.1128/AEM.03549-13,NA,"Roager HM, Licht TR, Poulsen SK, Larsen TM , Bahl MI","Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet",Applied and environmental microbiology,2014,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,before Average Danish Diet,6 months after Average Danish Diet,"the dietary intervention study of the NND compared to the ADD was performed as a 6-month, nonblinded, parallel, randomized, controlled, ad libitum dietary intervention trial and was carried out between October 2010 and July 2011.",26,26,NA,16S,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,10 August 2019,Lora Kasselman,WikiWorks743,"Changes in bacterial groups following the diet intervention within A) Firmicutes, B) Bacteroidetes, C) Actinobacteria, and D) γ-proteobacteria and other bacterial groups for the two diet groups ADD (n = 26, white bars) and NND (n = 36, black bars). Columns show means of log2 transformed data and error bars represent standard errors of the means. Asterisks indicate a significant difference (q < 0.05) compared to baseline. BCoAT: Butyryl-CoA:acetate CoAtransferase, NND: New Nordic Diet, ADD: Average Danish",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|1239|186801|186802|186803|2569097|39488;2|201174;2|1224|28221|213115|194924|872,Complete,Shaimaa Elsafoury
Study 134,randomized controlled trial,24296500,10.1128/AEM.03549-13,NA,"Roager HM, Licht TR, Poulsen SK, Larsen TM , Bahl MI","Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet",Applied and environmental microbiology,2014,Experiment 2,Denmark,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,before  New Nordic Diet,6 months after  New Nordic Diet,"the dietary intervention study of the NND compared to the ADD was performed as a 6-month, nonblinded, parallel, randomized, controlled, ad libitum dietary intervention trial and was carried out between October 2010 and July 2011.",36,36,NA,16S,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S3,4 May 2020,Shaimaa Elsafoury,WikiWorks743,"Changes in bacterial groups following the diet intervention within A) Firmicutes, B) Bacteroidetes, C) Actinobacteria, and D) γ-proteobacteria and other bacterial groups for the two diet groups ADD (n = 26, white bars) and NND (n = 36, black bars). Columns show means of log2 transformed data and error bars represent standard errors of the means. Asterisks indicate a significant difference (q < 0.05) compared to baseline. BCoAT: Butyryl-CoA:acetate CoAtransferase, NND: New Nordic Diet, ADD: Average Danish",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803|2569097|39488;2|1239|91061|186826|33958|1578|1579;2|201174;2|1224|1236|91347|543|561|562;2|1224|28221|213115|194924|872,Complete,Shaimaa Elsafoury
Study 134,randomized controlled trial,24296500,10.1128/AEM.03549-13,NA,"Roager HM, Licht TR, Poulsen SK, Larsen TM , Bahl MI","Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet",Applied and environmental microbiology,2014,Experiment 2,Denmark,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,before  New Nordic Diet,6 months after  New Nordic Diet,"the dietary intervention study of the NND compared to the ADD was performed as a 6-month, nonblinded, parallel, randomized, controlled, ad libitum dietary intervention trial and was carried out between October 2010 and July 2011.",36,36,NA,16S,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S3,4 May 2020,Shaimaa Elsafoury,WikiWorks743,"Changes in bacterial groups following the diet intervention within A) Firmicutes, B) Bacteroidetes, C) Actinobacteria, and D) γ-proteobacteria and other bacterial groups for the two diet groups ADD (n = 26, white bars) and NND (n = 36, black bars). Columns show means of log2 transformed data and error bars represent standard errors of the means. Asterisks indicate a significant difference (q < 0.05) compared to baseline. BCoAT: Butyryl-CoA:acetate CoAtransferase, NND: New Nordic Diet, ADD: Average Danish",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii",2|976|200643|171549|171550|239759;2157|28890|183925|2158|2159|2172|2173,Complete,Shaimaa Elsafoury
Study 135,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD , Lewis JD",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,low animal protein,High animal protein,high protein / low fiber,98,98,6 months,16S,12,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C and text,11 August 2019,Lora Kasselman,WikiWorks743,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 135,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD , Lewis JD",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,low animal protein,High animal protein,high protein / low fiber,98,98,6 months,16S,12,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C and text,11 August 2019,Lora Kasselman,WikiWorks743,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,2|976|200643|171549|171552,Complete,NA
Study 135,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD , Lewis JD",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber,Low fiber,high protein / low fiber,98,98,6 months,16S,12,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C and text,11 August 2019,Lora Kasselman,WikiWorks743,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Actinobacteria",2|976;2|201174,Complete,NA
Study 135,"cross-sectional observational, not case-control",21885731,10.1126/science.1208344,NA,"Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD , Lewis JD",Linking long-term dietary patterns with gut microbial enterotypes,"Science (New York, N.Y.)",2011,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber,Low fiber,high protein / low fiber,98,98,6 months,16S,12,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C and text,11 August 2019,Lora Kasselman,WikiWorks743,"The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.",decreased,k__Bacteria|p__Actinobacteria,2|201174,Complete,NA
Study 136,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV , Alexeev DG",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,Experiment 1,Russian Federation,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,"high vegetable, fruit, grain","Low vegetable, fruit, grains,",low fiber,215,215,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 and Figure 2,11 August 2019,Lora Kasselman,WikiWorks743,"Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary
recommendations. Red branches of the cladogram denote the taxa that were increased in abundance,
while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of
the effect size >2 in LEfSe method (n = 430 paired samples).",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|976|200643|171549|815;2|976|200643|171549|171551;2|976|200643|171549|171552;2|976|200643|171549|171550;2|1239|186801|186802|216572;2|1239|909932|1843488|909930;2|1239|909932|1843489|31977;2|1224|28216|80840|995019;2|1224|28221|213115|194924;2|1239|91061|186826|33958,Complete,NA
Study 136,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV , Alexeev DG",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,Experiment 1,Russian Federation,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,"high vegetable, fruit, grain","Low vegetable, fruit, grains,",low fiber,215,215,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 and Figure 2,11 August 2019,Lora Kasselman,WikiWorks743,"Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary
recommendations. Red branches of the cladogram denote the taxa that were increased in abundance,
while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of
the effect size >2 in LEfSe method (n = 430 paired samples).",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1239|186801|186802|31979|1485;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186803;2|1239|186801|186802|216572|459786;2157|28890|183925|2158|2159;2|201174|1760|85004|31953;2|201174|84998|84999|84107;2|1239|91061|1385|90964;2|1239|91061|186826|81852;2|1239|91061|186826|1300;2|1239|186801|186802|424536;2|1239|186801|186802|31979;2|1239|526524|526525|128827;2|1239;2|1224|28211|204457|41297;2|1224|1236|91347|543;2|74201|203494|48461|203557,Complete,NA
Study 136,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV , Alexeev DG",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,Experiment 2,Russian Federation,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,before dietary intervention,two weeks after a dietry intervention,NA,215,215,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure S8,7 May 2020,Shaimaa Elsafoury,WikiWorks743,"Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.",increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia",2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|404402|404403;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|1300|1357|1358;2|201174|1760|85004|31953|1678|216816|1679;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|1301;2|74201|203494|48461|203557;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300;2|1239|91061|186826|81852;2|74201|203494;2|74201|203494|48461;2|1239|186801|186802|186803|189330|88431;2|74201;2|1224|28211;2|1239|186801|186802|186806|1730;2|1239|91061;2|201174|1760|85004|31953|1678|1680;2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107|102106;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979;2|1239|186801|186802;2|1239|186801;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|1239|186801|186802|186803|572511,Complete,Shaimaa Elsafoury
Study 136,time series / longitudinal observational,29738477,10.3390/nu10050576,NA,"Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV , Alexeev DG",Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project,Nutrients,2018,Experiment 2,Russian Federation,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,before dietary intervention,two weeks after a dietry intervention,NA,215,215,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure S8,7 May 2020,Shaimaa Elsafoury,"WikiWorks743,Fatima","Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium succinatutens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum",2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|28111;2|1224|28221;2|1224|28221|213115|194924|872;2|1224|28221|213115;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|28050|39485;2|1239|91061|186826|33958;2|1239|909932|1843488|909930|33024|626940;2|976|200643|171549|815|909656|310297;2|1239|186801|186802|186803|841|301301;2|1239|186801|186802|216572|1263;2|201174|84998|1643822|1643826|84108;2|201174|84998|1643822|1643826|84108|572010;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|186801|186802|186803|2316020|46228;2|1239|186801|186802|216572|39492,Complete,Fatima
Study 137,case-control,31358825,10.1038/s41598-019-45588-z,NA,"Yang TW, Lee WH, Tu SJ, Huang WC, Chen HM, Sun TH, Tsai MC, Wang CC, Chen HY, Huang CC, Shiu BH, Yang TL, Huang HT, Chou YP, Chou CH, Huang YR, Sun YR, Liang C, Lin FM, Ho SY, Chen WL, Yang SF, Ueng KC, Huang HD, Huang CN, Jong YJ , Lin CC",Enterotype-based Analysis of Gut Microbiota along the Conventional Adenoma-Carcinoma Colorectal Cancer Pathway,Scientific reports,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,CRC,CRC positive during colonoscopy,104,62,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Figure 4A, Text",16 August 2019,Lora Kasselman,WikiWorks743,"Relative overall sample abundance in the 3 groups Binary logarithms of the relative abundance of a single genus in the normal, adenoma, and cancer groups. Each genus was present in more than 50% of the samples in the cancer group. Most of the significant differences were between the cancer group and the other 2 groups.",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1224|1236|135624|84642|642;2|32066|203490|203491|203492|848,Complete,NA
Study 137,case-control,31358825,10.1038/s41598-019-45588-z,NA,"Yang TW, Lee WH, Tu SJ, Huang WC, Chen HM, Sun TH, Tsai MC, Wang CC, Chen HY, Huang CC, Shiu BH, Yang TL, Huang HT, Chou YP, Chou CH, Huang YR, Sun YR, Liang C, Lin FM, Ho SY, Chen WL, Yang SF, Ueng KC, Huang HD, Huang CN, Jong YJ , Lin CC",Enterotype-based Analysis of Gut Microbiota along the Conventional Adenoma-Carcinoma Colorectal Cancer Pathway,Scientific reports,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,CRC,CRC positive during colonoscopy,104,62,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"Figure 4A, Text",16 August 2019,Lora Kasselman,WikiWorks743,"Relative overall sample abundance in the 3 groups Binary logarithms of the relative abundance of a single genus in the normal, adenoma, and cancer groups. Each genus was present in more than 50% of the samples in the cancer group. Most of the significant differences were between the cancer group and the other 2 groups.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|815|816;2|1224|28221|213115|194924|35832;2|1224|1236|91347|543|544;2|1224|1236|91347|543|413496;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186803|841,Complete,NA
Study 138,case-control,31065547,10.3389/fcimb.2019.00112,NA,"Zhuang H, Cheng L, Wang Y, Zhang YK, Zhao MF, Liang GD, Zhang MC, Li YG, Zhao JB, Gao YN, Zhou YJ , Liu SL",Dysbiosis of the Gut Microbiome in Lung Cancer,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,controls,lung cancer,NA,30,30,3 months,16S,34,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Supplementary Figure S3",27 August 2019,Rimsha Azhar,WikiWorks743,"The LDA score obtained by linear regression analysis (LDA), the larger the LDA score, the greater the influence of species abundance on the difference effect. LC, lung cancer",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|526524|526525|128827|1505663;2|1239|91061|1385|90964|69965;2|201174|1760|2037;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|1239|186801|186802|1392389;2|1224|1236|91347|543|160674;2|201174|84998|84999|1643824|1380;2|1239|526524|526525|128827|1573535;2|1239|91061|1385|90964,Complete,NA
Study 138,case-control,31065547,10.3389/fcimb.2019.00112,NA,"Zhuang H, Cheng L, Wang Y, Zhang YK, Zhao MF, Liang GD, Zhang MC, Li YG, Zhao JB, Gao YN, Zhou YJ , Liu SL",Dysbiosis of the Gut Microbiome in Lung Cancer,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,controls,lung cancer,NA,30,30,3 months,16S,34,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Supplementary Figure S3",27 August 2019,Rimsha Azhar,WikiWorks743,"The LDA score obtained by linear regression analysis (LDA), the larger the LDA score, the greater the influence of species abundance on the difference effect. LC, lung cancer",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lentibacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|201174|1760;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998|84999|84107|102106;2|1239|186801|186802|31979;2|1239|186801|186802|186803|189330;2|201174|84998|1643822|1643826|447020;2|1239|91061|1385|186817|175304;2|1224|1236|135622|72275|226;2|1239|186801|186802|216572|1508657;2|1224|1236|135622|72275;2|1239|186801|186802|186803|28050;2|1224|1236|135622;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|2005519|1348911;2|1239|186801|186802|186803|46205;2|1239|186801|186802|186803|437755;2|1224|28216|80840|995019|40544;2|1239|186801|186802|186804|1257,Complete,NA
Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,controls,HNSCC,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,129,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"ethnic group,sex","age,sex,smoking status",NA,NA,NA,NA,unchanged,unchanged,Signature 1,Table 2,4 September 2019,Utsav Patel,WikiWorks743,Median counts and Fold changes for the association between selected taxa and risk of HNSCC in a case-control study nested in 2 cohorts,increased,k__Bacteria|p__Actinobacteria,2|201174,Complete,Fatima Zohra
Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,controls,HNSCC,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,129,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"ethnic group,sex","age,sex,smoking status",NA,NA,NA,NA,unchanged,unchanged,Signature 2,Table 2,4 September 2019,Utsav Patel,WikiWorks743,Median counts and Fold changes for the association between selected taxa and risk of HNSCC in a case-control study nested in 2 cohorts,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria",2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|32257;2|976|200643|171549|171552|838|425941;2|976|117743|200644|49546|1016|327575;2|1239|909932|909929|1843491|970|69823;2|1224|28216,Complete,Fatima Zohra
Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,Experiment 2,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,controls,Larynx cancer cases,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,58,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"ethnic group,sex","age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 6, Text",4 September 2019,Utsav Patel,WikiWorks743,Median counts and Fold changes for the association between selected taxa and risk of HNSCC in a case-control study nested in 2 cohorts,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella denitrificans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales",2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|32257;2|1224|28216|206351|481|482;2|1239|91061|186826|186827|46123;2|976|117743|200644|49546|1016;2|1224|28216|206351|481|32257|502;2|1239|91061|186826|1300|1301|1305;2|1224|28216;2|1224|28216|206351,Complete,Fatima Zohra
Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,Experiment 3,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,controls,Pharynx cancer cases,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,30,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"ethnic group,sex","age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 6, Text",4 September 2019,Utsav Patel,WikiWorks743,Median counts and Fold changes for the association between selected taxa and risk of HNSCC in a case-control study nested in 2 cohorts,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella denticariosi,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella",2|201174|1760|2037|2049|1654|544580;2|1239|909932|1843489|31977|29465|419208;2|201174|1760|85007|1653|1716;2|1224|28216;2|1224|28216|206351;2|1224|28216|206351|481|32257,Complete,Fatima Zohra
Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,Experiment 4,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,controls,Oral cavity cancer cases,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,41,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"ethnic group,sex","age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Supplementary Table 6, Text",4 September 2019,Utsav Patel,WikiWorks743,Median counts and Fold changes for the association between selected taxa and risk of HNSCC in a case-control study nested in 2 cohorts,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,2|201174|1760|2037|2049|1654,Complete,Fatima Zohra
Study 139,case-control,29327043,10.1001/jamaoncol.2017.4777,NA,"Hayes RB, Ahn J, Fan X, Peters BA, Ma Y, Yang L, Agalliu I, Burk RD, Ganly I, Purdue MP, Freedman ND, Gapstur SM , Pei Z",Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer,JAMA oncology,2018,Experiment 4,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,controls,Oral cavity cancer cases,"histologically confirmed incident HNSCC including oral cavity, pharynx and larynx. (excluding salivary glands & nasopharynx)",254,41,NA,16S,34,Roche454,DESeq2,0.1,TRUE,NA,"ethnic group,sex","age,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Supplementary Table 6, Text",4 September 2019,Utsav Patel,WikiWorks743,Median counts and Fold changes for the association between selected taxa and risk of HNSCC in a case-control study nested in 2 cohorts,decreased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca",2|1239|1737404|1737405|1570339|543311|33033;2|1224|28216|206351|481|482|490,Complete,Fatima Zohra
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,controls,multiple sclerosis,multiple sclerosis,43,60,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq,increased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micromonosporales|f__Micromonosporaceae|g__Verrucosispora,k__Archaea|p__Euryarchaeota",2157|28890|183925|2158|2159|2172;2|74201|203494|48461|1647988|239934;2|201174|1760|85008|28056|84593;2157|28890,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,controls,multiple sclerosis,multiple sclerosis,43,60,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,2|976|200643|171549|1853231|574697,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,controls,multiple sclerosis,multiple sclerosis,43,60,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micromonosporales|f__Micromonosporaceae|g__Verrucosispora,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Archaea|p__Euryarchaeota",2|201174|1760|85008|28056|84593;2157|28890|183925|2158|2159|2172;2|74201|203494|48461|1647988|239934;2157|28890,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,controls,multiple sclerosis,multiple sclerosis,43,60,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,2|976|200643|171549|1853231|574697,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|74201|203494|48461|203557|2735;2|74201|203494|48461|1647988|239934,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|1853231|574697;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Verrucomicrobium,k__Archaea|p__Euryarchaeota,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|74201|203494|48461|203557|2735;2157|28890;2157|28890|183925|2158|2159|2172;2|74201|203494|48461|1647988|239934,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,controls,untreated multiple sclerosis,untreated multiple sclerosis,43,28,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|1853231|574697;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 5,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,untreated,treated multiple sclerosis,treated multiple sclerosis,28,32,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Illumina MiSeq,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 5,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,untreated,treated multiple sclerosis,treated multiple sclerosis,28,32,6 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Illumina MiSeq,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,2|1239|186801|186802|31979|1266,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 6,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,untreated,treated multiple sclerosis,treated multiple sclerosis,28,32,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Roche 454,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
Study 140,case-control,27352007,10.1038/ncomms12015,NA,"Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L , Weiner HL",Alterations of the human gut microbiome in multiple sclerosis,Nature communications,2016,Experiment 6,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,untreated,treated multiple sclerosis,treated multiple sclerosis,28,32,6 months,16S,345,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2c, Table 2",26 February 2020,Rimsha Azhar,WikiWorks743,Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Roche 454,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,2|1239|186801|186802|31979|1266,Complete,NA
Study 141,prospective cohort,30633889,10.1016/j.trsl.2018.12.005,NA,"Brown RG, Al-Memar M, Marchesi JR, Lee YS, Smith A, Chan D, Lewis H, Kindinger L, Terzidou V, Bourne T, Bennett PR , MacIntyre DA",Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes,Translational research : the journal of laboratory and clinical medicine,2019,Experiment 1,United Kingdom,Homo sapiens,vagina,UBERON:0000996,preterm premature rupture of the membranes,MONDO:0012511,controls,PPROM,(PPROM) preterm premature rupture of the membranes,36,60,9 months,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"body mass index,ethnic group,gestational age,maternal age",NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 3,8 September 2019,Rimsha Azhar,WikiWorks743,The effect size for each of the differentially abundant species was estimated using LDA,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|1737404|1737405|1570339|165779;2|201174|1760|2037|2049;2|1239|909932|1843489|31977|39948|309120;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|165779|33036;2|1239|1737404|1737405|1570339;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552|838|386414;2|1239|909932|1843489|31977;2|1239|909932;2|32066|203490|203491;2|32066;2|1239|186801|186802|186803|43996;2|1239|186801|186802|186803;2|976|200643|171549|171552;2|976|200643|171549;2|976;2|976|200643|171549|171552|838;2|976|200643;2|1239|91061|186826|1300|1301;2|1239|186801|186802;2|1239|186801;2|1239|91061|186826|1300,Complete,NA
Study 141,prospective cohort,30633889,10.1016/j.trsl.2018.12.005,NA,"Brown RG, Al-Memar M, Marchesi JR, Lee YS, Smith A, Chan D, Lewis H, Kindinger L, Terzidou V, Bourne T, Bennett PR , MacIntyre DA",Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes,Translational research : the journal of laboratory and clinical medicine,2019,Experiment 1,United Kingdom,Homo sapiens,vagina,UBERON:0000996,preterm premature rupture of the membranes,MONDO:0012511,controls,PPROM,(PPROM) preterm premature rupture of the membranes,36,60,9 months,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"body mass index,ethnic group,gestational age,maternal age",NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 3,8 September 2019,Rimsha Azhar,WikiWorks743,The effect size for each of the differentially abundant species was estimated using LDA,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes",2|1239|91061|186826|33958|2742598|1633;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061;2|1239,Complete,NA
Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,Controls,HNSCC,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) and had atleast one post-treatment salivary sample,25,17,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 6, Sup Fig1",11 September 2019,Utsav Patel,WikiWorks743,Relative abundance of oral microbiome in HNSCC patients and controls,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186804|1257;2|976|200643|171549|2005525|195950;2|1239|91061|1385|90964|1279;2|1239|1737404|1737405|1570339|543311;2|1239|909932|1843489|31977|29465,Complete,Rimsha Azhar
Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,Controls,HNSCC,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) and had atleast one post-treatment salivary sample,25,17,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 6, Sup Fig1",11 September 2019,Utsav Patel,WikiWorks743,Relative abundance of oral microbiome in HNSCC patients and controls,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1224|1236|135625|712|416916;2|1224|28216|80840|119060|47670;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|32066|203490|203491|1129771|32067,Complete,Rimsha Azhar
Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,Experiment 2,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,HPV -,HPV +,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) and had atleast one post-treatment salivary sample,4,7,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,"Figure 6, Text",11 September 2019,Utsav Patel,WikiWorks743,Relative abundance of oral microbiome in HNSCC HPV + and HPV -,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Weeksella",2|1239|91061|186826|33958|1578;2|976|117743|200644|2762318|1013,Complete,Rimsha Azhar
Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,Experiment 2,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,HPV -,HPV +,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) and had atleast one post-treatment salivary sample,4,7,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,"Figure 6, Text",11 September 2019,Utsav Patel,WikiWorks743,Relative abundance of oral microbiome in HNSCC HPV + and HPV -,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1224|28216|206351|481|538;2|1224|28216|206351|481|482;2|32066|203490|203491|1129771|32067,Complete,Rimsha Azhar
Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,Experiment 3,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,surgery,chemothrapy radiation and surgery,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) and had atleast one post-treatment salivary sample,NA,NA,NA,16S,345,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6, Text",11 September 2019,Utsav Patel,WikiWorks743,Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,Rimsha Azhar
Study 142,case-control,27259999,10.18632/oncotarget.9710,NA,"Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W , Sidransky D","16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment",Oncotarget,2016,Experiment 4,United States of America,Homo sapiens,oral gland,UBERON:0010047,squamous cell carcinoma,EFO:0000707,surgery,chemothrapy radiation and surgery,histopathologically confirmed HNSCC (Head & Neck Squamous Cell Cancer) and had atleast one post-treatment salivary sample,NA,NA,NA,16S,34,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6, Text",11 September 2019,Utsav Patel,WikiWorks743,Relative abundance of oral microbiome in chemo-radiation therapy/radiation and surgery,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1224|1236|135625|712|724;2|1224|1236|135625|712|416916;2|32066|203490|203491|1129771|32067,Complete,Rimsha Azhar
Study 143,"cross-sectional observational, not case-control",30239655,10.1093/ecco-jcc/jjy136,NA,"Kiernan MG, Coffey JC, McDermott K, Cotter PD, Cabrera-Rubio R, Kiely PA , Dunne CP",The Human Mesenteric Lymph Node Microbiome Differentiates Between Crohn's Disease and Ulcerative Colitis,Journal of Crohn's & colitis,2019,Experiment 1,Ireland,Homo sapiens,mesenteric lymph node,UBERON:0002509,inflammatory bowel disease,EFO:0003767,Ulcerative colitis,Crohn's disease,histopathologivally diagnosed ulcerative colitis and crohn's disease,8,5,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,increased,NA,NA,increased,Signature 1,Figure 3B,11 September 2019,Fatima Zohra,WikiWorks743,Abundance of phyla in MLN of crohn's disease (CD) and ulcerative colitis (UC) patients,increased,k__Bacteria|p__Proteobacteria,2|1224,Complete,Rimsha Azhar
Study 143,"cross-sectional observational, not case-control",30239655,10.1093/ecco-jcc/jjy136,NA,"Kiernan MG, Coffey JC, McDermott K, Cotter PD, Cabrera-Rubio R, Kiely PA , Dunne CP",The Human Mesenteric Lymph Node Microbiome Differentiates Between Crohn's Disease and Ulcerative Colitis,Journal of Crohn's & colitis,2019,Experiment 2,Ireland,Homo sapiens,mesenteric lymph node,UBERON:0002509,inflammatory bowel disease,EFO:0003767,Ulcerative colitis,Crohn's disease,histopathologivally diagnosed ulcerative colitis and crohn's disease,8,5,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,increased,NA,NA,increased,Signature 1,Figure 3B,11 September 2019,Fatima Zohra,WikiWorks743,Abundance of phyla in MLN of crohn's disease (CD) and ulcerative colitis (UC) patients,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,Rimsha Azhar
Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,air pollution,ENVO:02500037,lightly poluuted region (A),moderately polluted region (B),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,40,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,vital capacity,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, 4, 5, 6",19 September 2019,Rimsha Azhar,WikiWorks743,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239;2|201174;2|1239|186801;2|201174|1760;2|1239|186801|186802;2|201174|1760|2037;2|1239|186801|186802|186803;2|201174|1760|85006|1268;2|201174|1760|2037|2049;2|1239|186801|186802|541000;2|201174|1760|85006|1268|32207;2|1239|186801|186802|186803|265975;2|1224|28216|206351|481|482;2|201174|1760|2037|2049|1654,Complete,Shaimaa Elsafoury
Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,air pollution,ENVO:02500037,lightly poluuted region (A),moderately polluted region (B),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,40,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,vital capacity,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, 4, 5, 6",19 September 2019,Rimsha Azhar,WikiWorks743,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|976;2|32066;2|976|200643;2|32066|203490;2|976|200643|171549;2|32066|203490|203491;2|976|117743|200644;2|1224|1236|72274;2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|171551;2|32066|203490|203491|203492;2|1224|1236|2887326|468;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171551|836;2|32066|203490|203491|203492|848;2|1239|186801|186802|186804|1257;2|1224|1236|2887326|468|475,Complete,Shaimaa Elsafoury
Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,Experiment 2,China,Homo sapiens,throat,UBERON:0000341,air pollution,ENVO:02500037,lightly poluuted region (A),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,39,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,vital capacity,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, 4, 5, 6",19 September 2019,Rimsha Azhar,WikiWorks743,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239;2|1224;2|201174;2|1239|186801;2|1239|186801|186802|541000;2|1224|1236;2|1224|28211;2|1239|186801|186802;2|1239|186801|186802|186803,Complete,Shaimaa Elsafoury
Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,Experiment 2,China,Homo sapiens,throat,UBERON:0000341,air pollution,ENVO:02500037,lightly poluuted region (A),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",35,39,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,vital capacity,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, 4, 5, 6",19 September 2019,Rimsha Azhar,WikiWorks743,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",2|976;2|32066;2|976|200643;2|32066|203490;2|976|117743;2|976|200643|171549;2|32066|203490|203491;2|1224|28216|206351;2|976|117743|200644;2|1224|29547|213849;2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|171551;2|32066|203490|203491|203492;2|976|117743|200644|49546;2|1224|1236|2887326|468;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171551|836;2|32066|203490|203491|203492|848;2|976|117743|200644|49546|1016;2|1239|186801|186802|186804|1257;2|1224|1236|2887326|468|475;2|1224|29547|213849|72294|194,Complete,Shaimaa Elsafoury
Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,Experiment 3,China,Homo sapiens,throat,UBERON:0000341,air pollution,ENVO:02500037,moderately poluuted region (B),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",40,39,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,vital capacity,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, 4, 5, 6",19 September 2019,Rimsha Azhar,WikiWorks743,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales",2|1224;2|1224|1236;2|1224|28211;2|1224|1236|72274,Complete,Shaimaa Elsafoury
Study 144,"cross-sectional observational, not case-control",31126003,10.1016/j.envpol.2018.12.083,NA,"Li X, Sun Y, An Y, Wang R, Lin H, Liu M, Li S, Ma M , Xiao C",Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China,"Environmental pollution (Barking, Essex : 1987)",2019,Experiment 3,China,Homo sapiens,throat,UBERON:0000341,air pollution,ENVO:02500037,moderately poluuted region (B),heavily polluted region (C),"paticipants lived in any of those regions for more than 2 years. region A: (lightly polluted region of PM 2.5), region B: (moderately polluted region of PM 2.5) and region C: (heavily polluted region of PM 2.5)",40,39,3 months,16S,3,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,vital capacity,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, 4, 5, 6",19 September 2019,Rimsha Azhar,WikiWorks743,"Abundance analysis of the dominant bacterial taxa of A (lightly polluted region of PM 2.5), B (moderately polluted region of PM 2.5) and C (heavily polluted region of PM 2.5)",decreased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|32066;2|201174|1760;2|32066|203490;2|201174|1760|2037;2|32066|203490|203491;2|1224|28216|206351;2|1224|29547|213849;2|201174|1760|85006|1268;2|32066|203490|203491|203492;2|1224|28216|206351|481;2|32066|203490|203491|1129771;2|201174|1760|2037|2049;2|201174|1760|85006|1268|32207;2|32066|203490|203491|203492|848;2|1239|186801|186802|186803|265975;2|201174|1760|2037|2049|1654;2|1224|29547|213849|72294|194;2|1224|28216|206351|481|482,Complete,Shaimaa Elsafoury
Study 145,case-control,15987522,10.1186/1479-5876-3-27,NA,"Mager DL, Haffajee AD, Devlin PM, Norris CM, Posner MR , Goodson JM","The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects",Journal of translational medicine,2005,Experiment 1,United States of America,Homo sapiens,saliva,UBERON:0001836,oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"disgnosed oral squamous cell carcinoma via biopsy, age 18 years or older and immunocompetent",229,45,3 months,NA,NA,DNA-DNA Hybridization,Mann-Whitney (Wilcoxon),0.001,TRUE,NA,"age,sex,smoking behavior",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1 , Text",25 September 2019,Utsav Patel,WikiWorks743,Relative abundance of oral microbiome in oral squamous cell carcinoma patients and controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea",2|976|200643|171549|171552|838|28132;2|976|117743|200644|49546|1016|1017;2|1239|91061|186826|1300|1301|28037;2|976|117743|200644|49546|1016|1018,Complete,Rimsha Azhar
Study 145,case-control,15987522,10.1186/1479-5876-3-27,NA,"Mager DL, Haffajee AD, Devlin PM, Norris CM, Posner MR , Goodson JM","The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects",Journal of translational medicine,2005,Experiment 1,United States of America,Homo sapiens,saliva,UBERON:0001836,oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"disgnosed oral squamous cell carcinoma via biopsy, age 18 years or older and immunocompetent",229,45,3 months,NA,NA,DNA-DNA Hybridization,Mann-Whitney (Wilcoxon),0.001,TRUE,NA,"age,sex,smoking behavior",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1 , Text",25 September 2019,Utsav Patel,WikiWorks743,Relative abundance of oral microbiome in oral squamous cell carcinoma patients and controls,decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum",2|32066|203490|203491|1129771|32067|40542;2|1239|186801|186802|186803|1164882|467210,Complete,Rimsha Azhar
Study 146,case-control,28924229,10.1038/s41598-017-11779-9,NA,"Zhao H, Chu M, Huang Z, Yang X, Ran S, Hu B, Zhang C , Liang J",Variations in oral microbiota associated with oral cancer,Scientific reports,2017,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"subjects with oral squamous cell carcinoma and did not have detectable periodontal inflammation, visible carious lesions, oral mucosa disease or any sever systemic disorders such as diabetes, immune compromise or genetic diseases",40,40,2 weeks,16S,45,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 1,"Figure 1c, Figure 3b, 3c, Text",2 October 2019,Utsav Patel,WikiWorks743,Variations in oral microbiota associated with oral cancer,increased,"k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Spirochaetes",2|544448|31969|2085|2092|2093;2|203691|203692|136|2845253|157;2|1224|29547|213849|72294|194;2|1224|28216|206351|481|538;2|1239|909932|909929|1843491|82202;2|976|200643|171549|171552|1283313;2|32066|203490|203491|203492|848;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186804|1257;2|1239|186801|186802|186804|44259;2|1239|186801|186802|186807|2740;2|1239|186801|186802|186803|43996;2|1239|1737404|1737405|1570339|543311;2|976|117743|200644|49546|1016;2|1239|186801|186802|186804;2|1239|186801|186802|186803;2|976;2|32066;2|203691,Complete,Rimsha Azhar
Study 146,case-control,28924229,10.1038/s41598-017-11779-9,NA,"Zhao H, Chu M, Huang Z, Yang X, Ran S, Hu B, Zhang C , Liang J",Variations in oral microbiota associated with oral cancer,Scientific reports,2017,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,oral squamous cell carcinoma,EFO:0000199,Controls,oral squamous cell carcinoma (OSCC),"subjects with oral squamous cell carcinoma and did not have detectable periodontal inflammation, visible carious lesions, oral mucosa disease or any sever systemic disorders such as diabetes, immune compromise or genetic diseases",40,40,2 weeks,16S,45,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 2,"Figure 1c, Figure 3b, 3c, Text",2 October 2019,Utsav Patel,WikiWorks743,Variations in oral microbiota associated with oral cancer,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes",2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803|1213720;2|1239|91061|186826|186828|117563;2|1224|28216|80840|119060|47670;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|201174|1760|85004|31953|196081;2|201174|1760|85006|1268|32207;2|201174|1760|2037|2049|1654;2|201174;2|1239,Complete,Rimsha Azhar
Study 147,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y , Zhou L",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,squamous cell carcinoma,EFO:0000707,controls,laryngeal squamous cell carcinoma (LSCC),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Text, Supplementary Table S2",9 October 2019,Utsav Patel,WikiWorks743,Differences in bacterial communities in the throats of LSCC patients and control subjects,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186804|1257;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|43996;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|1224|28216|80840|119060|32008;2|1239|186801|186802|186804,Complete,Rimsha Azhar
Study 147,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y , Zhou L",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,squamous cell carcinoma,EFO:0000707,controls,laryngeal squamous cell carcinoma (LSCC),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Text, Supplementary Table S2",9 October 2019,Utsav Patel,WikiWorks743,Differences in bacterial communities in the throats of LSCC patients and control subjects,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207,Complete,Rimsha Azhar
Study 147,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y , Zhou L",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,Site 2 (site below the epiglottis in the throat),Site 1 (upper portion of throat near the epiglottis),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Text, Supplementary Table S2",9 October 2019,Utsav Patel,WikiWorks743,Differences in bacterial communities in the throats of LSCC patients and control subjects,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Candidatus Saccharibacteria",2|1239|909932|1843489|31977|29465;2|32066|203490|203491|1129771|32067;2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207;2|1239|91061|186826|186828|117563;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803|265975;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|186803|437755;2|95818,Complete,Rimsha Azhar
Study 147,case-control,25239901,10.1128/AEM.02329-14,NA,"Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, Hou D, Wang Y , Zhou L",Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma,Applied and environmental microbiology,2014,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,Site 2 (site below the epiglottis in the throat),Site 1 (upper portion of throat near the epiglottis),histopathological confirmation of Laryngeal squamous cell carcinoma and underwent total laryngectomy,28,27,3 months,16S,12,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 2, Text, Supplementary Table S2",9 October 2019,Utsav Patel,WikiWorks743,Differences in bacterial communities in the throats of LSCC patients and control subjects,decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186804|1257;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977|39948;2|544448|31969|2085|2092|2093;2|1239|186801|186802|186804|44259;2|1239|186801|186802|186803|43996;2|1224|28216|206351|481|538;2|203691|203692|136|2845253|157;2|1224|1236|135625|712|416916;2|1239|186801|186802|186804,Complete,Rimsha Azhar
Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,polycystic ovary syndrome,EFO:0000660,HC,NIR-PCOS,"diagnosed if two of the following were present: olig-/amenorrhea, clinical and/or biochemical hyperandrogenish, or polycystic ovaries",8,8,administration of antibiotics,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, Figure 3",9 October 2019,Fatima Zohra,WikiWorks743,Composition of gut microbial community among IR-PCOS  and NIR-PCOS patients and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira",2|976|200643|171549|815;2|1239|186801|186802|186803;2|976|200643|171549|815|816;2|1239|186801|186802|186803|28050,Complete,NA
Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,polycystic ovary syndrome,EFO:0000660,HC,NIR-PCOS,"diagnosed if two of the following were present: olig-/amenorrhea, clinical and/or biochemical hyperandrogenish, or polycystic ovaries",8,8,administration of antibiotics,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, Figure 3",9 October 2019,Fatima Zohra,WikiWorks743,Composition of gut microbial community among IR-PCOS  and NIR-PCOS patients and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552;2|976|200643|171549|171552|838,Complete,NA
Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,polycystic ovary syndrome,EFO:0000660,HC,IR-PCOS,"diagnosed if two of the following were present: olig-/amenorrhea, clinical and/or biochemical hyperandrogenish, or polycystic ovaries",8,9,administration of antibiotics,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, Figure 3",9 October 2019,Fatima Zohra,WikiWorks743,Composition of gut microbial community among IR-PCOS  and NIR-PCOS patients and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|1224|28216|80840|506;2|1239|186801|186802|186803|28050;2|976|200643|171549|815|816;2|976|200643|171549|815,Complete,NA
Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,polycystic ovary syndrome,EFO:0000660,HC,IR-PCOS,"diagnosed if two of the following were present: olig-/amenorrhea, clinical and/or biochemical hyperandrogenish, or polycystic ovaries",8,9,administration of antibiotics,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, Figure 3",9 October 2019,Fatima Zohra,WikiWorks743,Composition of gut microbial community among IR-PCOS  and NIR-PCOS patients and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552;2|976|200643|171549|171552|838,Complete,NA
Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,polycystic ovary syndrome,EFO:0000660,IR-PCOS,NIR-PCOS,"diagnosed if two of the following were present: olig-/amenorrhea, clinical and/or biochemical hyperandrogenish, or polycystic ovaries",8,9,administration of antibiotics,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 2, Figure 3",9 October 2019,Fatima Zohra,WikiWorks743,Composition of gut microbial community among IR-PCOS  and NIR-PCOS patients and healthy controls,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239;2|1239|186801|186802|541000;2|1239|186801|186802|186803;2|976|200643;2|976|200643|171549;2|976|200643|171549|815|816,Complete,NA
Study 148,case-control,30292647,10.1016/j.resmic.2018.09.002,NA,"Zeng B, Lai Z, Sun L, Zhang Z, Yang J, Li Z, Lin J , Zhang Z",Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study,Research in microbiology,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,polycystic ovary syndrome,EFO:0000660,IR-PCOS,NIR-PCOS,"diagnosed if two of the following were present: olig-/amenorrhea, clinical and/or biochemical hyperandrogenish, or polycystic ovaries",8,9,administration of antibiotics,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 2, Figure 3",9 October 2019,Fatima Zohra,WikiWorks743,Composition of gut microbial community among IR-PCOS  and NIR-PCOS patients and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia",2|976;2|976|200643|171549|815;2|1239|186801|186802|216572|216851;2|1239|186801|186802;2|1239|186801,Complete,NA
Study 149,case-control,30366118,10.1016/j.anaerobe.2018.10.009,NA,"Maya-Lucas O, Murugesan S, Nirmalkar K, Alcaraz LD, Hoyo-Vadillo C, Pizano-Zárate ML , García-Mena J",The gut microbiome of Mexican children affected by obesity,Anaerobe,2019,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,Obese,obesity,10,10,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 4A,16 October 2019,Rimsha Azhar,WikiWorks743,"Differentially abundant bacterial genera, families, or species",increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,2|1239|909932|909929|1843491|158846,Complete,NA
Study 149,case-control,30366118,10.1016/j.anaerobe.2018.10.009,NA,"Maya-Lucas O, Murugesan S, Nirmalkar K, Alcaraz LD, Hoyo-Vadillo C, Pizano-Zárate ML , García-Mena J",The gut microbiome of Mexican children affected by obesity,Anaerobe,2019,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,controls,Obese,obesity,10,10,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,Figure 4A,16 October 2019,Rimsha Azhar,WikiWorks743,"Differentially abundant bacterial genera, families, or species",decreased,"k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Archaea|p__Crenarchaeota|c__Thermoprotei|o__Desulfurococcales|f__Desulfurococcaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|1224|28221;2157|28889|183924|114380|2272;2|1224|28221|213118;2|1239|91061|186826|1300|1301|1308;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|186803|207244;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;2|1239|526524|526525|128827|61170;2|976|200643|171549|815|816|674529;2|1239|186801|186802|186803|2719313|358743;2|1224|28221|213115|194924|35832|35833;2|976|200643|171549|815|816|291644;2|976|200643|171549|815|816|371601;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816;2|976|200643|171549|815,Complete,NA
Study 150,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L, Yin G, Guo Y, Zhao Y, Zhao M, Lai Y, Sui P, Shi T, Guo W , Huang Z",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,head and neck carcinoma,MONDO:0002038,Healthy controls,Throat cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",29,32,6 months,16S,3,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 2, Figure 3, Text",16 October 2019,Utsav Patel,WikiWorks743,Variations in oral microbiota composition associated with a risk of Throat Cancer,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales",2|1224|1236|72274|135621|286;2|1224|1236|135625|712|416916;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1508657;2|1224|28216|80840|119060|47670;2|976|200643|171549|815|909656;2|976|200643|171549|815|816;2|976|200643|171549|171552;2|1224|1236|72274|135621|351;2|976|200643|171549|815;2|1224|28216|80840|119060;2|1224|28216|80840;2|1224|28211;2|1224|28211|766,Complete,Fatima Zohra
Study 150,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L, Yin G, Guo Y, Zhao Y, Zhao M, Lai Y, Sui P, Shi T, Guo W , Huang Z",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,head and neck carcinoma,MONDO:0002038,Healthy controls,Throat cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",29,32,6 months,16S,3,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,"Figure 2, Figure 3, Text",16 October 2019,Utsav Patel,"WikiWorks743,Lwaldron",Variations in oral microbiota composition associated with a risk of Throat Cancer,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetes|c__Spirochaetia,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|1236|135625|712|713;2|1239|186801|186802|543314|109326;2|976|117743|200644|2762318|59735;2|1224|29547|213849|72294|194;2|1224|29547|213849|72294;2|1224|29547|213849;2|363464;2|95818;2|1239|186801;2|201174|1760|85007|1653;2|201174|1760|85007;2|201174|1760|85007|1653|1716;2|1224|29547;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1239|186801|186802|186803|1506553;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1224|1236|2887326|468|475;2|1224|1236|2887326|468;2|1239|909932;2|1224|28216|206351|481|482;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186804;2|1239|186801|186802|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|186801|186802|186803|841;2|201174|1760|85006|1268|32207;2|1239|909932|909929;2|1239|909932|909929|1843491|970;2|203691|203692|136|137;2|203691|203692|136;2|203691|203692;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,Fatima
Study 150,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L, Yin G, Guo Y, Zhao Y, Zhao M, Lai Y, Sui P, Shi T, Guo W , Huang Z",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,head and neck carcinoma,MONDO:0002038,Vocal cord polyp,Cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",9,32,6 months,16S,3,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 2, Figure 3, Text",16 October 2019,Utsav Patel,WikiWorks743,Variations in oral microbiota composition associated with a risk of Throat Cancer,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",2|1224|1236|91347|543|547;2|1224|1236|135625|712|416916;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|351,Complete,Fatima Zohra
Study 150,case-control,31334130,10.3389/fcimb.2019.00205,NA,"Wang L, Yin G, Guo Y, Zhao Y, Zhao M, Lai Y, Sui P, Shi T, Guo W , Huang Z",Variations in Oral Microbiota Composition Are Associated With a Risk of Throat Cancer,Frontiers in cellular and infection microbiology,2019,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,head and neck carcinoma,MONDO:0002038,Vocal cord polyp,Cancer,"throat cancer including cancer of oropharynx, hypopharynx, nasopharynx and larynx",9,32,6 months,16S,3,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 2, Figure 3, Text",16 October 2019,Utsav Patel,WikiWorks743,Variations in oral microbiota composition associated with a risk of Throat Cancer,decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Lentimicrobiaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Defluviitaleaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales",2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|186801|186802|186804|44259;2|1224|1236|135625|712|713;2|1224|29547|213849|72293|209;2|976|200643|171549|171550;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186803|841;2|1239|186801|186802|543314|109326;2|1224|28221|213115|194924|872;2|1239|186801|186802|186803|43994;2|32066|203490;2|32066;2|32066|203490|203491;2|32066|203490|203491|203492;2|32066|203490|203491|1129771;2|1239|186801|186802|186804;2|95818;2|976|117747|200666;2|976|117747;2|976|200643|171549|1840213;2|1224|29547|213849|72293;2|363464;2|1224|28211|204458|76892;2|1224|28211|204458;2|1239|186801|186802|1185407;2|1224|28221|213115|194924;2|1224|28221|213115,Complete,Fatima Zohra
Study 151,case-control,30081953,10.1186/s40168-018-0515-3,NA,"Zhu J, Liao M, Yao Z, Liang W, Li Q, Liu J, Yang H, Ji Y, Wei W, Tan A, Liang S, Chen Y, Lin H, Zhu X, Huang S, Tian J, Tang R, Wang Q , Mo Z",Breast cancer in postmenopausal women is associated with an altered gut metagenome,Microbiome,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,breast cancer,MONDO:0007254,controls,Postmenopausal breast cancer patients,Postmenopausal breast cancer patients,46,44,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,unchanged,Signature 1,Table 2 and Supplementary Table S4,21 October 2019,Rimsha Azhar,WikiWorks743,Relative abundance of the different species between postmenopausal breast cancer patients and postmenopausal healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella boydii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio cholerae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia fergusonii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella flexneri,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter johnsonii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia rettgeri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia amylovora,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Bruguierivoracaceae|g__Sodalis|s__Sodalis glossinidius,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter radioresistens,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia enterocolitica,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella putrefaciens",2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|620|624;2|1224|1236|91347|1903414|583|584;2|1224|1236|91347|543|620|621;2|1224|1236|135623|641|662|666;2|1224|1236|91347|543|561|564;2|1224|1236|91347|543|620|623;2|1224|1236|2887326|468|469|470;2|1224|1236|2887326|468|469|40214;2|1224|1236|91347|1903414|586|587;2|1239|91061|186826|33958|2742598|97478;2|976|200643|171549|171551|836|281920;2|32066|203490|203491|203492|848|851;2|1224|1236|91347|543|544|545;2|1224|28221|213115|194924|872|901;2|1239|91061|186826|81852|1350|1353;2|1224|1236|91347|543|590|28901;2|1224|1236|91347|1903409|551|552;2|1224|1236|91347|2812006|84565|63612;2|1224|1236|2887326|468|469|40216;2|32066|203490|203491|203492|848|856;2|1239|909932|1843488|909930|904|187327;2|976|200643|171549|171552|838|419005;2|1224|1236|91347|1903411|629|630;2|1239|1737404|1737405|1570339|165779|33037;2|1224|1236|135622|267890|22|24,Complete,Fatima Zohra
Study 151,case-control,30081953,10.1186/s40168-018-0515-3,NA,"Zhu J, Liao M, Yao Z, Liang W, Li Q, Liu J, Yang H, Ji Y, Wei W, Tan A, Liang S, Chen Y, Lin H, Zhu X, Huang S, Tian J, Tang R, Wang Q , Mo Z",Breast cancer in postmenopausal women is associated with an altered gut metagenome,Microbiome,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,breast cancer,MONDO:0007254,controls,Postmenopausal breast cancer patients,Postmenopausal breast cancer patients,46,44,3 months,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,unchanged,Signature 2,Table 2 and Supplementary Table S4,21 October 2019,Rimsha Azhar,WikiWorks743,Relative abundance of the different species between postmenopausal breast cancer patients and postmenopausal healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia albertii,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella melitensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis",2|1239|186801|186802|186803|28050|39485;2|1224|1236|91347|543|561|208962;2|1224|29547|213849|72294|194|199;2|1239|186801|186802|186803|841|360807;2|1224|28211|356|118882|234|29459;2|1239|91061|186826|33958|2742598|1633,Complete,Fatima Zohra
Study 152,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z, Wang Q, Zhao J, Gong L, Zhang Y, Wang X , Yuan Z",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 3,22 October 2019,Fatima Zohra,WikiWorks743,Alpha diversity and composition of gut microbiome in patients with cervical cancer,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea",2|1224|1236|135624|83763|83770;2|1239|186801|186802|216572|1263;2|1224|1236|91347|1903414|581;2|1224|1236|135622|267890|22;2|1224|1236|91347|1903414|583;2|1239|186801|186802|186803|189330,Complete,NA
Study 152,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z, Wang Q, Zhao J, Gong L, Zhang Y, Wang X , Yuan Z",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 3,22 October 2019,Fatima Zohra,WikiWorks743,Alpha diversity and composition of gut microbiome in patients with cervical cancer,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1224|1236|135619|28256|2745;2|1239|909932|1843488|909930|33024,Complete,NA
Study 152,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z, Wang Q, Zhao J, Gong L, Zhang Y, Wang X , Yuan Z",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 4, Table 3, Figure 5",22 October 2019,Fatima Zohra,WikiWorks743,Alpha diversity and composition of gut microbiome in patients with cervical cancer,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris",2|976|200643|171549|815|909656|310297;2|1224;2|1224|1236;2|1224|1236|91347|543;2|1224|1236|91347;2|976|200643|171549|2005525|375288;2|976|200643|171549|2005525|375288|823;2|1224|1236|91347|543|561|562;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|841|360807;2|976|200643|171549|815|816|46506,Complete,NA
Study 152,case-control,30904962,10.1186/s13568-019-0763-z,NA,"Wang Z, Wang Q, Zhao J, Gong L, Zhang Y, Wang X , Yuan Z",Altered diversity and composition of the gut microbiome in patients with cervical cancer,AMB Express,2019,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer,pathology confirmed cervical cancer patients,5,8,2 months,16S,4,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 4, Table 3, Figure 5",22 October 2019,Fatima Zohra,WikiWorks743,Alpha diversity and composition of gut microbiome in patients with cervical cancer,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes",2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930;2|1239|909932|909929;2|1239|909932,Complete,NA
Study 153,case-control,31379800,10.3389/fmicb.2019.01664,NA,"Ma X, Chi C, Fan L, Dong B, Shao X, Xie S, Li M , Xue W",The Microbiome of Prostate Fluid Is Associated With Prostate Cancer,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,prostate gland secretion,UBERON:0004796,prostate cancer,MONDO:0008315,controls,prostate cancer,Prostate cancer,27,32,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,increased,NA,unchanged,Signature 1,Figure 5,23 October 2019,Rimsha Azhar,WikiWorks743,The differences in microbial species between the prostate cancer and non-prostate cancer patients were explored,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",2|1239|91061|186826|1300|1357;2|1239|91061|186826|186828|2747;2|1239|91061|186826|1300|1301;2|1239|91061|1385|186817|129337;2|1224|1236|91347|543|547,Complete,NA
Study 153,case-control,31379800,10.3389/fmicb.2019.01664,NA,"Ma X, Chi C, Fan L, Dong B, Shao X, Xie S, Li M , Xue W",The Microbiome of Prostate Fluid Is Associated With Prostate Cancer,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,prostate gland secretion,UBERON:0004796,prostate cancer,MONDO:0008315,controls,prostate cancer,Prostate cancer,27,32,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,increased,NA,unchanged,Signature 2,Figure 5,23 October 2019,Rimsha Azhar,WikiWorks743,The differences in microbial species between the prostate cancer and non-prostate cancer patients were explored,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus",2|1224|1236|91347|543|413496;2|1239|186801|186802|31979|114627;2|1239|91061|1385|186822|44249,Complete,NA
Study 154,case-control,31250341,10.1007/s11684-019-0695-7,NA,"Zhang H, Chang Y, Zheng Q, Zhang R, Hu C , Jia W",Altered intestinal microbiota associated with colorectal cancer,Frontiers of medicine,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy controls,colorectal cancer,diagnosed only with colorectal cancer with endoscopy,14,9,30 days,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,"Figure 3, Supplementary table 2, table 2",24 October 2019,Fatima Zohra,WikiWorks743,Altered intestinal microbiota associated with colorectal cancer,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium",2|1224|28211|356|45401;2|1224|28211|356|2831106|46913;2|1224|28211|356;2|1224|28211;2|1239|91061|1385|186822|44249;2|1239|91061|1385|186822;2|976|117743|200644|2762318|59732,Complete,NA
Study 154,case-control,31250341,10.1007/s11684-019-0695-7,NA,"Zhang H, Chang Y, Zheng Q, Zhang R, Hu C , Jia W",Altered intestinal microbiota associated with colorectal cancer,Frontiers of medicine,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy controls,colorectal cancer,diagnosed only with colorectal cancer with endoscopy,14,9,30 days,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,"Figure 3, Supplementary table 2, table 2",24 October 2019,Fatima Zohra,WikiWorks743,Altered intestinal microbiota associated with colorectal cancer,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1239|186801|186802|31979;2|1224|28221;2|1224|28221|213115;2|1239|186801|186802|186806|1730;2|1224|1236|91347|543|570;2|32066|203490|203491|1129771|32067;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|543314|86331;2|1224|1236|91347|1903411|613,Complete,NA
Study 155,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters BA, Wu J, Pei Z, Yang L, Purdue MP, Freedman ND, Jacobs EJ, Gapstur SM, Hayes RB , Ahn J",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,esophageal cancer,MONDO:0007576,controls,Esophageal Adenocarcinoma (EAC),diagnosed with easophageal cancer anytime after oral wash sample collection,160,81,NA,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1, Text",29 October 2019,Utsav Patel,WikiWorks743,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|976|200643|171549|2005525|195950|28112;2|201174|1760|2037|2049|2529408|181487;2|1239|909932|1843489|31977|29465;2|1239|909932|909929|1843491|970,Complete,Fatima Zohra
Study 155,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters BA, Wu J, Pei Z, Yang L, Purdue MP, Freedman ND, Jacobs EJ, Gapstur SM, Hayes RB , Ahn J",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,esophageal cancer,MONDO:0007576,controls,Esophageal Adenocarcinoma (EAC),diagnosed with easophageal cancer anytime after oral wash sample collection,160,81,NA,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1, Text",29 October 2019,Utsav Patel,WikiWorks743,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|976|200643|171549|171552|1283313;2|1239|186801|186802|186803|265975;2|1239|526524|526525|128827|123375;2|1224|28216|206351|481|482;2|201174|1760|85007|1653|1716|61592;2|976|200643|171549|171552|838|425941;2|1239|91061|186826|1300|1301|1313;2|1239|186801|186802|186803|1164882|617123;2|1239|186801|186802|186803|265975|1501329;2|1239|526524|526525|128827|123375|102148;2|1224|28216|206351|481|482|484;2|1224|28216|206351|481|482|490;2|1224|1236|135625|712|724,Complete,Fatima Zohra
Study 155,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters BA, Wu J, Pei Z, Yang L, Purdue MP, Freedman ND, Jacobs EJ, Gapstur SM, Hayes RB , Ahn J",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,esophageal cancer,MONDO:0007576,controls,Esophageal Squamous cell carcinoma (ESCC),diagnosed with easophageal cancer anytime after oral wash sample collection,50,25,NA,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1, Text",29 October 2019,Utsav Patel,WikiWorks743,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria weaveri,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema vincentii",2|976|200643|171549|171552|838|425941;2|976|117743|200644|2762318|59735;2|1224|28216|206351|481|482|28091;2|203691|203692|136|2845253|157|69710,Complete,Fatima Zohra
Study 155,case-control,29196415,10.1158/0008-5472.CAN-17-1296,NA,"Peters BA, Wu J, Pei Z, Yang L, Purdue MP, Freedman ND, Jacobs EJ, Gapstur SM, Hayes RB , Ahn J",Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers,Cancer research,2017,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,esophageal cancer,MONDO:0007576,controls,Esophageal Squamous cell carcinoma (ESCC),diagnosed with easophageal cancer anytime after oral wash sample collection,50,25,NA,16S,4,Illumina,Logistic Regression,0.05,FALSE,NA,"age,race,sex","alcohol drinking,body mass index,smoking behavior",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1, Text",29 October 2019,Utsav Patel,WikiWorks743,"Oral Microbiome composition and prospective risk for esophageal cancer, no significance for q-value",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus",2|1239|186801|186802|186803;2|976|200643|171549|171552|838;2|1224|1236|135625|712|416916|732,Complete,Fatima Zohra
Study 156,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi YF, Sun JN, Ren LF, Cao XL, Dong JH, Tao K, Guan XM, Cui YN , Su W","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,88,116,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,30 October 2019,Fatima Zohra,WikiWorks743,Most differentially abundant taxa between healthy controls and gastric cancer patients,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543;2|1224;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|91061;2|1239|91061|186826;2|1224|1236|91347|543|570;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|976|200643|171549|171551;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|201174|1760;2|201174;2|1239|909932|1843489|31977|29465;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|186802|990719|990721;2|1239|186801|186802|990719;2|976|200643|171549|2005525|375288,Complete,Shaimaa Elsafoury
Study 156,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi YF, Sun JN, Ren LF, Cao XL, Dong JH, Tao K, Guan XM, Cui YN , Su W","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,88,116,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,30 October 2019,Fatima Zohra,WikiWorks743,Most differentially abundant taxa between healthy controls and gastric cancer patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rectale CAG:36,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium",2|1239|186801|186802;2|1239|186801;2|1239;2|1239|186801|186802|186803;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186806|1730|1263079;2|1239|186801|186802|541000;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|1506553,Complete,Shaimaa Elsafoury
Study 156,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi YF, Sun JN, Ren LF, Cao XL, Dong JH, Tao K, Guan XM, Cui YN , Su W","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,48,48,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary figure 3,30 October 2019,Fatima Zohra,WikiWorks743,Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched,increased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae",2|1239|526524|526525|128827|1729679;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|91061;2|1239|91061|186826;2|1224|1236|91347|543|570;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|201174|1760;2|201174;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|990719,Complete,Shaimaa Elsafoury
Study 156,case-control,30535886,10.1007/s10620-018-5411-y,NA,"Qi YF, Sun JN, Ren LF, Cao XL, Dong JH, Tao K, Guan XM, Cui YN , Su W","Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China",Digestive diseases and sciences,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,gastric adenocarcinoma,EFO:0000503,healthy controls,Gastric cancer,gastric carcinoma confirmed by pathological examination,48,48,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary figure 3,30 October 2019,Fatima Zohra,WikiWorks743,Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rectale CAG:36,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium",2|1224|28216|80840;2|1224|28216;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186803;2|1239|186801|186802|186806|1730|1263079;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|1506553,Complete,Shaimaa Elsafoury
Study 157,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X, Winckler B, Lu M, Cheng H, Yuan Z, Yang Y, Jin L , Ye W",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,esophageal cancer,MONDO:0007576,Dysplasia,Esophageal Squamous cell carcinoma (ESCC),"Histopathological confirmation, complete questionnaire with saliva sample",63,87,1 month,16S,34,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,"Fig 1, Table 2, Table 3",5 November 2019,Utsav Patel,WikiWorks743,Oral microbiota and Risk for Esophageal Squamous cell carcinoma,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|976|200643|171549|171551|836;2|1239|91061|186826|33958|1578,Complete,NA
Study 157,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X, Winckler B, Lu M, Cheng H, Yuan Z, Yang Y, Jin L , Ye W",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,esophageal cancer,MONDO:0007576,Dysplasia,Esophageal Squamous cell carcinoma (ESCC),"Histopathological confirmation, complete questionnaire with saliva sample",63,87,1 month,16S,34,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,"Fig 1, Table 2, Table 3",5 November 2019,Utsav Patel,WikiWorks743,Oral microbiota and Risk for Esophageal Squamous cell carcinoma,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum",2|1239|909932|1843489|31977|29465;2|1224|28216|206351|481|482;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|201174|1760|85006|1268|32207;2|32066|203490|203491|1129771|32067;2|1224|29547|213849|72294|194;2|1224|1236|135625|712|416916;2|1239|186801|186802|186803|265975;2|201174|84998|84999|1643824|1380;2|1224|28216|80840|119060|47670;2|1239|526524|526525|128827|118747;2|1239|186801|186802|186803|43996;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186807|2740;2|1224|1236|135615|868|2717;2|1224|28216|80840|75682|963,Complete,NA
Study 157,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X, Winckler B, Lu M, Cheng H, Yuan Z, Yang Y, Jin L , Ye W",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,esophageal cancer,MONDO:0007576,controls,Esophageal Squamous cell carcinoma (ESCC),"Histopathological confirmation, complete questionnaire with saliva sample",85,87,1 month,16S,34,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Fig 1, Table 2, Table 3",5 November 2019,Utsav Patel,WikiWorks743,Oral microbiota and Risk for Esophageal Squamous cell carcinoma,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|976|200643|171549|171551|836;2|976|117743|200644|49546|1016;2|976|117743|200644|2762318|308865;2|976|200643|171549|815|816,Complete,NA
Study 157,case-control,26641451,10.1371/journal.pone.0143603,NA,"Chen X, Winckler B, Lu M, Cheng H, Yuan Z, Yang Y, Jin L , Ye W",Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China,PloS one,2015,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,esophageal cancer,MONDO:0007576,controls,Esophageal Squamous cell carcinoma (ESCC),"Histopathological confirmation, complete questionnaire with saliva sample",85,87,1 month,16S,34,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Fig 1, Table 2, Table 3",5 November 2019,Utsav Patel,WikiWorks743,Oral microbiota and Risk for Esophageal Squamous cell carcinoma,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",2|1239|909932|1843489|31977|29465;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|201174|1760|85006|1268|32207;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|906;2|1224|29547|213849|72294|194;2|1239|909932|909929|1843491|970;2|1224|1236|135625|712|416916;2|1239|186801|186802|186804|1257;2|1239|186801|186802|186803|265975;2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|1224|28216|80840|119060|47670;2|1239|526524|526525|128827|118747;2|1239|186801|186802|186803|43996;2|1239|186801|186802|186804|44259;2|201174|1760|85007|1653|1716;2|544448|31969|186329|2146|2147;2|1239|186801|186802|186803|830;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186807|2740;2|1224|1236|135615|868|2717,Complete,NA
Study 158,case-control,30416659,NA,NA,"Zhang WQ, Zhao SK, Luo JW, Dong XP, Hao YT, Li H, Shan L, Zhou Y, Shi HB, Zhang ZY, Peng CL , Zhao XG",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,healthy volunteers,lung cancer,patients had a definite postoperative pathological diagnosis,41,41,12 months,16S,12,Illumina,Metastats,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,6 November 2019,Fatima Zohra,WikiWorks743,Significant differences of the predominant taxa from lung cancer patients and healthy volunteers,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976;2|32066;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|203492|848;2|1239|909932|1843488|909930|33024,Complete,NA
Study 158,case-control,30416659,NA,NA,"Zhang WQ, Zhao SK, Luo JW, Dong XP, Hao YT, Li H, Shan L, Zhou Y, Shi HB, Zhang ZY, Peng CL , Zhao XG",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,healthy volunteers,lung cancer,patients had a definite postoperative pathological diagnosis,41,41,12 months,16S,12,Illumina,Metastats,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,6 November 2019,Fatima Zohra,WikiWorks743,Significant differences of the predominant taxa from lung cancer patients and healthy volunteers,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1239;2|1224|1236|91347|543|579;2|1239|186801|186802|216572|216851;2|1224|1236|91347|543|547;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,NA
Study 158,case-control,30416659,NA,NA,"Zhang WQ, Zhao SK, Luo JW, Dong XP, Hao YT, Li H, Shan L, Zhou Y, Shi HB, Zhang ZY, Peng CL , Zhao XG",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,healthy volunteers,lung cancer,patients had a definite postoperative pathological diagnosis,41,41,12 months,16S,12,Illumina,LEfSe,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,6 November 2019,Fatima Zohra,WikiWorks743,Different structures of fecal microbiota from patients with lung cancer and healthy volunteers,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae",2|976;2|976|200643;2|976|200643|171549;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552;2|976|200643|171549|815|909656|310297;2|1224|1236|91347|543|570;2|32066;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492,Complete,NA
Study 158,case-control,30416659,NA,NA,"Zhang WQ, Zhao SK, Luo JW, Dong XP, Hao YT, Li H, Shan L, Zhou Y, Shi HB, Zhang ZY, Peng CL , Zhao XG",Alterations of fecal bacterial communities in patients with lung cancer,American journal of translational research,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,healthy volunteers,lung cancer,patients had a definite postoperative pathological diagnosis,41,41,12 months,16S,12,Illumina,LEfSe,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,6 November 2019,Fatima Zohra,WikiWorks743,Different structures of fecal microbiota from patients with lung cancer and healthy volunteers,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1239|186801|186802|186803;2|1239|909932|1843489|31977|39948;2|1224|1236|91347|543|547;2|1239|186801|186802|216572|216851;2|1239|186801|186802|541000;2|1239|186801|186802;2|1239|186801;2|1224;2|1239;2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,NA
Study 159,time series / longitudinal observational,30542916,10.1007/s00284-018-1610-1,NA,"Guo R, Liu H, Li X, Yang Q, Jia L, Zheng Y , Li W",Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients,Current microbiology,2019,Experiment 1,China,Homo sapiens,dental plaque,UBERON:0016482,gingival disease,EFO:0009670,before,1 month after the placement of the brackets,subgingial microbial changes during fixed appliance treatment,10,10,1 month,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 5,6 November 2019,Rimsha Azhar,WikiWorks743,Relative abundance of microbiota that showed statistically significant differences among three different time points,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|1224|1236|135625|712|713;2|976|117743|200644|49546|1016,Complete,NA
Study 159,time series / longitudinal observational,30542916,10.1007/s00284-018-1610-1,NA,"Guo R, Liu H, Li X, Yang Q, Jia L, Zheng Y , Li W",Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients,Current microbiology,2019,Experiment 2,China,Homo sapiens,dental plaque,UBERON:0016482,gingival disease,EFO:0009670,before,3 months after the placement of the brackets,subgingial microbial changes during fixed appliance treatment,10,10,1 month,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 1,Figure 5,6 November 2019,Rimsha Azhar,WikiWorks743,Relative abundance of microbiota that showed statistically significant differences among three different time points,increased,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,2|976|117743|200644|49546|1016,Complete,NA
Study 159,time series / longitudinal observational,30542916,10.1007/s00284-018-1610-1,NA,"Guo R, Liu H, Li X, Yang Q, Jia L, Zheng Y , Li W",Subgingival Microbial Changes During the First 3 Months of Fixed Appliance Treatment in Female Adult Patients,Current microbiology,2019,Experiment 2,China,Homo sapiens,dental plaque,UBERON:0016482,gingival disease,EFO:0009670,before,3 months after the placement of the brackets,subgingial microbial changes during fixed appliance treatment,10,10,1 month,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,unchanged,unchanged,Signature 2,Figure 5,6 November 2019,Rimsha Azhar,"WikiWorks743,Fatima",Relative abundance of microbiota that showed statistically significant differences among three different time points,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. tigurinus",2|1239|91061|186826|186828|117563;2|1239|91061|186826|1300|1301|1303|1077464,Complete,NA
Study 160,case-control,30123780,10.3389/fcimb.2018.00267,NA,"Lim Y, Fukuma N, Totsika M, Kenny L, Morrison M , Punyadeera C",The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers,Frontiers in cellular and infection microbiology,2018,Experiment 1,Australia,Homo sapiens,mouth,UBERON:0000165,head and neck carcinoma,MONDO:0002038,High-risk individuals,OCC & OPC,Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer),11,31,NA,16S,678,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1B, Supp. Table 2, Text",6 November 2019,Utsav Patel,WikiWorks743,The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia",2|976|200643|171549|2005523|346096;2|201174|1760|85007|1653|1716;2|976|200643|171549|171551|836;2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|713;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|416916;2|1224|28216|80840|119060|47670,Complete,NA
Study 160,case-control,30123780,10.3389/fcimb.2018.00267,NA,"Lim Y, Fukuma N, Totsika M, Kenny L, Morrison M , Punyadeera C",The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers,Frontiers in cellular and infection microbiology,2018,Experiment 2,Australia,Homo sapiens,mouth,UBERON:0000165,head and neck carcinoma,MONDO:0002038,Normal Healthy Controls,OCC & OPC,Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer),20,31,NA,16S,678,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1B, Supp. Table 2, Text",6 November 2019,Utsav Patel,WikiWorks743,The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,2|1239|186801|186802|186803|265975,Complete,NA
Study 160,case-control,30123780,10.3389/fcimb.2018.00267,NA,"Lim Y, Fukuma N, Totsika M, Kenny L, Morrison M , Punyadeera C",The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers,Frontiers in cellular and infection microbiology,2018,Experiment 2,Australia,Homo sapiens,mouth,UBERON:0000165,head and neck carcinoma,MONDO:0002038,Normal Healthy Controls,OCC & OPC,Newly diagnosed OCC(Oral Cavity Cancer) and OPC (Oropharyngeal Cancer),20,31,NA,16S,678,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 1B, Supp. Table 2, Text",6 November 2019,Utsav Patel,WikiWorks743,The Performance of an Oral Microbiome in Predicting Oral Cavity and Oropharyngeal Cancers,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|201174|1760|85006|1268|32207;2|1224|1236|135625|712|724;2|201174|1760|85007|1653|1716;2|976|200643|171549|2005523|346096;2|976|200643|171549|171551|836;2|976|117743|200644|49546|1016,Complete,NA
Study 161,case-control,31205521,10.7150/jca.28077,NA,"Zhang W, Luo J, Dong X, Zhao S, Hao Y, Peng C, Shi H, Zhou Y, Shan L, Sun Q, Li Y , Zhao X",Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients,Journal of Cancer,2019,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,lung cancer,MONDO:0008903,healthy controls,NSCLC,newly diagnosed NSCLC (non small cell lung cancer) patients,20,39,6 months,16S,12,Illumina,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 2,13 November 2019,Fatima Zohra,WikiWorks743,Salivary microbial dysbiosis in non-small cell lung cancer,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174;2|1239;2|1224;2|1224|1236|135625|712|416916;2|201174|1760|85006|1268|32207;2|32066|203490|203491|1129771|32067;2|1224|28216|80840|119060|47670;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 161,case-control,31205521,10.7150/jca.28077,NA,"Zhang W, Luo J, Dong X, Zhao S, Hao Y, Peng C, Shi H, Zhou Y, Shan L, Sun Q, Li Y , Zhao X",Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients,Journal of Cancer,2019,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,lung cancer,MONDO:0008903,healthy controls,NSCLC,newly diagnosed NSCLC (non small cell lung cancer) patients,20,39,6 months,16S,12,Illumina,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figure 2,13 November 2019,Fatima Zohra,WikiWorks743,Salivary microbial dysbiosis in non-small cell lung cancer,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976;2|1239|186801|186802|216572|216851;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|976|200643|171549|171552|1283313;2|976|200643|171549|171551|836,Complete,NA
Study 161,case-control,31205521,10.7150/jca.28077,NA,"Zhang W, Luo J, Dong X, Zhao S, Hao Y, Peng C, Shi H, Zhou Y, Shan L, Sun Q, Li Y , Zhao X",Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients,Journal of Cancer,2019,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,lung cancer,MONDO:0008903,healthy controls,NSCLC,newly diagnosed NSCLC (non small cell lung cancer) patients,20,39,6 months,16S,12,Illumina,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 3,13 November 2019,Fatima Zohra,WikiWorks743,Salivary microbial dysbiosis in non-small cell lung cancer,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia",2|1224;2|1224|28216;2|1224|28216|80840;2|1239|91061;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826;2|1224|28216|80840|119060;2|1224|28216|80840|119060|47670,Complete,NA
Study 161,case-control,31205521,10.7150/jca.28077,NA,"Zhang W, Luo J, Dong X, Zhao S, Hao Y, Peng C, Shi H, Zhou Y, Shan L, Sun Q, Li Y , Zhao X",Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients,Journal of Cancer,2019,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,lung cancer,MONDO:0008903,healthy controls,NSCLC,newly diagnosed NSCLC (non small cell lung cancer) patients,20,39,6 months,16S,12,Illumina,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figure 3,13 November 2019,Fatima Zohra,WikiWorks743,Salivary microbial dysbiosis in non-small cell lung cancer,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552;2|976;2|976|200643;2|976|200643|171549,Complete,NA
Study 162,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H , Cai X",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,healthy control,lung cancer group,newly diagnosed lung cancer patients by histopathology and computed tomography,16,30,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,13 November 2019,Fatima Zohra,WikiWorks743,Comparison of relative abundant microbiome at family level between cancer groups and healthy controls,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,2|1239|186801|186802|186803,Complete,NA
Study 162,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H , Cai X",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,others,CEA group,newly diagnosed lung cancer patients by histopathology and computed tomography,16,30,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,13 November 2019,Fatima Zohra,WikiWorks743,Comparison of relative abundant microbiome at family level between cancer groups and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|976|200643|171549|815;2|1239|91061|186826|1300,Complete,NA
Study 162,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H , Cai X",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,others,NSE group,newly diagnosed lung cancer patients by histopathology and computed tomography,16,30,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,13 November 2019,Fatima Zohra,WikiWorks743,Comparison of relative abundant microbiome at family level between cancer groups and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|1224|1236|91347|543;2|32066|203490|203491|203492;2|74201|203494|48461|203557,Complete,NA
Study 162,case-control,31595156,10.7150/ijbs.35980,NA,"Liu F, Li J, Guan Y, Lou Y, Chen H, Xu M, Deng D, Chen J, Ni B, Zhao L, Li H, Sang H , Cai X",Dysbiosis of the Gut Microbiome is associated with Tumor Biomarkers in Lung Cancer,International journal of biological sciences,2019,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,lung cancer,MONDO:0008903,healthy controls,CYF group,newly diagnosed lung cancer patients by histopathology and computed tomography,16,30,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 3B,13 November 2019,Fatima Zohra,WikiWorks743,Comparison of relative abundant microbiome at family level between cancer groups and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,NA
Study 163,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A, Moissl-Eichinger C, Perras A, Koskinen K, Tomazic PV , Thurnher D",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,Experiment 1,Austria,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,"Figure 3, Text",13 November 2019,Utsav Patel,WikiWorks743,microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Schwartzia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|32066|203490|203491|1129771;2|1224|28221|213115|194924|872;2|1239|909932|909929|1843491|55506;2|1239|186801|186802|186803|437755;2|203691|203692|136|2845253|157;2|201174|1760|85004|31953|1678;2|201174|1760|2037|2049|1654;2|1239|909932|909929|1843491|970,Complete,NA
Study 163,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A, Moissl-Eichinger C, Perras A, Koskinen K, Tomazic PV , Thurnher D",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,Experiment 1,Austria,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,"Figure 3, Text",13 November 2019,Utsav Patel,WikiWorks743,microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1224|1236|135625|712;2|1239|186801|186802|186803|43996;2|1239|909932|1843489|31977|29465;2|1224|28216|206351|481|482;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838;2|1224|1236|135625|712|724;2|976|200643|171549|171552,Complete,NA
Study 163,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A, Moissl-Eichinger C, Perras A, Koskinen K, Tomazic PV , Thurnher D",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,Experiment 2,Austria,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Supplementary Figure S4,13 November 2019,Utsav Patel,WikiWorks743,microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",2|1224;2|203691|203692|136|137;2|203691|203692|136;2|203691;2|203691|203692|136|137|146;2|201174;2|1224|28221;2|1224|28211;2|976;2|976|200643;2|976|200643|171549;2|1239|909932|909929;2|1239|909932;2|1239|526524|526525;2|1239|526524;2|976|200643|171549|171552;2|1224|1236|135625|712;2|976|117747;2|976|117747|200666;2|201174|1760|85004;2|976|117743|200644|49546;2|976|117743|200644;2|976|117743;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|201174|1760|85007|1653;2|1224|1236|135624;2|1224|1236|135624|83763,Complete,NA
Study 163,case-control,28725009,10.1038/s41598-017-06361-2,NA,"Wolf A, Moissl-Eichinger C, Perras A, Koskinen K, Tomazic PV , Thurnher D",The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study,Scientific reports,2017,Experiment 2,Austria,Homo sapiens,saliva,UBERON:0001836,squamous cell carcinoma,EFO:0000707,Healthy Controls,Oropharyngeal Squamous Cell Carcinoma,diagnosed with OSCC and SCC of the oral cavity,11,11,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,Supplementary Figure S4,13 November 2019,Utsav Patel,WikiWorks743,microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria",2|1239|186801|186802|186803|1213720;2|1239|91061;2|1239|186801|186802|186804;2|1224|1236,Complete,NA
Study 164,case-control,26457297,10.1155/2015/173729,NA,"Hu J, Han S, Chen Y , Ji Z",Variations of Tongue Coating Microbiota in Patients with Gastric Cancer,BioMed research international,2015,Experiment 1,China,Homo sapiens,tongue,UBERON:0001723,gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer,16,34,2 months,16S,234,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Table 4, text",13 November 2019,Rimsha Azhar,WikiWorks743,Relative abundances of selected tongue coating microbial taxa in 34 gastric cancer subjects and 16 control subjects.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinobacteria",2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|201174|1760|2037|2049|1654;2|32066|203490|203491|1129771|32067;2|201174,Complete,NA
Study 164,case-control,26457297,10.1155/2015/173729,NA,"Hu J, Han S, Chen Y , Ji Z",Variations of Tongue Coating Microbiota in Patients with Gastric Cancer,BioMed research international,2015,Experiment 1,China,Homo sapiens,tongue,UBERON:0001723,gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer,16,34,2 months,16S,234,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Table 4, text",13 November 2019,Rimsha Azhar,WikiWorks743,Relative abundances of selected tongue coating microbial taxa in 34 gastric cancer subjects and 16 control subjects.,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria",2|1224|28216|206351|481|482;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|976|200643|171549|171551|836;2|1224,Complete,NA
Study 165,case-control,31245306,10.3389/fcimb.2019.00206,NA,"Li F, Wang M, Wang J, Li R , Zhang Y",Alterations to the Gut Microbiota and Their Correlation With Inflammatory Factors in Chronic Kidney Disease,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease,diagnosed with chronic kidney disease because they exhibited an effective glomerular filtration rate,22,50,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure2,18 November 2019,Fatima Zohra,WikiWorks743,Taxonomic differences in fecal microbiota exhibited by patients with chronic kidney disease,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria",2|201174|1760|2037;2|1224|28211|356|119045|407;2|1224|28211|356|119045;2|1239|186801|186802|31979;2|1224|28221|213115|194924|872;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|1283313;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|186801|186802|31979|1485;2|201174|1760;2|201174,Complete,NA
Study 165,case-control,31245306,10.3389/fcimb.2019.00206,NA,"Li F, Wang M, Wang J, Li R , Zhang Y",Alterations to the Gut Microbiota and Their Correlation With Inflammatory Factors in Chronic Kidney Disease,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease,diagnosed with chronic kidney disease because they exhibited an effective glomerular filtration rate,22,50,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure2,18 November 2019,Fatima Zohra,"WikiWorks743,Lwaldron",Taxonomic differences in fecal microbiota exhibited by patients with chronic kidney disease,decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales,k__Bacteria|p__Deferribacteres,k__Bacteria|p__Deferribacteres|c__Deferribacteres,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Mucispirillum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Parvibacter,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacteria|p__Synergistetes,k__Bacteria|p__Synergistetes|c__Synergistia,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales",2|74201|203494|48461|1647988|239934;2|1239|526524|526525|128827|174708;2|1239|91061;2|1224|28216;2|1224|28216|80840;2|1224|29547|213849;2|200930|68337|191393|191394;2|200930|68337|191393;2|200930;2|200930|68337;2|201174|84998|1643822|1643826|580024;2|1224|29547;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1224|29547|213849|72293|209;2|1224|29547|213849|72293;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|91061|186826|33958|1243;2|201174|1760|85006|1268;2|200930|68337|191393|191394|248038;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186803|265975;2|1224|28216|80840|995019|577310;2|201174|84998|84999|84107|1427376;2|508458|649775|649776|649777|638847;2|201174|1760|85006|1268|32207;2|1224|28216|80840|995019;2|508458|649775|649776|649777;2|508458|649775|649776;2|508458|649775|649776|649777|2753;2|508458;2|508458|649775;2|74201;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461,Complete,NA
Study 166,case-control,30088332,10.1002/mbo3.678,NA,"Lun H, Yang W, Zhao S, Jiang M, Xu M, Liu F , Wang Y",Altered gut microbiota and microbial biomarkers associated with chronic kidney disease,MicrobiologyOpen,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease,patients with chronic kidney disease,24,49,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,20 November 2019,Fatima Zohra,WikiWorks743,Comparison of gut bacteria between the HC and chronic kidney disease groups,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__[Ruminococcus] gnavus CAG:126,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__[Ruminococcus] torques CAG:61,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",2|976|200643;2|976|200643|171549;2|976;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|1236;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|976|200643|171549|171551;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|1263|1263106;2|1239|186801|186802|216572|1263|1263108;2|1239|91061|186826|33958|46255;2|1239|91061|186826|81850;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|186803|1769710;2|1239|526524|526525|128827|1505663;2|201174|84998|1643822|1643826|84111,Complete,NA
Study 166,case-control,30088332,10.1002/mbo3.678,NA,"Lun H, Yang W, Zhao S, Jiang M, Xu M, Liu F , Wang Y",Altered gut microbiota and microbial biomarkers associated with chronic kidney disease,MicrobiologyOpen,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,chronic kidney disease,EFO:0003884,healthy controls,chronic kidney disease,patients with chronic kidney disease,24,49,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,20 November 2019,Fatima Zohra,WikiWorks743,Comparison of gut bacteria between the HC and chronic kidney disease groups,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rectale CAG:36,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes",2|1239|186801|186802|186803;2|1239|186801|186802|186803|1506577;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|541000;2|201174|84998|84999|84107|102106;2|1239|186801|186802|31979|580596;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186804;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|292632;2|1239|186801|186802|186803|28050;2|1239|91061|186826|186828|2747;2|1239|186801|186802|186806|1730|1263079;2|976|200643|171549|171552;2|1239|909932|1843489|31977|39948;2|1239|909932|909929;2|1239|909932;2|1239|909932|1843489|31977;2|1239|186801;2|1239|186801|186802;2|1239,Complete,NA
Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,Experiment 1,China,Homo sapiens,mouth,UBERON:0000165,squamous cell carcinoma,EFO:0000707,healthy controls,Stage 4,OSCC  confirmed by biopsy and pathological findings,51,90,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 1,"Figure 1, Figure 5, Text",20 November 2019,Utsav Patel,WikiWorks743,Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.",2|32066|203490|203491|203492|848|860;2|1239|1737404|1737405|1570339|543311|33033;2|1239|91061|186826|1300|1301|76860;2|1224|1236|135625|712|724|727;2|1239|186801|186802|186804|44259|143361;2|1224|1236|135625|712|416916|739;2|1239|909932|909929|1843491|970|69823;2|1239|91061|186826|186828|117563|137732;2|1224|28216|206351|481|482|495;2|1224|28216|206351|481|538|539;2|1239|186801|186802|186803|265975|1969407;2|976|200643|171549|171551|836|1924944;2|1239|909932|1843489|31977|39948|39950;2|1224|29547|213849|72294|194|205;2|1224|29547|213849|72294|194|824;2|976|200643|171549|815|816|28113;2|1239|909932|909929|1843491|82202;2|1224|28216|206351|481|482|1107316;2|1239|186801|186802|186804;2|1224|1236|91347|543|561|562;2|201174|1760|85004|31953|419014|419015;2|1239|909932|909929|1843491|970|2053611;2|1239|909932|1843489|31977|156454|156456;2|32066|203490|203491|1129771|32067|104608;2|976|200643|171549|171552|1283313|1872471,Complete,NA
Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,Experiment 1,China,Homo sapiens,mouth,UBERON:0000165,squamous cell carcinoma,EFO:0000707,healthy controls,Stage 4,OSCC  confirmed by biopsy and pathological findings,51,90,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 2,"Figure 1, Figure 5, Text",20 November 2019,Utsav Patel,WikiWorks743,Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens",2|976|200643|171549|171552|838|425941;2|32066|203490|203491|1129771|2755140|157692;2|201174|1760|2037|2049|2529408|52768;2|201174|1760|2037|2049|1654|52769;2|976|200643|171549|171552|838|28132;2|1239|91061|186826|186828|117563|46124,Complete,NA
Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,Experiment 2,China,Homo sapiens,mouth,UBERON:0000165,squamous cell carcinoma,EFO:0000707,healthy controls,Stage 1,OSCC  confirmed by biopsy and pathological findings,51,41,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 1,"Figure 1, Supplementary Figure 5A , Text",20 November 2019,Utsav Patel,WikiWorks743,Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.",2|1239|91061|186826|1300|1301|76860;2|1224|1236|135625|712|724|727;2|1239|1737404|1737405|1570339|543311|33033;2|32066|203490|203491|203492|848|860;2|1239|91061|186826|186828|117563|137732;2|1239|186801|186802|186804|44259|143361;2|1224|28216|206351|481|482|1107316;2|976|200643|171549|171551|836|1924944;2|1224|29547|213849|72294|194|205,Complete,NA
Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,Experiment 2,China,Homo sapiens,mouth,UBERON:0000165,squamous cell carcinoma,EFO:0000707,healthy controls,Stage 1,OSCC  confirmed by biopsy and pathological findings,51,41,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 2,"Figure 1, Supplementary Figure 5A , Text",20 November 2019,Utsav Patel,WikiWorks743,Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",2|976|200643|171549|171552|838|28132;2|201174|1760|2037|2049|2529408|1660;2|1239|909932|1843489|31977|29465|29466;2|976|200643|171549|171551|836|1583331;2|1224|1236|135625|712|724|729;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|28037,Complete,NA
Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,Experiment 3,China,Homo sapiens,mouth,UBERON:0000165,squamous cell carcinoma,EFO:0000707,healthy controls,Stage 2 & 3,OSCC  confirmed by biopsy and pathological findings,51,66,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 1,"Figure 1, Supplementary Figure 5B,  Text",20 November 2019,Utsav Patel,WikiWorks743,Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|32066|203490|203491|203492|848|860;2|1239|1737404|1737405|1570339|543311|33033;2|1224|1236|135625|712|724|727;2|1239|91061|186826|1300|1301|76860;2|1239|186801|186802|186804|44259|143361;2|1239|91061|186826|186828|117563|137732;2|1224|1236|135625|712|416916|739;2|976|200643|171549|171551|836|1924944;2|1239|909932|909929|1843491|970|69823;2|1224|29547|213849|72294|194|205;2|1239|909932|1843489|31977|156454|156456;2|1224|29547|213849|72294|194|824;2|1239|186801|186802|186806|1730,Complete,NA
Study 167,case-control,29774014,10.3389/fmicb.2018.00862,NA,"Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP , Chang YL",Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,Frontiers in microbiology,2018,Experiment 3,China,Homo sapiens,mouth,UBERON:0000165,squamous cell carcinoma,EFO:0000707,healthy controls,Stage 2 & 3,OSCC  confirmed by biopsy and pathological findings,51,66,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,unchanged,NA,NA,Signature 2,"Figure 1, Supplementary Figure 5B , Text",20 November 2019,Utsav Patel,WikiWorks743,Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis",2|976|200643|171549|171552|838|28132;2|201174|1760|2037|2049|2529408|1660;2|1239|909932|1843489|31977|29465|29466;2|976|200643|171549|171551|836|1583331;2|1224|1236|135625|712|724|729;2|1239|91061|186826|1300|1301|28037,Complete,NA
Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,Experiment 1,China,Homo sapiens,tongue,UBERON:0001723,chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B yellow tongue coating patients,chronic hepatitis B,22,28,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2B, Figure 3A",20 November 2019,Rimsha Azhar,WikiWorks743,Differentially abundant taxa in chronic hepatitis B yellow and white tongue coating patients,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria",2|1224|1236|135615|868;2|1224|28216|80840|80864;2|1224|28216|80840|119060;2|1224|28216|206351|481;2|1224|28216|80840|80864|283;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|1224,Complete,NA
Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,Experiment 1,China,Homo sapiens,tongue,UBERON:0001723,chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B yellow tongue coating patients,chronic hepatitis B,22,28,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2B, Figure 3A",20 November 2019,Rimsha Azhar,WikiWorks743,Differentially abundant taxa in chronic hepatitis B yellow and white tongue coating patients,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptoclostridium,k__Bacteria|p__Candidatus Saccharibacteria|g__Candidatus Saccharimonas,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|201174|1760|85004|31953;2|1224|29547|213849|72294;2|201174|1760|85004|31953|196081;2|1239|186801|186802|186804|1481960;2|95818|1331051;2|1224|29547|213849|72294|194;2|1239|1737404|1737405|1570339|543311,Complete,NA
Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,Experiment 2,China,Homo sapiens,tongue,UBERON:0001723,chronic hepatitis B virus infection,EFO:0004239,chronic hepatitis B white tongue coating patients,chronic hepatitis B yellow tongue coating patients,chronic hepatitis B,25,28,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2B, Figure 3A",20 November 2019,Rimsha Azhar,"WikiWorks743,Fatima",Differentially abundant taxa in chronic hepatitis B yellow and white tongue coating patients,increased,"k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Candidatus Gracilibacteria",2|544448|31969|2085|2092|2093;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224;2|363464,Complete,NA
Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,Experiment 2,China,Homo sapiens,tongue,UBERON:0001723,chronic hepatitis B virus infection,EFO:0004239,chronic hepatitis B white tongue coating patients,chronic hepatitis B yellow tongue coating patients,chronic hepatitis B,25,28,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2B, Figure 3A",20 November 2019,Rimsha Azhar,WikiWorks743,Differentially abundant taxa in chronic hepatitis B yellow and white tongue coating patients,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Bacteroidetes",2|976|200643|171549|171552|838;2|1239|186801|186802|186803|43996;2|976,Complete,NA
Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,Experiment 3,China,Homo sapiens,tongue,UBERON:0001723,chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B white tongue coating patients,chronic hepatitis B,22,25,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2B, Figure 3A",20 November 2019,Rimsha Azhar,WikiWorks743,Differentially abundant taxa in chronic hepatitis B yellow and white tongue coating patients,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|200643|171549|171551;2|1239|526524|526525|128827|118747;2|1239|909932|909929|1843491|82202;2|976|117743|200644|2762318|59735;2|976|200643|171549|171551|836,Complete,NA
Study 168,case-control,30122883,10.3748/wjg.v24.i30.3448,NA,"Zhao Y, Mao YF, Tang YS, Ni MZ, Liu QH, Wang Y, Feng Q, Peng JH , Hu YY",Altered oral microbiota in chronic hepatitis B patients with different tongue coatings,World journal of gastroenterology,2018,Experiment 3,China,Homo sapiens,tongue,UBERON:0001723,chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B white tongue coating patients,chronic hepatitis B,22,25,3 months,16S,3,Ion Torrent,Metastats,0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2B, Figure 3A",20 November 2019,Rimsha Azhar,WikiWorks743,Differentially abundant taxa in chronic hepatitis B yellow and white tongue coating patients,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Alysiella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1224|1236|135615|868;2|201174|1760|2037|2049;2|544448|31969|2085|2092;2|1239|186801|186802|186806|113286;2|1224|28216|206351|481|194195;2|201174|1760|85004|31953|196081;2|201174|1760|2037|2049|1654,Complete,NA
Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,Experiment 1,China,Homo sapiens,tongue,UBERON:0001723,gastric cancer,MONDO:0001056,other coatings,white-thin tongue coating GC patient,gastric cancer with different tongue coatings,90,25,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 1,2,4",21 November 2019,Rimsha Azhar,WikiWorks743,LEfSe analysis of microbial taxa from tongue coating in GC patients,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis",2|1224|28216|80840|119060|47670;2|976|117743|200644|49546|1016|44737;2|1239|909932|1843489|31977|906|187326,Complete,NA
Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,Experiment 1,China,Homo sapiens,tongue,UBERON:0001723,gastric cancer,MONDO:0001056,other coatings,white-thin tongue coating GC patient,gastric cancer with different tongue coatings,90,25,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 1,2,4",21 November 2019,Rimsha Azhar,WikiWorks743,LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.",2|1239|186801|186802|186803|1213720;2|1239|186801|186802|186806|1730|142586,Complete,NA
Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,Experiment 2,China,Homo sapiens,tongue,UBERON:0001723,gastric cancer,MONDO:0001056,other coatings,white-thick tongue coating GC patient,gastric cancer with different tongue coatings,72,43,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 1,2,4",21 November 2019,Rimsha Azhar,WikiWorks743,LEfSe analysis of microbial taxa from tongue coating in GC patients,increased,"k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella maculosa",2|95818;2|1239|186801|186802|541000;2|1239|186801|186802|186806|1730;2|1239|909932|1843489|31977|906|187326;2|1239|909932|909929|1843491|970|69823;2|976|200643|171549|171552|838|439703,Complete,NA
Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,Experiment 2,China,Homo sapiens,tongue,UBERON:0001723,gastric cancer,MONDO:0001056,other coatings,white-thick tongue coating GC patient,gastric cancer with different tongue coatings,72,43,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 1,2,4",21 November 2019,Rimsha Azhar,WikiWorks743,LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius",2|1224|1236|2887326|468|469|108980;2|1239|91061|186826|33958|2767887|1624,Complete,NA
Study 169,case-control,30508628,10.1016/j.micpath.2018.11.051,NA,"Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J , Zhan Z",Microbial biomarkers of common tongue coatings in patients with gastric cancer,Microbial pathogenesis,2019,Experiment 3,China,Homo sapiens,tongue,UBERON:0001723,gastric cancer,MONDO:0001056,other coatings,yellow-thick tongue coating GC patient,gastric cancer with different tongue coatings,95,20,4 weeks,16S,345,RT-qPCR,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 1,2,4",21 November 2019,Rimsha Azhar,WikiWorks743,LEfSe analysis of microbial taxa from tongue coating in GC patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|1239|186801|186802|541000;2|1224|28216|80840|119060|47670;2|1224|28216|206351|481|482;2|1239|186801|186802|186804|1257;2|1239|91061|1385|1378|84135;2|976|117743|200644|49546|1016|1019;2|1224|1236|135625|712|724|729,Complete,NA
Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,Experiment 1,China,Homo sapiens,lung,UBERON:0002048,lung cancer,MONDO:0008903,controls,cancerous site,diagnosis of lung cancer established by histological confirmation,18,24,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 3,25 November 2019,Fatima Zohra,WikiWorks743,"Differentially abundant taxa between T (patients in cancerous site), TN (contralateral non-cancerous site), and N (normal)groups",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|201174|1760|85007,Complete,NA
Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,Experiment 1,China,Homo sapiens,lung,UBERON:0002048,lung cancer,MONDO:0008903,controls,cancerous site,diagnosis of lung cancer established by histological confirmation,18,24,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 3,25 November 2019,Fatima Zohra,WikiWorks743,"Differentially abundant taxa between T (patients in cancerous site), TN (contralateral non-cancerous site), and N (normal)groups",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1224|1236|2887326|468;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279,Complete,NA
Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,Experiment 2,China,Homo sapiens,lung,UBERON:0002048,lung cancer,MONDO:0008903,controls,paired contralateral non-cancerous site,diagnosis of lung cancer established by histological confirmation,18,24,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,25 November 2019,Fatima Zohra,WikiWorks743,"Differentially abundant taxa between T (patients in cancerous site), TN (contralateral non-cancerous site), and N (normal)groups",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|1239|91061|186826;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|1236|135625|712|724;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|976|117743|200644|49546|237;2|1224|28216|206351;2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|976|117743|200644|49546;2|976|117743|200644;2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067;2|976|117743|200644|49546|1016;2|1239|909932|909929|1843491|970,Complete,NA
Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,Experiment 2,China,Homo sapiens,lung,UBERON:0002048,lung cancer,MONDO:0008903,controls,paired contralateral non-cancerous site,diagnosis of lung cancer established by histological confirmation,18,24,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3,25 November 2019,Fatima Zohra,WikiWorks743,"Differentially abundant taxa between T (patients in cancerous site), TN (contralateral non-cancerous site), and N (normal)groups",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales",2|1224|1236|2887326|468|469;2|1239|186801|186802|186803;2|1224|1236|2887326|468;2|1224|1236|72274,Complete,NA
Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,Experiment 3,China,Homo sapiens,lung,UBERON:0002048,lung cancer,MONDO:0008903,paired contralateral non-cancerous site,cancerous site,diagnosis of lung cancer established by histological confirmation,18,24,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,25 November 2019,Fatima Zohra,WikiWorks743,"Differentially abundant taxa between T (patients in cancerous site), TN (contralateral non-cancerous site), and N (normal)groups",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Candidatus Saccharibacteria",2|1239|91061|1385;2|1239|909932|1843489|31977|39948;2|95818,Complete,NA
Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,Experiment 4,China,Homo sapiens,lung,UBERON:0002048,lung cancer,MONDO:0008903,control groups with no antibiotics,cacerous site with no antibiotics,diagnosis of lung cancer established by histological confirmation,8,13,NA,16S,34,Illumina,LEfSe,0.5,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 1,Supplemental Figure S1,25 November 2019,Fatima Zohra,WikiWorks743,Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No(normal samples who received no antibiotics),increased,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,2|976|117743|200644|49546|1016,Complete,NA
Study 170,case-control,29023689,10.1002/ijc.31098,NA,"Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM , Qu JM",Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects,International journal of cancer,2018,Experiment 4,China,Homo sapiens,lung,UBERON:0002048,lung cancer,MONDO:0008903,control groups with no antibiotics,cacerous site with no antibiotics,diagnosis of lung cancer established by histological confirmation,8,13,NA,16S,34,Illumina,LEfSe,0.5,FALSE,3.5,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 2,Supplemental Figure S1,25 November 2019,Fatima Zohra,WikiWorks743,Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No(normal samples who received no antibiotics),decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Myxococcales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964;2|1224|28211|204455|31989|265;2|1224|28211|204455|31989;2|1224|28211|204455;2|1224|28221|29;2|1224|28221;2|1224|28216|80840|80864;2|1224|1236|2887326|468,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,digestive system cancer,MONDO:0002516,controls,digestive track cancers,digestive track cancers,118,59,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 1,"Figure 3, Figure S1",27 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|201174|1760|2037|2049|2529408|1660;2|1239|91061|186826|1300|1301|1318;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836|837;2|1239|91061|186826|1300|1301|1306;2|1224|28216|206351|481|482|495;2|1239|91061|186826|1300|1301|1305;2|1239|909932|1843489|31977|29465;2|32066|203490|203491|203492|848,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,digestive system cancer,MONDO:0002516,controls,digestive track cancers,digestive track cancers,118,59,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 2,"Figure 3, Figure S1",27 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|201174|1760|85006|1268|32207|2047;2|976|200643|171549|171552|838;2|976|200643|171549|171551|836|1924944;2|1239|526524|526525|128827|123375|102148;2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,tongue neoplasm,EFO:0003871,controls,tongue/pharylgeal cancer,tongue/pharyngeal cancer,26,13,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 1,"Figure S3, Figure 5",29 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis",2|1224|28216|206351|481|482;2|201174|1760|85007|1653|1716;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|32067;2|1224|1236|135625|712|416916|739;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1318;2|976|200643|171549|171551|836|837;2|1239|91061|186826|1300|1301|1305,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,tongue neoplasm,EFO:0003871,controls,tongue/pharylgeal cancer,tongue/pharyngeal cancer,26,13,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,unchanged,NA,NA,Signature 2,"Figure S3, Figure 5",29 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica",2|1224|28216|206351|481|482;2|201174|1760|85006|1268|32207|2047;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|113107;2|976|200643|171549|171552|838|28132,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 3,China,Homo sapiens,saliva,UBERON:0001836,esophageal cancer,MONDO:0007576,controls,esophageal cancer,esophageal cancer,24,12,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,increased,NA,NA,Signature 1,"Figure S3, Figure 5",29 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1239|91061|186826|1300|1301|1306;2|1224|1236|135625|712|416916|739;2|32066|203490|203491|1129771|32067|104608;2|201174|1760|85007|1653|1716;2|32066|203490|203491|1129771|32067|157688;2|976|200643|171549|171551|836|837;2|1239|909932|1843489|31977|906|187326;2|1224|28216|206351|481|482,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 3,China,Homo sapiens,saliva,UBERON:0001836,esophageal cancer,MONDO:0007576,controls,esophageal cancer,esophageal cancer,24,12,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,increased,increased,NA,NA,Signature 2,"Figure S3, Figure 5",29 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica",2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207|2047;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838|28132,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 4,China,Homo sapiens,saliva,UBERON:0001836,colorectal cancer,EFO:0005842,controls,colorectal cancer,colorectal cancer,48,24,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Figure S3, Figure 5",29 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces paraguayensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus",2|201174|1760|2037|2049|2529408|1660;2|201174|1760|85011|2062|1883|68251;2|201174|1760|85007|1653|1716;2|976|200643|171549|171551|836|837;2|1239|909932|1843489|31977|906|187326;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838|59823;2|1239|186801|186802|186803|265975|237576,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 4,China,Homo sapiens,saliva,UBERON:0001836,colorectal cancer,EFO:0005842,controls,colorectal cancer,colorectal cancer,48,24,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Figure S3, Figure 5",29 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica",2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|59823;2|1239|91061|186826|1300|1301;2|976|200643|171549|171551|836|1583331;2|976|200643|171549|171552|838|28132,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 5,China,Homo sapiens,saliva,UBERON:0001836,gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer,20,10,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure S3, Figure 5",29 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis",2|1224|1236|135625|712|724|729;2|32066|203490|203491|203492|848|860;2|1239|91061|1385|1378|84135;2|1239|91061|186826|1300|1301;2|1224|28216|206351|481|482;2|976|200643|171549|171551|836|837,Complete,NA
Study 171,case-control,31428073,10.3389/fmicb.2019.01780,NA,"Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T , Yamashita Y",Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers,Frontiers in microbiology,2019,Experiment 5,China,Homo sapiens,saliva,UBERON:0001836,gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer,20,10,1 month,16S,12,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure S3, Figure 5",29 November 2019,Rimsha Azhar,WikiWorks743,Bacterial species corresponding to the differentially abundant OTUs between patients and control subjects,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.",2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803;2|976|200643|171549|171552|838;2|976|200643|171549|171551|836|1924944,Complete,NA
Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,Experiment 1,United States of America,Homo sapiens,saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1, Figure 3, Text",3 December 2019,Utsav Patel,WikiWorks743,Microbiomic differences at cancerprone oral mucosa sites with marijuana usage,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea vestrisii,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Leptothrix,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium",2|1224|28216|80840|80864;2|1224|28216|80840|80864|80865|80866;2|1224|28216|80840|80864|80865;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207|43675;2|1239|909932|1843489|31977|29465|39777;2|1224|28211|356|2831100|85413|151416;2|1224|28211|356|2831100|85413;2|201174|1760|2037|2049|1654|55565;2|1224|28216|80840|88;2|1239|186801|186802|543314|86331,Complete,NA
Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,Experiment 1,United States of America,Homo sapiens,saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the lateral border of the tongue",19,20,1 month,16S,123,Illumina,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1, Figure 3, Text",3 December 2019,Utsav Patel,WikiWorks743,Microbiomic differences at cancerprone oral mucosa sites with marijuana usage,decreased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes",2|976|117743|200644|2762318|59735|1962306;2|976|200643|171549|171552|838|425941;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|976|117743|200644|2762318|59735;2|32066;2|32066|203490;2|32066|203490|203491;2|976|117743;2|976|117743|200644|49546;2|976|117743|200644;2|976|200643|171549|171551|836;2|976|200643|171549|171551;2|976,Complete,NA
Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,Experiment 2,United States of America,Homo sapiens,saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1, Figure 3, Text",3 December 2019,Utsav Patel,WikiWorks743,Microbiomic differences at cancerprone oral mucosa sites with marijuana usage,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|909932;2|1239|909932|1843489;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977;2|1239|909932|909929|1843491|970;2|1239|909932|909929|1843491;2|1239|909932|909929;2|1239|186801|186802|543314|86331;2|1239|186801|186802|541000,Complete,NA
Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,Experiment 2,United States of America,Homo sapiens,saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (oral pharynx),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,1 month,16S,123,Illumina,LEfSe,NA,FALSE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1, Figure 3, Text",3 December 2019,Utsav Patel,WikiWorks743,Microbiomic differences at cancerprone oral mucosa sites with marijuana usage,decreased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales",2|976|117743|200644|2762318|59735;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|91061|186826,Complete,NA
Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,Experiment 3,United States of America,Homo sapiens,saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,2 month,16S,123,Illumina,DESeq2,NA,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1, Figure 3, Table 1, Text",3 December 2019,Utsav Patel,WikiWorks743,Microbiomic differences at cancerprone oral mucosa sites with marijuana usage,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Leptothrix,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1224|28216|80840|80864|80865;2|1224|28216|80840|88;2|1224|1236|72274|135621|286;2|1224|28211|356|2831100|85413;2|1224|28216|80840|119060|47670;2|201174|1760|85006|1268|32207,Complete,NA
Study 172,case-control,31481657,10.1038/s41598-019-48768-z,NA,"Newman TM, Krishnan LP, Lee J , Adami GR",Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage,Scientific reports,2019,Experiment 3,United States of America,Homo sapiens,saliva,UBERON:0001836,Cannabis use,EFO:0007585,controls (lateral border of tongue),marijuana usage group,"using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.",19,20,2 month,16S,123,Illumina,DESeq2,NA,TRUE,NA,"age,sex",NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1, Figure 3, Table 1, Text",3 December 2019,Utsav Patel,WikiWorks743,Microbiomic differences at cancerprone oral mucosa sites with marijuana usage,decreased,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,2|976|117743|200644|2762318|59735,Complete,NA
Study 173,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Wang W , Zheng S",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,healthy controls,pancreatic cancer,diagnosed according to international guidelines by comprehensive consideration of clinical symptoms,57,85,8 weeks,16S,345,Illumina,LEfSe,0.05,FALSE,NA,age,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 4,4 December 2019,Fatima Zohra,WikiWorks743,Composition and differences of fecal microbial communities between PC patients and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Paraliobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465;2|1224|1236|91347|543|570;2|1239|909932|909929|1843491|970;2|1239|526524|526525|2810280|135858;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|52228;2|1239|909932|1843488|909930|904;2|1224|1236|91347|543|547;2|1239|91061|1385|186817|200903;2|1239|909932|909929|1843491|82202;2|1224|29547|213849|72294|194;2|32066|203490|203491|1129771|32067;2|1224|1236|91347|543|413496;2|1224|1236|135625|712|416916,Complete,NA
Study 173,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Wang W , Zheng S",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,healthy controls,pancreatic cancer,diagnosed according to international guidelines by comprehensive consideration of clinical symptoms,57,85,8 weeks,16S,345,Illumina,LEfSe,0.05,FALSE,NA,age,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 4,4 December 2019,Fatima Zohra,WikiWorks743,Composition and differences of fecal microbial communities between PC patients and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Paraeggerthella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger",2|1239|186801|186802|216572|244127;2|201174|84998|1643822|1643826|651554;2|1224|1236|91347|1903414|583;2|1239|186801|186802|543314|86331;2|1239|186801|186802|31979|1485;2|1239|186801|186802|216572|44748;2|201174|84998|1643822|1643826|84111;2|1224|28211|356|82115|379;2|1224|28211|204458|76892|41275;2|74201|203494|48461|1647988|239934;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|946234;2|1239|186801|186802|31979|580596;2|1224|28221|213115|194924|35832;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|207244;2|1239|909932|909929|1843491|158846;2|201174|1760|85004|31953|1678;2|976|200643|171549|171550|239759;2|1224|28216|80840|995019|577310;2|1239|186801|186802|204475,Complete,NA
Study 173,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Wang W , Zheng S",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,without cancer,pancreatic head cancer with obstruction,pancreatic head cancer with obstruction of common bile duct,32,22,8 weeks,16S,345,Illumina,LEfSe,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,4 December 2019,Fatima Zohra,WikiWorks743,Identification of crucial bacteria associated with the bile in the gut for PC,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Parasporobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",2|1239|186801|186802|186803|46205;2|1224|28216|80840|80864|283;2|1239|186801|186802|216572|1200657;2|32066|203490|203491|1129771|32067;2|1239|186801|186802|186803|140625;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|115543;2|1239|91061|186826|186828|117563,Complete,NA
Study 173,case-control,29221120,10.18632/oncotarget.18820,NA,"Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Wang W , Zheng S",Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China,Oncotarget,2017,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,without cancer,pancreatic head cancer with obstruction,pancreatic head cancer with obstruction of common bile duct,32,22,8 weeks,16S,345,Illumina,LEfSe,0.05,FALSE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,4 December 2019,Fatima Zohra,WikiWorks743,Identification of crucial bacteria associated with the bile in the gut for PC,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Anaerorhabdus",2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|526524|526525|128827|118966,Complete,NA
Study 174,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen XH, Wang A, Chu AN, Gong YH , Yuan Y",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,paired adjacent non-cacerous tissue,cacerous tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3,11 December 2019,Valentina Pineda,WikiWorks743,Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Actinobacteria|c__Thermoleophilia,k__Bacteria|p__Acidobacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oris,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter baumannii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Firmicutes",2|1224|28211|356;2|201174|1497346;2|57723;2|1239|909932|909929|1843491|970;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|28135;2|1239|186801|186802|186803|1164882;2|1239|91061|186826|1300|1301;2|1239|909932|909929;2|1239|909932;2|1239|909932|1843489|31977;2|1239|186801|186802|186804|1257;2|1239|186801|186802|186803;2|1224|28211|204457|41297|13687;2|201174;2|1239|186801|186802|186804;2|976|200643|171549|171552|838|28129;2|1224|1236|2887326|468|469;2|1224|1236|2887326|468;2|976|200643|171549|171552;2|1224|1236|2887326|468|469|470;2|1239|186801|186802;2|1239|186801;2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386;2|976|200643|171549;2|976|200643;2|1239|91061;2|976;2|1239|91061|1385;2|1224|1236|72274|135621|286|287;2|1239,Complete,NA
Study 174,case-control,31231345,10.3389/fmicb.2019.01261,NA,"Chen XH, Wang A, Chu AN, Gong YH , Yuan Y",Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,paired adjacent non-cacerous tissue,cacerous tissue,gastric cancer patients who underwent subtotal gastrectomy,62,62,1 month,16S,45,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure3,11 December 2019,Valentina Pineda,WikiWorks743,Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Niveispirillum,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus|s__Levilactobacillus brevis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales",2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|1903411|613;2|1224|29547|213849|72293|209|210;2|1224|29547|213849|72293;2|1224|29547|213849|72293|209;2|1224|1236|91347|1903411|613|615;2|1224|29547|213849;2|1224|29547;2|1224|28211|204441|2829815|1543704;2|1224|28211|204441|41295;2|1224|28211|204441;2|1239|91061|186826|33958|2767886|1580;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|1357|1358;2|1224|1236|135614,Complete,NA
Study 175,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the two cohorts with incident primary pancreatic adenocarcinoma,371,361,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,11 December 2019,Fatima Zohra,WikiWorks743,Median relative abundance of selected oral microbiota in pancreatic cancer,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|976;2|976|200643|171549|171552|1283313,Complete,NA
Study 175,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the two cohorts with incident primary pancreatic adenocarcinoma,371,361,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,11 December 2019,Fatima Zohra,WikiWorks743,Median relative abundance of selected oral microbiota in pancreatic cancer,decreased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|32066;2|32066|203490;2|32066|203490|203491;2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067,Complete,NA
Study 175,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the CPSII cohorts with incident primary pancreatic adenocarcinoma,170,170,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemenatry table 3a,11 December 2019,Fatima Zohra,WikiWorks743,Median relative abundance of selected oral microbiota in pancreatic cancer cases and controls in the Cancer Prevention Study(CPS) cohort,decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria",2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067;2|976|200643|171549|171552|1283313;2|32066|203490|203491;2|32066|203490;2|32066,Complete,NA
Study 175,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,Experiment 3,United States of America,Homo sapiens,mouth,UBERON:0000165,pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer cases,subjects from the PLCO cohorts with incident primary pancreatic adenocarcinoma,201,191,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemenatry table 3b,11 December 2019,Fatima Zohra,WikiWorks743,Median relative abundance of selected oral microbiota in pancreatic cancer cases and controls in the Cancer Prevention Study(CPS) cohort,decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067,Complete,NA
Study 176,case-control,28320465,10.1186/s40168-017-0250-1,NA,"Chua LL, Rajasuriar R, Azanan MS, Abdullah NK, Tang MS, Lee SC, Woo YL, Lim YA, Ariffin H , Loke P",Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation,Microbiome,2017,Experiment 1,Malaysia,Homo sapiens,caecum,UBERON:0001153,leukemia,EFO:0000565,controls,survivors of acute lymphoblastic leukemia,adult surviors of childhood leukemia,61,73,NA,16S,4,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,"Figure 2,Supplementary table S1",12 December 2019,Fatima Zohra,WikiWorks743,Alterations to microbial communities in adult survivors of acute lymphoblastic leukemia,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Archaea,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|201174;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|150022;2157;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|201174|1760|2037|2049|1654,Complete,NA
Study 176,case-control,28320465,10.1186/s40168-017-0250-1,NA,"Chua LL, Rajasuriar R, Azanan MS, Abdullah NK, Tang MS, Lee SC, Woo YL, Lim YA, Ariffin H , Loke P",Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation,Microbiome,2017,Experiment 1,Malaysia,Homo sapiens,caecum,UBERON:0001153,leukemia,EFO:0000565,controls,survivors of acute lymphoblastic leukemia,adult surviors of childhood leukemia,61,73,NA,16S,4,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,"Figure 2,Supplementary table S1",12 December 2019,Fatima Zohra,WikiWorks743,Alterations to microbial communities in adult survivors of acute lymphoblastic leukemia,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae",2|976|200643|171549;2|976|200643;2|976;2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|976|200643|171549|171550;2|1239|186801|186802|186803|28050;2|1224|28221|213115;2|1224|28221;2|1224|28221|213115|194924,Complete,NA
Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,Experiment 1,Sweden,Homo sapiens,mucosa,UBERON:0000344,colorectal cancer,EFO:0005842,control,mucosa,patients diagnosed with stage I-III colon cancer,14,12,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Table 2, supplemental table S1",16 December 2019,Fatima Zohra,"WikiWorks743,Fatima",Microbiota alterations in colon cancer mucosa and tumor samples compared with non cancer control mucosa at colonoscopy,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Tenericutes",2|976;2|1224|28221|213115|194924|35832;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|39948;2157|28890;2|32066;2|32066|203490|203491|203492|848;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|119852;2|1239|186801|186802|186804|1257;2|544448,Complete,NA
Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,Experiment 1,Sweden,Homo sapiens,mucosa,UBERON:0000344,colorectal cancer,EFO:0005842,control,mucosa,patients diagnosed with stage I-III colon cancer,14,12,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"Table 2, supplemental table S1",16 December 2019,Fatima Zohra,"WikiWorks743,Fatima",Microbiota alterations in colon cancer mucosa and tumor samples compared with non cancer control mucosa at colonoscopy,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,Experiment 2,Sweden,Homo sapiens,colon,UBERON:0001155,colorectal cancer,EFO:0005842,control,tumor,patients diagnosed with stage I-III colon cancer,14,12,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Table 2, supplemental table S1",16 December 2019,Fatima Zohra,WikiWorks743,Microbiota alterations in colon cancer mucosa and tumor samples compared with non cancer control mucosa at colonoscopy,increased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus",2157|28890|183925|2158|2159|2172;2|1239|909932|909929|1843491|970;2|1239|186801|186802|186804|1257,Complete,NA
Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,Experiment 3,Sweden,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,control,fecal,patients diagnosed with stage I-III colon cancer,21,14,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supppemental table S2, text",16 December 2019,Fatima Zohra,"WikiWorks743,Fatima",Microbiota alterations in colon cancer mucosa and tumor samples compared with non cancer control mucosa at colonoscopy,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1239|186801|186802|186803|189330;2|1239|186801|186802|186804|1257,Complete,NA
Study 177,case-control,28944067,10.1136/bmjgast-2017-000145,NA,"Hibberd AA, Lyra A, Ouwehand AC, Rolny P, Lindegren H, Cedgård L , Wettergren Y",Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention,BMJ open gastroenterology,2017,Experiment 3,Sweden,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,control,fecal,patients diagnosed with stage I-III colon cancer,21,14,recent,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supppemental table S2,16 December 2019,Fatima Zohra,WikiWorks743,Microbiota alterations in colon cancer mucosa and tumor samples compared with non cancer control mucosa at colonoscopy,decreased,"k__Bacteria|p__Tenericutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|544448;2|1239|186801|186802|186803|841,Complete,NA
Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal,gastric cancer peritumor group,gastric cancer,60,61,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 3,18 December 2019,Rimsha Azhar,WikiWorks743,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae",2|1224|1236|135619;2|1224|1236|135619|28256|2745;2|1224|1236|135619|28256;2|1224|1236|135622|267890;2|1224|1236|135622|267890|22;2|1224|1236|135622;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1224|28211|204458|76892|41275;2|201174|1760|85006|1268|1663;2|201174|1760|85007|1762|1763;2|201174|1760|85007|1762,Complete,NA
Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal,gastric cancer peritumor group,gastric cancer,60,61,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 3,18 December 2019,Rimsha Azhar,WikiWorks743,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae|g__Legionella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales",2|1224|28216|80840|119060|106589;2|1224|28216|80840|119060;2|976|200643|171549|171551;2|1224|1236|118969|444;2|1224|1236|118969|444|445;2|1224|1236|118969,Complete,NA
Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,Experiment 2,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,peritumor,gastric cancer tumor group,gastric cancer,61,59,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 1,Figure 3,18 December 2019,Rimsha Azhar,WikiWorks743,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia",2|1239|91061;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|909932|909929|1843491|970;2|1224|1236|135619;2|1224|1236|135619|28256|2745;2|1224|1236|135619|28256;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|1224|1236|91347|543;2|1224|1236|91347;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|1263;2|976|200643|171549|171550;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|459786;2|1239|186801|186802|186803|33042;2|1239|186801|186802|541000;2|1239|186801|186802|186803|841;2|1239|909932|1843489|31977|906;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|186801|186802|186803|572511,Complete,NA
Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,Experiment 2,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,peritumor,gastric cancer tumor group,gastric cancer,61,59,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 2,Figure 3,18 December 2019,Rimsha Azhar,WikiWorks743,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria",2|1224|28211|356|82115|379;2|1224|28211|356|82115;2|976;2|1239|909932|909929|1843491|158846;2|1224|1236|135622|267890;2|1224|1236|135622|267890|22;2|1224|1236|135622;2|201174|1760|85007|1762|1763;2|201174|1760|85007|1762;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1224,Complete,NA
Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,Experiment 3,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal,gastric cancer tumor group,gastric cancer,60,59,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,Figure 3,18 December 2019,Rimsha Azhar,"WikiWorks743,Lwaldron",LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174;2|1224|1236|135622;2|1224|28216|80840|92793;2|1239|91061;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|572511;2|1224|28216|80840;2|1239|91061|186826|186828;2|1239|186801|186802|186803|33042;2|1239|909932|1843489|31977|39948;2|1224|1236|91347;2|1224|1236|91347|543;2|1239;2|1239|91061|1385|1378;2|1239|186801|186802|204475;2|1239|91061|186826|186828|117563;2|1224|2008785|119069|206349;2|1224|2008785|119069;2|1224|2008785|119069|206349|70774;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045;2|1224|28211|356|119045|407;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1239|186801|186802|541000;2|1224|28216|80840|75682;2|1239|186801|186802|186804;2|1239|186801|186802|186804|1257;2|201174|1760|85009|31957;2|201174|1760|85009|31957|1743;2|1239|186801|186802|186803|841;2|201174|84995|84996|84997|42255;2|201174|84995|84996|84997;2|201174|84995|84996;2|1239|186801|186802|216572|1263;2|1224|1236|135622|267890|22;2|1224|1236|135622|267890;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977,Complete,NA
Study 178,case-control,30936882,10.3389/fimmu.2019.00533,NA,"Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F , Liu X",Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study,Frontiers in immunology,2019,Experiment 3,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal,gastric cancer tumor group,gastric cancer,60,59,1 month,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,Figure 3,18 December 2019,Rimsha Azhar,WikiWorks743,LEfSe identifies the taxa with the greatest differences in abundance among the three stomach microhabitats,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|976;2|976|200643|171549|171551;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653;2|1224|28216|80840|119060;2|1224|28216|80840|119060|106589;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279,Complete,NA
Study 179,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q, Rao Y, Guo X, Liu N, Liu S, Wen P, Li S , Li Y",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,oesophageal cancer,21,20,1 month,16S,34,Illumina,Metastats,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 2, Figure 5, Figure 6",18 December 2019,Utsav Patel,WikiWorks743,Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",2|201174|1760|2037|2049|1654;2|201174|84998|84999|1643824|1380;2|1224|1236|135615|868|2717,Complete,NA
Study 179,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q, Rao Y, Guo X, Liu N, Liu S, Wen P, Li S , Li Y",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,oesophageal cancer,21,20,1 month,16S,34,Illumina,Metastats,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 2, Figure 5, Figure 6",18 December 2019,Utsav Patel,WikiWorks743,Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836,Complete,NA
Study 179,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q, Rao Y, Guo X, Liu N, Liu S, Wen P, Li S , Li Y",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,oesophageal cancer,21,20,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 2, Figure 5, Figure 6",18 December 2019,Utsav Patel,WikiWorks743,Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|201174|84998|84999|1643824|1380;2|201174|84998|84999;2|201174|84998;2|201174|84998|84999|1643824;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654,Complete,NA
Study 179,case-control,31836795,10.1038/s41598-019-55667-w,NA,"Wang Q, Rao Y, Guo X, Liu N, Liu S, Wen P, Li S , Li Y",Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma,Scientific reports,2019,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,esophageal squamous cell carcinoma,EFO:0005922,Healthy controls,Oesophageal cancer,oesophageal cancer,21,20,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 2, Figure 5, Figure 6",18 December 2019,Utsav Patel,WikiWorks743,Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC),decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|32066|203490|203491|203492|848;2|32066|203490|203491|203492;2|976|200643|171549|171551;2|976|200643|171549|171551|836,Complete,NA
Study 180,case-control,29102920,10.1136/gutjnl-2017-314205,NA,"Ferreira RM, Pereira-Marques J, Pinto-Ribeiro I, Costa JL, Carneiro F, Machado JC , Figueiredo C",Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota,Gut,2018,Experiment 1,Portugal,Homo sapiens,stomach,UBERON:0000945,gastric carcinoma,EFO:0000178,chronic gastritis,gastric carcinoma,gastric carcinoma,23,23,NA,16S,56,Ion Torrent,LEfSe,0.05,TRUE,4,age,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,"Figure 3, Figure S4",18 December 2019,Rimsha Azhar,WikiWorks743,LEfSe analysis showing the assiciation of specific microbiota taxa with the group of chronic gastritis and gastric carcinoma,increased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium|s__Phyllobacterium sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter|s__Achromobacter sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria",2|976|117743|200644|2762318|59732|1871047;2|201174|1760|85007|85025|1827|1831;2|201174|1760|85007|85025;2|201174;2|1224|28211|356|69277|28100|1871046;2|1224|1236|91347|543;2|1224|1236|91347|543|544|1896336;2|1239|186801|186802|31979|1485|1506;2|1224|1236|91347;2|1224|1236|135614;2|1224|1236|135614|32033;2|1224|28216|80840|506|222|134375;2|1224|28216|80840;2|1224;2|1224|1236|72274|135621|286|306;2|1224|1236,Complete,NA
Study 180,case-control,29102920,10.1136/gutjnl-2017-314205,NA,"Ferreira RM, Pereira-Marques J, Pinto-Ribeiro I, Costa JL, Carneiro F, Machado JC , Figueiredo C",Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota,Gut,2018,Experiment 1,Portugal,Homo sapiens,stomach,UBERON:0000945,gastric carcinoma,EFO:0000178,chronic gastritis,gastric carcinoma,gastric carcinoma,23,23,NA,16S,56,Ion Torrent,LEfSe,0.05,TRUE,4,age,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,"Figure 3, Figure S4",18 December 2019,Rimsha Azhar,WikiWorks743,LEfSe analysis showing the assiciation of specific microbiota taxa with the group of chronic gastritis and gastric carcinoma,decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter sp.,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria",2|1224|29547;2|1224|29547|213849;2|1224|29547|213849|72293|209|218;2|1224|29547|213849|72293;2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|1300|1301|1306;2|1239|91061|186826|1300;2|1239;2|1224|28216|206351;2|976;2|1224|28216|206351|481|482|192066;2|976|200643;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552;2|32066|203490;2|32066,Complete,NA
Study 181,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer,pancreatic cancer,371,361,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 3, Table 3a",1 January 2020,Rimsha Azhar,WikiWorks743,Median relative abundance of selected oral microbial taxa in pancreatic cancer cases and controls,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,2|976|200643|171549|171552|1283313,Complete,NA
Study 181,case-control,27742762,10.1136/gutjnl-2016-312580,NA,"Fan X, Alekseyenko AV, Wu J, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Abnet CC, Stolzenberg-Solomon R, Miller G, Ravel J, Hayes RB , Ahn J",Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,Gut,2018,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,pancreatic carcinoma,EFO:0002618,controls,pancreatic cancer,pancreatic cancer,371,361,NA,16S,34,Roche454,Logistic Regression,0.05,FALSE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Table 3, Table 3a",1 January 2020,Rimsha Azhar,WikiWorks743,Median relative abundance of selected oral microbial taxa in pancreatic cancer cases and controls,decreased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|32066;2|32066|203490;2|32066|203490|203491;2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067,Complete,NA
Study 182,"cross-sectional observational, not case-control",31215600,10.1590/1678-7757-2018-0635,NA,"Yokoi A, Ekuni D, Hata H, Yamane-Takeuchi M, Maruyama T, Yamanaka R , Morita M",Relationship between acetaldehyde concentration in mouth air and characteristics of microbiota of tongue dorsum in Japanese healthy adults: a cross-sectional study,Journal of applied oral science : revista FOB,2019,Experiment 1,Japan,Homo sapiens,mouth,UBERON:0000165,acetaldehyde,CHEBI:15343,low acetaldehyde concentration group,high acetaldehyde concentration group,"The Sensor Gas Chromatograph SGEA-P2 (FIS Inc., Itami, Japan) was used to measure acetaldehyde concentrations in mouth air.",6,6,current use,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,8 January 2020,Shaimaa Elsafoury,WikiWorks743,Difference in relative abundance of tongue microbiome between High acetaldehyde concentration group and Low acetaldehyde concentration group.,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens",2|1239|91061|1385|1378|84135;2|1239|909932|1843489|31977|29465|29466;2|1224|28216|206351|481|482|484,Complete,NA
Study 182,"cross-sectional observational, not case-control",31215600,10.1590/1678-7757-2018-0635,NA,"Yokoi A, Ekuni D, Hata H, Yamane-Takeuchi M, Maruyama T, Yamanaka R , Morita M",Relationship between acetaldehyde concentration in mouth air and characteristics of microbiota of tongue dorsum in Japanese healthy adults: a cross-sectional study,Journal of applied oral science : revista FOB,2019,Experiment 1,Japan,Homo sapiens,mouth,UBERON:0000165,acetaldehyde,CHEBI:15343,low acetaldehyde concentration group,high acetaldehyde concentration group,"The Sensor Gas Chromatograph SGEA-P2 (FIS Inc., Itami, Japan) was used to measure acetaldehyde concentrations in mouth air.",6,6,current use,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,8 January 2020,Shaimaa Elsafoury,WikiWorks743,Difference in relative abundance of tongue microbiome between High acetaldehyde concentration group and Low acetaldehyde concentration group.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola",2|1239|91061|186826|1300|1301|1318;2|976|200643|171549|171552|838|470565,Complete,NA
Study 183,case-control,31764438,10.1097/MPG.0000000000002461,NA,"Kansal S, Catto-Smith AG, Boniface K, Thomas S, Cameron DJ, Oliver M, Alex G, Kirkwood CD , Wagner J",Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease,Journal of pediatric gastroenterology and nutrition,2019,Experiment 1,Australia,Homo sapiens,ileum,UBERON:0002116,Crohn's disease,EFO:0000384,crohn disease ASCA negative patients,crohn disease ASCA positive patients,Crohn disease anti-Saccharomyces cerevisiae antibody status,39,38,3 months,16S,2,Non-quantitative PCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 1,8 January 2020,Rimsha Azhar,WikiWorks743,Bacterial species significantly associated with Crohn disease Anti-Saccharomyces cerevisiae antibody status (ASCA) positive patients and CD ASCA-negative patients,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,2|1239|186801|186802|186803|2316020|33039,Complete,NA
Study 183,case-control,31764438,10.1097/MPG.0000000000002461,NA,"Kansal S, Catto-Smith AG, Boniface K, Thomas S, Cameron DJ, Oliver M, Alex G, Kirkwood CD , Wagner J",Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease,Journal of pediatric gastroenterology and nutrition,2019,Experiment 1,Australia,Homo sapiens,ileum,UBERON:0002116,Crohn's disease,EFO:0000384,crohn disease ASCA negative patients,crohn disease ASCA positive patients,Crohn disease anti-Saccharomyces cerevisiae antibody status,39,38,3 months,16S,2,Non-quantitative PCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 1,8 January 2020,Rimsha Azhar,WikiWorks743,Bacterial species significantly associated with Crohn disease Anti-Saccharomyces cerevisiae antibody status (ASCA) positive patients and CD ASCA-negative patients,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1224|1236|91347|543|547|550;2|1239|186801|186802|216572|216851|853,Complete,NA
Study 184,prospective cohort,30117171,10.1002/pros.23713,NA,"Alanee S, El-Zawahry A, Dynda D, Dabaja A, McVary K, Karr M , Braundmeier-Fleming A",A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis,The Prostate,2019,Experiment 1,United States of America,Homo sapiens,urine,UBERON:0001088,prostate cancer,MONDO:0008315,controls,prostate cancer patients,the association of urinary and fecal microbiota with prostate cancer diagnosis,16,14,28 days,16S,345,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 1, Text",8 January 2020,Rimsha Azhar,WikiWorks743,Significant differential OTU frequencies in urine samples of patients with or without prostate cancer,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 184,prospective cohort,30117171,10.1002/pros.23713,NA,"Alanee S, El-Zawahry A, Dynda D, Dabaja A, McVary K, Karr M , Braundmeier-Fleming A",A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis,The Prostate,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,prostate cancer,MONDO:0008315,controls,prostate cancer patients,the association of urinary and fecal microbiota with prostate cancer diagnosis,16,14,28 days,16S,345,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 1, Text",8 January 2020,Rimsha Azhar,WikiWorks743,Significant differential OTU frequencies in urine samples of patients with or without prostate cancer,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|186802|186803|28050;2|1239|186801|186802|216572|258514;2|1239|186801|186802|216572|216851,Complete,NA
Study 185,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W, Yang Y, Wang H, Wang H, Yu X, Lu Y, Shen S , Teng L",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer patients,22,20,1 month,16S,NA,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,increased,unchanged,NA,increased,Signature 1,"Figure 2, Sup. figure 2A, Sup. figure 2B",8 January 2020,Valentina Pineda,WikiWorks743,Comparision of gut microbiota between Gastric Cancer patients and Healthy Controls,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales",2|1224;2|1224|1236|91347|543;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|29465;2|1224|1236;2|1224|1236|91347,Complete,NA
Study 185,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W, Yang Y, Wang H, Wang H, Yu X, Lu Y, Shen S , Teng L",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,controls,gastric cancer,gastric cancer patients,22,20,1 month,16S,NA,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,decreased,increased,unchanged,NA,increased,Signature 2,"Figure 2, Sup. figure 2A, Sup. figure 2B",8 January 2020,Valentina Pineda,WikiWorks743,Comparision of gut microbiota between Gastric Cancer patients and Healthy Controls,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643;2|976|200643|171549,Complete,NA
Study 185,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W, Yang Y, Wang H, Wang H, Yu X, Lu Y, Shen S , Teng L",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,healthy gastric cancer,gastric cancer,gastric cancer patients,22,20,1 month,16S,NA,Illumina,LEfSe,NA,FALSE,3.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5,8 January 2020,Valentina Pineda,WikiWorks743,LEfSe analysis of enriched bacterial taxa in gut microbiota between gastric cancer group and healthy gastric cancer group,increased,"k__Bacteria|p__Synergistetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",2|508458;2|1239|186801|186802|186803;2|1224|1236|91347|543|570,Complete,NA
Study 185,case-control,31464899,10.1097/MD.0000000000016626,NA,"Liang W, Yang Y, Wang H, Wang H, Yu X, Lu Y, Shen S , Teng L",Gut microbiota shifts in patients with gastric cancer in perioperative period,Medicine,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,healthy gastric cancer,gastric cancer,gastric cancer patients,22,20,1 month,16S,NA,Illumina,LEfSe,NA,FALSE,3.5,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5,8 January 2020,Valentina Pineda,WikiWorks743,LEfSe analysis of enriched bacterial taxa in gut microbiota between gastric cancer group and healthy gastric cancer group,decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|74201|203494;2|74201|203494|48461;2|74201|203494|48461|203557;2|74201;2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543|620;2|95818;2|1239|909932|909929;2|1239|909932;2|1239|909932|1843489|31977;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|39948;2|976|200643|171549|171552,Complete,NA
Study 186,case-control,31379800,10.3389/fmicb.2019.01664,NA,"Ma X, Chi C, Fan L, Dong B, Shao X, Xie S, Li M , Xue W",The Microbiome of Prostate Fluid Is Associated With Prostate Cancer,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,prostate gland secretion,UBERON:0004796,prostate cancer,MONDO:0008315,non prostrate cancer,prostrate cancer,pathology after prostate biopsy,27,32,4 week,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 1,Figure 5a,8 January 2020,Fatima Zohra,WikiWorks743,Differences in microbial species between prostate cancer and non cancer group,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",2|1239|91061|186826|1300|1357;2|1239|91061|186826|186828|2747;2|1239|91061|186826|1300|1301;2|1239|91061|1385|186817|129337;2|1224|1236|91347|543|547,Complete,NA
Study 186,case-control,31379800,10.3389/fmicb.2019.01664,NA,"Ma X, Chi C, Fan L, Dong B, Shao X, Xie S, Li M , Xue W",The Microbiome of Prostate Fluid Is Associated With Prostate Cancer,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,prostate gland secretion,UBERON:0004796,prostate cancer,MONDO:0008315,non prostrate cancer,prostrate cancer,pathology after prostate biopsy,27,32,4 week,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,increased,NA,NA,Signature 2,Figure 5a,8 January 2020,Fatima Zohra,WikiWorks743,Differences in microbial species between prostate cancer and non cancer group,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus",2|1224|1236|91347|543|413496;2|1239|186801|186802|31979|114627;2|1239|91061|1385|186822|44249,Complete,NA
Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,Experiment 1,United States of America,Homo sapiens,vagina,UBERON:0000996,medroxyprogesterone acetate,CHEBI:6716,depot mdroxyprogesterone Acetate vaginal microbiome (visit 2) among black participants,naive (baseline visit),NA,16,16,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,13 January 2020,Shaimaa Elsafoury,WikiWorks743,Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,Experiment 2,United States of America,Homo sapiens,vagina,UBERON:0000996,medroxyprogesterone acetate,CHEBI:6716,black naive vaginal microbiome (the baseline visit ),white naiive vaginal microbiome,NA,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,13 January 2020,Shaimaa Elsafoury,WikiWorks743,Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women,increased,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,2|1239|1737404|1737405|1570339|150022,Complete,NA
Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,Experiment 2,United States of America,Homo sapiens,vagina,UBERON:0000996,medroxyprogesterone acetate,CHEBI:6716,black naive vaginal microbiome (the baseline visit ),white naiive vaginal microbiome,NA,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,13 January 2020,Shaimaa Elsafoury,WikiWorks743,Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia",2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803|177971,Complete,NA
Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,Experiment 3,United States of America,Homo sapiens,vagina,UBERON:0000996,medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone  (the second visit ),white participants after using depot medroxyprogesterone,NA,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,decreased,Signature 1,Figure 3,13 January 2020,Shaimaa Elsafoury,WikiWorks743,Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,Experiment 3,United States of America,Homo sapiens,vagina,UBERON:0000996,medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone  (the second visit ),white participants after using depot medroxyprogesterone,NA,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,decreased,Signature 2,Figure 3,13 January 2020,Shaimaa Elsafoury,WikiWorks743,Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella",2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|168808;2|1239|186801|186802|31979|1485;2|32066|203490|203491|203492|848;2|1239|91061|1385|1378,Complete,NA
Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,Experiment 4,United States of America,Homo sapiens,vagina,UBERON:0000996,medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone  (the third visit ),white participants after using depot medroxyprogesterone,NA,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 1,Figure 3,13 January 2020,Shaimaa Elsafoury,WikiWorks743,Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women,increased,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,2|1239|1737404|1737405|1570339|150022,Complete,NA
Study 187,time series / longitudinal observational,30866773,10.1080/22221751.2018.1563458,NA,"Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL , Pei Z",Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women,Emerging microbes & infections,2019,Experiment 4,United States of America,Homo sapiens,vagina,UBERON:0000996,medroxyprogesterone acetate,CHEBI:6716,black participants after using depot medroxyprogesterone  (the third visit ),white participants after using depot medroxyprogesterone,NA,16,9,before sample collection,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.2,TRUE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 2,Figure 3,13 January 2020,Shaimaa Elsafoury,WikiWorks743,Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus",2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|906;2|1239|91061|186826|186827|1375,Complete,NA
Study 188,case-control,30854760,10.1111/1471-0528.15600,NA,"Brown RG, Chan D, Terzidou V, Lee YS, Smith A, Marchesi JR, MacIntyre DA , Bennett PR",Prospective observational study of vaginal microbiota pre- and post-rescue cervical cerclage,BJOG : an international journal of obstetrics and gynaecology,2019,Experiment 1,United Kingdom,Homo sapiens,vagina,UBERON:0000996,cervical cerclage,NCIT:C102763,Vaginal microbiome of asymptomatic women prior to cerclage,Vaginal microbiome of symptomatic women prior ro cerclage,NA,13,7,NA,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2,15 January 2020,Shaimaa Elsafoury,WikiWorks743,Cladogram describing differentially abundant vaginal microbial clades and nodes observed between asymptomatic women and those with symptoms as identified using LEfSe analysis,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|1239|91061|186826|1300|1301|257758;2|976|200643|171549|171552|838|28130;2|201174|1760|85004|31953|2701|2702;2|201174|1760|85004|31953|2701,Complete,NA
Study 188,case-control,30854760,10.1111/1471-0528.15600,NA,"Brown RG, Chan D, Terzidou V, Lee YS, Smith A, Marchesi JR, MacIntyre DA , Bennett PR",Prospective observational study of vaginal microbiota pre- and post-rescue cervical cerclage,BJOG : an international journal of obstetrics and gynaecology,2019,Experiment 1,United Kingdom,Homo sapiens,vagina,UBERON:0000996,cervical cerclage,NCIT:C102763,Vaginal microbiome of asymptomatic women prior to cerclage,Vaginal microbiome of symptomatic women prior ro cerclage,NA,13,7,NA,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2,15 January 2020,Shaimaa Elsafoury,WikiWorks743,Cladogram describing differentially abundant vaginal microbial clades and nodes observed between asymptomatic women and those with symptoms as identified using LEfSe analysis,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,2|1239|91061|186826|33958|1578|47770,Complete,NA
Study 189,case-control,29180991,10.3389/fmicb.2017.02222,NA,"Wang J, Wang Y, Zhang X, Liu J, Zhang Q, Zhao Y, Peng J, Feng Q, Dai J, Sun S, Zhao Y, Zhao L, Zhang Y, Hu Y , Zhang M",Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients,Frontiers in microbiology,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B patients,Chronic hepatitis B patients,22,85,1 month,16S,34,Illumina,LEfSe,0.01,FALSE,2,body mass index,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 2,14 January 2020,Rimsha Azhar,WikiWorks743,Differentail OTU selected by LDA effect size(LEfSe),increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,2|1239|909932|909929|1843491|158846,Complete,NA
Study 189,case-control,29180991,10.3389/fmicb.2017.02222,NA,"Wang J, Wang Y, Zhang X, Liu J, Zhang Q, Zhao Y, Peng J, Feng Q, Dai J, Sun S, Zhao Y, Zhao L, Zhang Y, Hu Y , Zhang M",Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients,Frontiers in microbiology,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B patients,Chronic hepatitis B patients,22,85,1 month,16S,34,Illumina,LEfSe,0.01,FALSE,2,body mass index,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 2,14 January 2020,Rimsha Azhar,"WikiWorks743,Fatima",Differentail OTU selected by LDA effect size(LEfSe),decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|976|200643|171549|815|816;2|976|200643|171549|1853231|574697;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1239|186801|186802|186803;2|1224|1236|91347|543,Complete,NA
Study 190,prospective cohort,30813950,10.1186/s40168-019-0645-2,NA,"Iszatt N, Janssen S, Lenters V, Dahl C, Stigum H, Knight R, Mandal S, Peddada S, González A, Midtvedt T , Eggesbø M",Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month,Microbiome,2019,Experiment 1,Norway,Homo sapiens,feces,UBERON:0001988,breast milk measurement,EFO:0009092,one-month age infants exposed to low chemical breast milk,one-month age infants exposed to high chemical breast milk,low chemical exposure is < 20th percentile breast milk toxicant exposure and high chemical exposure is ≥ 80th percentile breast milk toxicant exposure.,NA,NA,more than two weeks prior sampling,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,gestational age,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2,15 January 2020,Shaimaa Elsafoury,"WikiWorks743,Fatima",Differentially abundant sequences in the high vs. low chemical exposure groups.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Poales|f__Juncaceae|g__Oxychloe",2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300;2759|33090|35493|3398|38820|14101|13623,Complete,NA
Study 190,prospective cohort,30813950,10.1186/s40168-019-0645-2,NA,"Iszatt N, Janssen S, Lenters V, Dahl C, Stigum H, Knight R, Mandal S, Peddada S, González A, Midtvedt T , Eggesbø M",Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month,Microbiome,2019,Experiment 1,Norway,Homo sapiens,feces,UBERON:0001988,breast milk measurement,EFO:0009092,one-month age infants exposed to low chemical breast milk,one-month age infants exposed to high chemical breast milk,low chemical exposure is < 20th percentile breast milk toxicant exposure and high chemical exposure is ≥ 80th percentile breast milk toxicant exposure.,NA,NA,more than two weeks prior sampling,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,gestational age,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2,15 January 2020,Shaimaa Elsafoury,WikiWorks743,Differentially abundant sequences in the high vs. low chemical exposure groups.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|29465,Complete,NA
Study 191,"cross-sectional observational, not case-control",30791484,10.3390/nu11020433,NA,"Iino C, Shimoyama T, Iino K, Yokoyama Y, Chinda D, Sakuraba H, Fukuda S , Nakaji S",Daidzein Intake Is Associated with Equol Producing Status through an Increase in the Intestinal Bacteria Responsible for Equol Production,Nutrients,2019,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,equol,CHEBI:34741,equol non-producers,equol producers,The equol production status was defined by a urinary log 10 - transformed equol/daidzein ratio of −1.75 or more as described previously,586,458,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Table 2,15 January 2020,Shaimaa Elsafoury,WikiWorks743,Relative abundance of species (percentage of the total bacterial 16sRNA).,increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens|s__Adlercreutzia equolifaciens subsp. celatus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens",2|201174|84998|1643822|1643826|447020|446660|394340;2|201174|84998|1643822|1643826|84108|572010,Complete,NA
Study 192,case-control,22339879,10.1111/j.1365-2982.2012.01891.x,NA,"Carroll IM, Ringel-Kulka T, Siddle JP , Ringel Y",Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,healthy controls,diarrhea-predominant irritable bowel syndrome,Diarrhea-Predominant irritable bowel syndrome,23,23,2 months,16S,123,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Table 2,15 January 2020,Rimsha Azhar,WikiWorks743,Bacterial taxa that differ between D-IBS patients and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347;2|1224|1236|91347|543,Complete,NA
Study 192,case-control,22339879,10.1111/j.1365-2982.2012.01891.x,NA,"Carroll IM, Ringel-Kulka T, Siddle JP , Ringel Y",Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,healthy controls,diarrhea-predominant irritable bowel syndrome,Diarrhea-Predominant irritable bowel syndrome,23,23,2 months,16S,123,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Table 2,15 January 2020,Rimsha Azhar,WikiWorks743,Bacterial taxa that differ between D-IBS patients and healthy controls,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,NA
Study 192,case-control,22339879,10.1111/j.1365-2982.2012.01891.x,NA,"Carroll IM, Ringel-Kulka T, Siddle JP , Ringel Y",Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,healthy controls,diarrhea-predominant irritable bowel syndrome,Diarrhea-Predominant irritable bowel syndrome,23,23,2 months,16S,6,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table 2,15 January 2020,Rimsha Azhar,WikiWorks743,Bacterial taxa that differ between D-IBS patients and healthy controls,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens",2|1224;2|1224|1236;2|1224|1236|91347|543;2|1239|186801|186802|216572|253238,Complete,NA
Study 193,case-control,25052961,10.1111/hel.12145,NA,"Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS , Kim JF","Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods",Helicobacter,2014,Experiment 1,South Korea,Homo sapiens,mucosa of stomach,UBERON:0001199,gastric cancer,MONDO:0001056,chronic gastritis and intestinal metaplasia,gastric cancer,diagnosis confirmed by hisotpathology,21,10,6 months,16S,5,Roche454,NA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Supplemental Fig S1, S2",22 January 2020,Fatima Zohra,WikiWorks743,"Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer",increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|91061;2|1239|91061|186826|1300,Complete,NA
Study 193,case-control,25052961,10.1111/hel.12145,NA,"Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS , Kim JF","Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods",Helicobacter,2014,Experiment 1,South Korea,Homo sapiens,mucosa of stomach,UBERON:0001199,gastric cancer,MONDO:0001056,chronic gastritis and intestinal metaplasia,gastric cancer,diagnosis confirmed by hisotpathology,21,10,6 months,16S,5,Roche454,NA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Supplemental Fig S1, S2",22 January 2020,Fatima Zohra,WikiWorks743,"Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer",decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae",2|1224|29547;2|1224|29547|213849|72293,Complete,NA
Study 193,case-control,25052961,10.1111/hel.12145,NA,"Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS , Kim JF","Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods",Helicobacter,2014,Experiment 2,South Korea,Homo sapiens,mucosa of stomach,UBERON:0001199,gastric cancer,MONDO:0001056,H. pylori negative,H. pylori postive,by conventional laboratory method including rapid urease test and histopathology,3,7,6 months,16S,5,Roche454,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Fig S3,22 January 2020,Fatima Zohra,WikiWorks743,Comparison of the gastric microbial profiles between H. pylori positive and H. pylori negative chronic gastritis patients,decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae",2|1224|28211|356|41294;2|1224|28211|204458|76892;2|1239|91061|186826|33958;2|1224|28216|80840|119060,Complete,NA
Study 194,case-control,30737418,10.1038/s41598-018-38031-2,NA,"Zhou B, Sun C, Huang J, Xia M, Guo E, Li N, Lu H, Shan W, Wu Y, Li Y, Xu X, Weng D, Meng L, Hu J, Gao Q, Ma D , Chen G",The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients,Scientific reports,2019,Experiment 1,China,Homo sapiens,uterus,UBERON:0000995,ovarian cancer,MONDO:0008170,normal tissue,ovarian cancer,women diagnosed with high grade ovarian cancer,25,25,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,unchanged,NA,NA,Signature 1,"Figure 2, Fig S3",22 January 2020,Fatima Zohra,WikiWorks743,Differentially abundant taxons between ovarian cancer tissues and normal tissues,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Acidobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus piscium",2|1239;2|201174;2|57723;2|1239|186801|186802|216572|236752;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|1357|1364,Complete,NA
Study 194,case-control,30737418,10.1038/s41598-018-38031-2,NA,"Zhou B, Sun C, Huang J, Xia M, Guo E, Li N, Lu H, Shan W, Wu Y, Li Y, Xu X, Weng D, Meng L, Hu J, Gao Q, Ma D , Chen G",The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients,Scientific reports,2019,Experiment 1,China,Homo sapiens,uterus,UBERON:0000995,ovarian cancer,MONDO:0008170,normal tissue,ovarian cancer,women diagnosed with high grade ovarian cancer,25,25,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,decreased,NA,unchanged,NA,NA,Signature 2,"Figure 2, Fig S3",22 January 2020,Fatima Zohra,WikiWorks743,Differentially abundant taxons between ovarian cancer tissues and normal tissues,decreased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Schlegelella,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella osloensis,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia vermicola,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter lwoffii,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas azotifigens",2|1224;2|1224|28211|356|212791;2|1224|28216|80840|80864|283;2|1239|91061|1385|90964|1279;2|1224|28211|204457|41297|165695;2|1224|28211|356|119045|407;2|1224|28216|80840|119060|106589;2|1224|1236|91347|1903414|586;2|1224|28216|80840|80864|215579;2|976|1853228|1853229|563835|504481;2|1224|28216|80840|80864|12916;2|1224|28211|204457|41297|13687;2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|475|34062;2|1224|28211|204457|41297|165695|13690;2|1224|1236|91347|1903414|586|333965;2|1224|1236|2887326|468|469|28090;2|1224|28211|204457|41297|13687|330920,Complete,NA
Study 195,case-control,26606973,10.1038/srep17098,NA,"Ling Z, Liu X, Cheng Y, Jiang X, Jiang H, Wang Y , Li L",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,Experiment 1,China,Homo sapiens,dental plaque,UBERON:0016482,chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,"Figure 3, Text",24 January 2020,Rimsha Azhar,WikiWorks743,LEfSe was used to identify the most differentially abundant taxa in healthy control and CHB patient samples,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia",2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|1903411|629;2|1224|1236|135614;2|1239|186801|186802|186804|44259;2|1224|1236|135614|32033;2|1239|186801|186802|186804;2|1239|186801|186802;2|1239|186801,Complete,NA
Study 195,case-control,26606973,10.1038/srep17098,NA,"Ling Z, Liu X, Cheng Y, Jiang X, Jiang H, Wang Y , Li L",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,Experiment 1,China,Homo sapiens,dental plaque,UBERON:0016482,chronic hepatitis B virus infection,EFO:0004239,healthy controls,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,"Figure 3, Text",24 January 2020,Rimsha Azhar,WikiWorks743,LEfSe was used to identify the most differentially abundant taxa in healthy control and CHB patient samples,decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067;2|976|117743|200644;2|976|117743|200644|49546;2|976|117743;2|976|117743|200644|49546|1016,Complete,NA
Study 195,case-control,26606973,10.1038/srep17098,NA,"Ling Z, Liu X, Cheng Y, Jiang X, Jiang H, Wang Y , Li L",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,Experiment 2,China,Homo sapiens,dental plaque,UBERON:0016482,chronic hepatitis B virus infection,EFO:0004239,liver cirrhosis,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 4, Text",1 February 2020,Rimsha Azhar,WikiWorks743,Taxanomic differences in oral microbiota of the CHB and LC groups,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Spirochaetes|c__Spirochaetia",2|1239|186801|186802|186804|44259;2|203691|203692|136|2845253|157;2|203691|203692|136|137;2|203691|203692|136;2|203691;2|203691|203692,Complete,NA
Study 195,case-control,26606973,10.1038/srep17098,NA,"Ling Z, Liu X, Cheng Y, Jiang X, Jiang H, Wang Y , Li L",Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project,Scientific reports,2015,Experiment 2,China,Homo sapiens,dental plaque,UBERON:0016482,chronic hepatitis B virus infection,EFO:0004239,liver cirrhosis,chronic hepatitis B,chronic hepatitis B,10,10,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 4, Text",1 February 2020,Rimsha Azhar,WikiWorks743,Taxanomic differences in oral microbiota of the CHB and LC groups,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1224|28216;2|1224|28216|206351|481;2|1224|28216|206351;2|1224|28216|206351|481|482,Complete,NA
Study 196,case-control,29525681,10.1016/j.intimp.2018.03.003,NA,"Wang X, Zhang L, Wang Y, Liu X, Zhang H, Liu Y, Shen N, Yang J , Gai Z",Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,70,85,NA,16S,12,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 6b,24 January 2020,Rimsha Azhar,WikiWorks743,The most differentially abundant taxa between Henoch-Schönlein Purpura (HSP) and controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239|909932|1843489|31977|29465;2|32066|203490;2|32066;2|32066|203490|203491;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|909932|1843489|31977;2|1239|909932|909929|1843491|158846;2|976|200643|171549|171551;2|976|200643|171549|2005525|375288,Complete,NA
Study 196,case-control,29525681,10.1016/j.intimp.2018.03.003,NA,"Wang X, Zhang L, Wang Y, Liu X, Zhang H, Liu Y, Shen N, Yang J , Gai Z",Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,70,85,NA,16S,12,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 6b,24 January 2020,Rimsha Azhar,"WikiWorks743,Fatima",The most differentially abundant taxa between Henoch-Schönlein Purpura (HSP) and controls,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|1224|28216|80840|506;2|1224|28216;2|1224|28216|80840;2|1239|186801|186802|990719;2|1239|186801;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239;2|1224|1236|135625|712|724;2|1224|1236|91347|543|570;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|28050|39485;2|1239|186801|186802|186803;2|1224|28216|80840|995019|577310;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|39491,Complete,NA
Study 197,case-control,29031597,10.1016/j.jaci.2017.09.018,NA,"Goldman DL, Chen Z, Shankar V, Tyberg M, Vicencio A , Burk R",Lower airway microbiota and mycobiota in children with severe asthma,The Journal of allergy and clinical immunology,2018,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,asthma,MONDO:0004979,non-asthma,severe asthma,severe asthma,11,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1a, 1b",24 January 2020,Rimsha Azhar,"WikiWorks743,Fatima",Differentially abundant genera between between severe asthma and non-asthma patients,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Leucosporidiales|f__Leucosporidiaceae|g__Leucosporidium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pneumocystidomycetes|o__Pneumocystidales|f__Pneumocystidaceae|g__Pneumocystis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|207244;2|976|200643|171549|815|816;2|976|117743|200644|49546|1016;2|1239|186801|186802|186803|1432051;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2759|4751|5204|162481|231212|1163720|5277;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2759|4751|4890|147553|37987|44281|4753;2759|4751|5204|162481|231213|1799696|5533;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263,Complete,NA
Study 197,case-control,29031597,10.1016/j.jaci.2017.09.018,NA,"Goldman DL, Chen Z, Shankar V, Tyberg M, Vicencio A , Burk R",Lower airway microbiota and mycobiota in children with severe asthma,The Journal of allergy and clinical immunology,2018,Experiment 1,United States of America,Homo sapiens,oral gland,UBERON:0010047,asthma,MONDO:0004979,non-asthma,severe asthma,severe asthma,11,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1a, 1b",24 January 2020,Rimsha Azhar,WikiWorks743,Differentially abundant genera between between severe asthma and non-asthma patients,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricostilbomycetes|o__Agaricostilbales|f__Agaricostilbaceae|g__Sterigmatomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Davidiella",2|1224|1236|91347|1903414|583;2759|4751|5204|162480|48846|48847|5615;2759|4751|5204|155616|5234|1884633|5206;2759|4751|4890|147541|2726946|452563|237557,Complete,NA
Study 198,case-control,30342346,10.1016/j.intimp.2018.10.017,NA,"Chen B, Wang J, Wang Y, Zhang J, Zhao C, Shen N, Yang J, Gai Z , Zhang L",Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,Experiment 1,China,Homo sapiens,mouth,UBERON:0000165,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,66,98,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 6b, 6c",24 January 2020,Rimsha Azhar,WikiWorks743,"Histogram of the LDA scores computed for different abundance levels between children with HSP and healthy children, as detected by the LEfSe tool",increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|1224|28216|206351;2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|1239|909932|1843489|31977|29465;2|1239|909932;2|1239|909932|1843489;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976;2|976|200643;2|976|200643|171549,Complete,NA
Study 198,case-control,30342346,10.1016/j.intimp.2018.10.017,NA,"Chen B, Wang J, Wang Y, Zhang J, Zhao C, Shen N, Yang J, Gai Z , Zhang L",Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children,International immunopharmacology,2018,Experiment 1,China,Homo sapiens,mouth,UBERON:0000165,Henoch-Schoenlein purpura,EFO:1000965,controls,Henoch-Schönlein Purpura,Henoch-Schönlein Purpura in children,66,98,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,3.5,"age,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 6b, 6c",24 January 2020,Rimsha Azhar,WikiWorks743,"Histogram of the LDA scores computed for different abundance levels between children with HSP and healthy children, as detected by the LEfSe tool",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria",2|1224|1236|135625|712|724;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|28211;2|1224|1236|2887326|468|469;2|1224|1236|2887326|468;2|1224|1236|72274;2|1224|1236;2|1224,Complete,NA
Study 199,case-control,31954395,10.1186/s13048-019-0603-4,NA,"Wang Q, Zhao L, Han L, Fu G, Tuo X, Ma S, Li Q, Wang Y, Liang D, Tang M, Sun C, Wang Q, Song Q , Li Q",The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ,Journal of ovarian research,2020,Experiment 1,China,Homo sapiens,uterus,UBERON:0000995,ovarian cancer,MONDO:0008170,controls,ovarian cancer,preliminary diagnosis of suspected ovarian cancer and undergoing laparotomy,10,6,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 3, Table 2",24 January 2020,Fatima Zohra,WikiWorks743,Differential relative abundance of taxa in ovarian communities between patients in cancer an control group,increased,"k__Bacteria|p__Planctomycetes,k__Bacteria|p__Aquificae,k__Bacteria|p__Verrucomicrobia|c__Spartobacteria,k__Bacteria|p__Planctomycetes|c__Planctomycetia|o__Planctomycetales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Thermales|f__Thermaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Chloroflexi|c__Ktedonobacteria|o__Thermogemmatisporales|f__Thermogemmatisporaceae",2|203682;2|200783;2|74201|134549;2|203682|203683|112;2|1224|1236|72274;2|1224|1236|91347;2157|28890|183925|2158;2|1224|29547|213849;2157|28890|183925|2158|2159;2|1224|1236|2887326|468;2|1297|188787|68933|188786;2|201174|1760|85006|85023;2|1239|91061|1385|90964;2|200795|388447|768667|768668,Complete,NA
Study 199,case-control,31954395,10.1186/s13048-019-0603-4,NA,"Wang Q, Zhao L, Han L, Fu G, Tuo X, Ma S, Li Q, Wang Y, Liang D, Tang M, Sun C, Wang Q, Song Q , Li Q",The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ,Journal of ovarian research,2020,Experiment 1,China,Homo sapiens,uterus,UBERON:0000995,ovarian cancer,MONDO:0008170,controls,ovarian cancer,preliminary diagnosis of suspected ovarian cancer and undergoing laparotomy,10,6,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 3, Table 2",24 January 2020,Fatima Zohra,WikiWorks743,Differential relative abundance of taxa in ovarian communities between patients in cancer an control group,decreased,"k__Archaea|p__Crenarchaeota,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Archaea|p__Euryarchaeota|c__Archaeoglobi|o__Archaeoglobales|f__Archaeoglobaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanocorpusculaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Haloferacales|f__Haloferacaceae|g__Haloferax",2157|28889;2|976|117747;2157|28890|183963|2235;2|976|117743|200644|49546;2157|28890|183980|2231|2232;2|32066|203490|203491|1129771;2157|28890|224756|2191|88404;2|201174|1760|1643682|85030;2|1239|91061|1385|186822|44249;2157|28890|183963|1644055|1644056|2251,Complete,NA
Study 200,"cross-sectional observational, not case-control",31844128,10.1038/s41598-019-55720-8,NA,"Walsh DM, Hokenstad AN, Chen J, Sung J, Jenkins GD, Chia N, Nelson H, Mariani A , Walther-Antonio MRS",Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome),Scientific reports,2019,Experiment 1,United States of America,Homo sapiens,lower part of vagina,UBERON:0015243,endometrial cancer,MONDO:0011962,pre,post,patients undergoing hysterectomy,NA,NA,2 weeks,16S,345,Illumina,Linear Regression,0.1,TRUE,NA,NA,vaginal pH,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 2, Table S1",25 January 2020,Fatima Zohra,WikiWorks743,Bacterial OTUs differentially enriched among patients without EC by menopause status,increased,k__Archaea|p__candidate phylum NAG2,2157|1448937,Complete,NA
Study 200,"cross-sectional observational, not case-control",31844128,10.1038/s41598-019-55720-8,NA,"Walsh DM, Hokenstad AN, Chen J, Sung J, Jenkins GD, Chia N, Nelson H, Mariani A , Walther-Antonio MRS",Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome),Scientific reports,2019,Experiment 1,United States of America,Homo sapiens,lower part of vagina,UBERON:0015243,endometrial cancer,MONDO:0011962,pre,post,patients undergoing hysterectomy,NA,NA,2 weeks,16S,345,Illumina,Linear Regression,0.1,TRUE,NA,NA,vaginal pH,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 2, Table S1",25 January 2020,Fatima Zohra,WikiWorks743,Bacterial OTUs differentially enriched among patients without EC by menopause status,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae|g__Tepidimicrobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Luteococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|1224|29547|213849|72294|194;2|201174|1760|2037|2049|1654;2|201174|1760|85009|31957|72763;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|186807|2740;2|976|200643|171549|815|816;2|1239|1737404|1737405|1737406|285105;2|1239|186801|186802|31979|1485;2|201174|1760|85009|31957|33983;2|1239|1737404|1737405|1570339|162290;2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|216851;2|201174|1760|2037|2049|184869,Complete,NA
Study 200,"cross-sectional observational, not case-control",31844128,10.1038/s41598-019-55720-8,NA,"Walsh DM, Hokenstad AN, Chen J, Sung J, Jenkins GD, Chia N, Nelson H, Mariani A , Walther-Antonio MRS",Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome),Scientific reports,2019,Experiment 2,United States of America,Homo sapiens,lower part of vagina,UBERON:0015243,endometrial cancer,MONDO:0011962,benign,endometrial cancer,patients undergoing hysterectomy for endometrial cancer,75,66,2 weeks,16S,345,Illumina,Linear Regression,0.1,TRUE,NA,NA,vaginal pH,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,25 January 2020,Fatima Zohra,WikiWorks743,Bacterial OTUs differentially enriched among patients with and without EC,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|1737404|1737405|1570339|165779;2|1239|91061|186826|33958|1578,Complete,NA
Study 200,"cross-sectional observational, not case-control",31844128,10.1038/s41598-019-55720-8,NA,"Walsh DM, Hokenstad AN, Chen J, Sung J, Jenkins GD, Chia N, Nelson H, Mariani A , Walther-Antonio MRS",Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome),Scientific reports,2019,Experiment 2,United States of America,Homo sapiens,lower part of vagina,UBERON:0015243,endometrial cancer,MONDO:0011962,benign,endometrial cancer,patients undergoing hysterectomy for endometrial cancer,75,66,2 weeks,16S,345,Illumina,Linear Regression,0.1,TRUE,NA,NA,vaginal pH,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,25 January 2020,Fatima Zohra,WikiWorks743,Bacterial OTUs differentially enriched among patients with and without EC,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium",2|1239|91061|186826|33958|1578;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|32066|203490|203491|203492|848;2|1224|29547|213849|72294|194;2|201174|1760|2037|2049|1654;2|1239|186801|186802|186807|2740;2|1239|1737404|1737405|1570339|162290;2|201174|1760|2037|2049|184869;2|201174|1760|2037|2049|28263,Complete,NA
Study 201,time series / longitudinal observational,30988420,10.1038/s41598-019-42652-6,NA,"Rashidi A, Kaiser T, Shields-Cutler R, Graiziger C, Holtan SG, Rehman TU, Wasko J, Weisdorf DJ, Dunny G, Khoruts A , Staley C",Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia,Scientific reports,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,leukemia,EFO:0000565,repeat therapy,induction,acute leukemia patients undergoing chemotherapy,7,13,NA,16S,4,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,25 January 2020,Fatima Zohra,WikiWorks743,Composition of microbial communities during induction and repeat therapy in leukemia patients,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|976|200643|171549|2005525|375288;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|459786,Complete,NA
Study 201,time series / longitudinal observational,30988420,10.1038/s41598-019-42652-6,NA,"Rashidi A, Kaiser T, Shields-Cutler R, Graiziger C, Holtan SG, Rehman TU, Wasko J, Weisdorf DJ, Dunny G, Khoruts A , Staley C",Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia,Scientific reports,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,leukemia,EFO:0000565,repeat therapy,induction,acute leukemia patients undergoing chemotherapy,7,13,NA,16S,4,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,25 January 2020,Fatima Zohra,WikiWorks743,Composition of microbial communities during induction and repeat therapy in leukemia patients,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|216572|292632;2|1239|526524|526525|128827|1573536;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|81852|1350,Complete,NA
Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,children with autism non-mental regression ANMR,children with autism mental regression AMR,"clinical diagnosis used the criteria of the International Classification Disease 10th Edition for ASD and DSM-5. The diagnosis was confirmed by scores above the cut-off points of two tests, the Autism Diagnostic Observation Schedule test, with revised algorithms, and the Pervasive Developmental Disorders. The ASD group was also classified according to whether the children presented developmental delay (a score lower than 70 in the cognitive quotient of the Battelle developmental test) or not",30,18,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & Table 3,28 January 2020,Shaimaa Elsafoury,WikiWorks743,Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1224;2|1239|91061|186826|81852|1350,Complete,NA
Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,healthy control,children with autism non-mental regression ANMR,"clinical diagnosis used the criteria of the International Classification Disease 10th Edition for ASD and DSM-5. The diagnosis was confirmed by scores above the cut-off points of two tests, the Autism Diagnostic Observation Schedule test, with revised algorithms, and the Pervasive Developmental Disorders. The ASD group was also classified according to whether the children presented developmental delay (a score lower than 70 in the cognitive quotient of the Battelle developmental test) or not",57,30,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 & Table 3",28 January 2020,Shaimaa Elsafoury,WikiWorks743,Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae",2|201174;2|201174|1760;2|201174|1760|85004|31953;2|201174|1760|85006|85023;2|1239|186801|68295|186814;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|2719313|208479,Complete,NA
Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,Experiment 3,Spain,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,healthy control,children with autism mental regression AMR,"clinical diagnosis used the criteria of the International Classification Disease 10th Edition for ASD and DSM-5. The diagnosis was confirmed by scores above the cut-off points of two tests, the Autism Diagnostic Observation Schedule test, with revised algorithms, and the Pervasive Developmental Disorders. The ASD group was also classified according to whether the children presented developmental delay (a score lower than 70 in the cognitive quotient of the Battelle developmental test) or not",57,18,NA,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Table 2, Figure 2 & Table 3",28 January 2020,Shaimaa Elsafoury,WikiWorks743,Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae",2|1224;2|201174|1760|85004|31953;2|201174|1760|85006|85023;2|1239|186801|68295|186814;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852|1350;2|1239|186801|186802|186803|2719313|208479,Complete,NA
Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,Experiment 4,Spain,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,healthy controls,children with autism spectrum disordorders ASD,"clinical diagnosis used the criteria of the International Classification Disease 10th Edition for ASD and DSM-5. The diagnosis was confirmed by scores above the cut-off points of two tests, the Autism Diagnostic Observation Schedule test, with revised algorithms, and the Pervasive Developmental Disorders. The ASD group was also classified according to whether the children presented developmental delay (a score lower than 70 in the cognitive quotient of the Battelle developmental test) or not",57,48,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,28 January 2020,Shaimaa Elsafoury,WikiWorks743,Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Thermoactinomycetaceae",2|1239|91061|1385|186817;2|201174|1760|85004|31953;2|201174|1760|85007|1653;2|1224|28221|213115|213117;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|526524|526525|128827;2|201174|1760|85006|85023;2|1239|91061|1385|186824,Complete,NA
Study 202,case-control,30764497,10.3390/nu11020337,NA,"Plaza-Díaz J, Gómez-Fernández A, Chueca N, Torre-Aguilar MJ, Gil Á, Perez-Navero JL, Flores-Rojas K, Martín-Borreguero P, Solis-Urra P, Ruiz-Ojeda FJ, Garcia F , Gil-Campos M",Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota,Nutrients,2019,Experiment 4,Spain,Homo sapiens,feces,UBERON:0001988,autism,EFO:0003758,healthy controls,children with autism spectrum disordorders ASD,"clinical diagnosis used the criteria of the International Classification Disease 10th Edition for ASD and DSM-5. The diagnosis was confirmed by scores above the cut-off points of two tests, the Autism Diagnostic Observation Schedule test, with revised algorithms, and the Pervasive Developmental Disorders. The ASD group was also classified according to whether the children presented developmental delay (a score lower than 70 in the cognitive quotient of the Battelle developmental test) or not",57,48,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,28 January 2020,Shaimaa Elsafoury,WikiWorks743,Relative abundances of bacteria in fecal microbiota of children with ASD (AMR or ANMR) and healthy children.,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,2|1239|186801|186802|186803,Complete,NA
Study 203,case-control,30707176,10.1097/CM9.0000000000000086,NA,"Bai W, Chen S, Tang CS, Qi JG, Cui QH, Xu M, Du JB , Jin HF",Gut microbiota analysis and its significance in vasovagal syncope in children,Chinese medical journal,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Syncope,HP:0001279,healthy children,children with vasovagal syncope,NA,20,20,8 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,4,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,29 January 2020,Shaimaa Elsafoury,WikiWorks743,The predominant bacteria in vasovagal syncope group using LEfSe.,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|541000,Complete,NA
Study 204,case-control,29791775,10.1111/1471-0528.15299,NA,"Tabatabaei N, Eren AM, Barreiro LB, Yotova V, Dumaine A, Allard C , Fraser WD",Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case-control study,BJOG : an international journal of obstetrics and gynaecology,2019,Experiment 1,Canada,Homo sapiens,vagina,UBERON:0000996,premature birth,EFO:0003917,mothers whose newborns were delivered at ≥37 getastional weeks,mothers whose newborns were delivered at <34 gestational week,NA,365,17,NA,16S,4,Illumina,NLMIXED,0.05,TRUE,NA,NA,"body mass index,ethnic group,maternal age,parity,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Table 2 & S2,3 February 2020,Shaimaa Elsafoury,WikiWorks743,Vaginal microbial oligotype differential relative abundance composition between pregnant women who had early (<34 weeks of gestation) preterm versus full term (≥37 weeks gestation) deliveries,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus acidophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia solanacearum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|1578|33959;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|1685;2|1239|91061|186826|33958|1578|1579;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|1578|147802;2|1224|28216|80840|119060|48736|305;2|201174|1760|85004|31953|1678,Complete,NA
Study 205,"cross-sectional observational, not case-control",23758857,10.1186/1471-2334-13-271,NA,"Gao W, Weng J, Gao Y , Chen X",Comparison of the vaginal microbiota diversity of women with and without human papillomavirus infection: a cross-sectional study,BMC infectious diseases,2013,Experiment 1,China,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV negative,HPV positive,HPV infection,38,32,1 month,16S,23,NA,NA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Table 4,5 February 2020,Fatima Zohra,WikiWorks743,Number of times genus was identified in HPV positive and HPV negative women,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",2|1239|91061|186826|33958|1578|1596;2|201174|1760|85004|31953|2701|2702,Complete,NA
Study 206,case-control,29317709,10.1038/s41598-017-18596-0,NA,"Hsieh YY, Tung SY, Pan HY, Yen CW, Xu HW, Lin YJ, Deng YF, Hsu WT, Wu CS , Li C",Increased Abundance of Clostridium and Fusobacterium in Gastric Microbiota of Patients with Gastric Cancer in Taiwan,Scientific reports,2018,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,patients diagnosed with gastritis,patients diagnosed with gastric cancer,Patients with gastric cancer,16,11,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,4 February 2020,Valentina Pineda,WikiWorks743,Bacteria specifically found in patients with gastric cancer compared with the average counts gastritis specimens,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium colicanis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium canifelinum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oris,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|1239|186801|186802|31979|1485|179628;2|32066|203490|203491|203492|848|285729;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|2742598|1598;2|1239|909932|1843489|31977|906|187326;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|28135;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|1318,Complete,NA
Study 207,case-control,24265786,10.1371/journal.pone.0079812,NA,"Liu MB, Xu SR, He Y, Deng GH, Sheng HF, Huang XM, Ouyang CY , Zhou HW",Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis,PloS one,2013,Experiment 1,China,Homo sapiens,vagina,UBERON:0000996,vulvovaginitis,EFO:1001240,NC,BV,BV assessment with a gram-stain score => 7,30,10,1 month,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Figure 1,6 February 2020,Fatima Zohra,WikiWorks743,Vaginal microbiome differences in candida vulvovaginitis,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|201174;2|201174|1760|85004|31953|2701;2|1239|186801;2|201174|1760|85004|31953;2|201174|1760|85004;2|1239|186801|186802;2|32066|203490|203491|1129771|168808;2|1239|526524|526525;2|201174|84998|84999|1643824|1380;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239|526524|526525|128827;2|32066;2|1239|526524|526525|128827|118747;2|1239|909932|1843489|31977;2|1224;2|32066|203490|203491;2|1239|526524;2|1239|909932|1843489|31977|39948;2|201174|1760|2037|2049|2050;2|201174|1760|2037|2049;2|201174|1760|2037;2|976|200643|171549|171551;2|976|200643|171549|171551|836,Complete,NA
Study 207,case-control,24265786,10.1371/journal.pone.0079812,NA,"Liu MB, Xu SR, He Y, Deng GH, Sheng HF, Huang XM, Ouyang CY , Zhou HW",Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis,PloS one,2013,Experiment 1,China,Homo sapiens,vagina,UBERON:0000996,vulvovaginitis,EFO:1001240,NC,BV,BV assessment with a gram-stain score => 7,30,10,1 month,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplemental Figure 1,6 February 2020,Fatima Zohra,WikiWorks743,Vaginal microbiome differences in candida vulvovaginitis,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,NA
Study 207,case-control,24265786,10.1371/journal.pone.0079812,NA,"Liu MB, Xu SR, He Y, Deng GH, Sheng HF, Huang XM, Ouyang CY , Zhou HW",Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis,PloS one,2013,Experiment 2,China,Homo sapiens,vagina,UBERON:0000996,vulvovaginitis,EFO:1001240,NC,BV.VVC,had both BV and VVC,30,16,1 month,16S,6,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplemental Figure 1,6 February 2020,Fatima Zohra,WikiWorks743,Vaginal microbiome differences in candida vulvovaginitis,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549;2|976|200643;2|976|200643|171549|171552;2|976;2|976|200643|171549|171552|838,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1a, Text",13 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between infants with food allergy and health controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Cytophagaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae",2|1239|186801|186802|31979;2|976|768503|768507|89373;2|201174|1760|85007|85025,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 1a, Text",13 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between infants with food allergy and health controls,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",2|1224|28216|80840|506;2|1239|186801|186802|543314;2|1224|28211|356|69277;2|1224|1236|135614|32033;2|976|117743|200644|49546;2|1224|1236|2887326|468,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 3,"Supplemental Table 3, Text",13 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between infants with food allergy and health controls,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Fusobacteria",2|1239;2|32066,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 4,"Supplemental Table 3, Text",13 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between infants with food allergy and health controls,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Verrucomicrobia",2|976;2|1224;2|201174;2|74201,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 5,"Supplemental Table 4, Text",13 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between infants with food allergy and health controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1239|91061|1385|90964|1279;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|207244;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|946234,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,Metastats,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 6,"Supplemental Table 4, Text",13 February 2020,Lucy Mellor,"WikiWorks743,Fatima",Differentially abundant taxons between infants with food allergy and health controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|976|200643|171549|815|816;2|1239|186801|186802|186803|572511;2|1224|1236|91347|543|570;2|1239|186801|186802|186803;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|186804,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1d, Text",6 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between infants with food allergy and health controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae,k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Cytophagaceae",2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2;2|1239|186801|186802|31979|580596;2|201174|1760|2037;2|201174|1760|85007|85025|1827;2|201174|1760|85007|85025;2|976|768503|768507|89373,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,infants with food allergies,infant with food allergy,45,34,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 1d, Text",6 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between infants with food allergy and health controls,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas",2|1239|909932|1843489|31977|906;2|1239|186801|186802|541000;2|976|117743|200644|49546;2|1224|28211|356|69277;2|1224|28211|356|69277|68287;2|1224|28216|80840|506|222;2|1224|28216|80840|506;2|976|117743|200644;2|201174|84998|1643822|1643826|84111;2|976|117743|200644|49546|237;2|1224|1236|135614|32033;2|1224|1236|135614|32033|40323;2|1239|186801|186802|543314|86331;2|976|117743|200644|2762318|59732;2|1239|186801|186802|543314;2|1224|1236|135614;2|1224|28211|204458|76892;2|1224|28216|80840|80864|283,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Text",6 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia",2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1239|186801|186802;2|1239|186801,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Text",6 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae",2|1239|186801|186802|186803;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|526524|526525;2|1239|526524|526525|128827;2|1239|526524;2|201174|1760|85007|85025|1827;2|201174|1760|85007|85025,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2c, Text",13 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,NA
Study 208,case-control,24532064,10.1128/AEM.00003-14,NA,"Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L , Xiang C",Altered fecal microbiota composition associated with food allergy in infants,Applied and environmental microbiology,2014,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,infants non-IgE mediated,infants IgE mediated,infant IgE mediated,17,17,1 month,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2c, Text",13 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between IgE-mediated food allergy infants and non-IgE-mediated food allergy infants,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 209,"cross-sectional observational, not case-control",32012716,10.3390/microorganisms8020179,NA,"Wong WSW, Sabu P, Deopujari V, Levy S, Shah AA, Clemency N, Provenzano M, Saadoon R, Munagala A, Baker R, Baveja R, Mueller NT, Dominguez-Bello MG, Huddleston K, Niederhuber JE , Hourigan SK",Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome,Microorganisms,2020,Experiment 1,United States of America,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,"meconium defined as the first stool passed, other than meconium staining of amniotic fluid.",62,43,"Mothers of infants born by CS received significantly more peripartum antibiotics than those born by VD (43/43 (100%) in CS vs. 19/62 (31%) in VD, p < 0.001).",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 1,Figure 4 & text,10 February 2020,Shaimaa Elsafoury,WikiWorks743,Differentially abundant OTUs(FDR< 0.05) according to deliverymode,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae|g__Bradyrhizobium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Chelatococcaceae|g__Chelatococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Leptothrix,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Rubrivivax,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium",2|1239|909932|1843489|31977|29465;2|1224|28211|356|119045|407;2|1224|1236|91347|543|544;2|1239|91061|1385|90964|1279;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|1224|28216|80840|80864|12916;2|201174|1760|85009|31957|1743;2|1239|91061|186826|186828|117563;2|1224|1236|2887326|468|469;2|1224|28211|356|41294|374;2|1224|28216|80840|80864|80865;2|201174|1760|85004|31953|1302778;2|1239|91061|186826|33958|1578;2|1224|28216|80840|506|222;2|1297|188787|68933|188786|65551;2|1224|28211|356|2036754|28209;2|1224|1236|135614|32033|40323;2|1224|28216|80840|114248;2|1224|1236|135625|712|724;2|1224|28216|80840|88;2|1224|28216|80840|80864|283;2|1224|28216|80840|28067;2|976|1853228|1853229|563835|504481;2|1239|91061|186826|1300|1357;2|1224|1236|91347|543|547;2|1239|91061|1385|186817|150247;2|1224|28211|356|82115|357,Complete,NA
Study 209,"cross-sectional observational, not case-control",32012716,10.3390/microorganisms8020179,NA,"Wong WSW, Sabu P, Deopujari V, Levy S, Shah AA, Clemency N, Provenzano M, Saadoon R, Munagala A, Baker R, Baveja R, Mueller NT, Dominguez-Bello MG, Huddleston K, Niederhuber JE , Hourigan SK",Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome,Microorganisms,2020,Experiment 1,United States of America,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,"meconium defined as the first stool passed, other than meconium staining of amniotic fluid.",62,43,"Mothers of infants born by CS received significantly more peripartum antibiotics than those born by VD (43/43 (100%) in CS vs. 19/62 (31%) in VD, p < 0.001).",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 2,Figure 4 & text,10 February 2020,Shaimaa Elsafoury,WikiWorks743,Differentially abundant OTUs(FDR< 0.05) according to deliverymode,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|91347|543|561;2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|544;2|1224|1236|91347|543|570;2|1224|1236|91347|543|158851;2|1224|1236|91347|543|620;2|1239|91061|1385|90964|1279;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301,Complete,NA
Study 210,case-control,26663491,10.1111/pai.12522,NA,"Chen CC, Chen KJ, Kong MS, Chang HJ , Huang JL",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,T-Test,0.01,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Table 2, Text",12 February 2020,Lucy Mellor,"WikiWorks743,Fatima",Differentially abundant taxons between food sensitization children and healthy control,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|91061|186826|81852|1350;2|1239|186801|186802|216572|216851;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263;2|1224|28211|204457|41297|13687;2|1239|186801|186802|216572|292632;2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572,Complete,NA
Study 210,case-control,26663491,10.1111/pai.12522,NA,"Chen CC, Chen KJ, Kong MS, Chang HJ , Huang JL",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,T-Test,0.01,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Table 2, Text",12 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between food sensitization children and healthy control,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|976|200643|171549|171550|239759;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 210,case-control,26663491,10.1111/pai.12522,NA,"Chen CC, Chen KJ, Kong MS, Chang HJ , Huang JL",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,"Figure 3, Text",12 February 2020,Lucy Mellor,"WikiWorks743,Fatima",Differentially abundant taxons between food sensitization children and healthy control,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1224|28211;2|1239|186801;2|1239|186801|186802;2|1239;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572,Complete,NA
Study 210,case-control,26663491,10.1111/pai.12522,NA,"Chen CC, Chen KJ, Kong MS, Chang HJ , Huang JL",Alterations in the gut microbiotas of children with food sensitization in early life,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2016,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy controls,children with food sensitization,child with food sensitization,22,23,1 week,16S,345,Roche454,LEfSe,0.05,FALSE,2,age,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,"Figure 3, Text",12 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons between food sensitization children and healthy control,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976;2|976|200643;2|976|200643|171549;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465,Complete,NA
Study 211,case-control,30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber (Q3 and Q4),low fiber (Q1 and Q2),lower quartiles (Q1 and Q2) of fiber intake vs control (Q3 and Q4),38,37,"no ""long term"" antibiotics use",16S,34,Roche454,DESeq2,0.05,TRUE,NA,NA,"age,body height,body mass index,body weight,race,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2.,19 February 2020,Lora Kasselman,WikiWorks743,Table 2. Meta-analysis of the association between total fibre intake and genera and species in National Cancer Institute (NCI) and New York University (NYU) study populations - NCI data,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,2|201174|1760|2037|2049|1654,Complete,NA
Study 212,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber (Q3 and Q4),low fiber (Q1 and Q2),lower quartiles (Q1 and Q2) of fiber intake vs control (Q3 and Q4),38,38,"no ""long term"" antibiotics use",16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body height,body mass index,body weight,race,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2.,19 February 2020,Lora Kasselman,WikiWorks743,Table 2. Meta-analysis of the association between total fibre intake and genera and species in National Cancer Institute (NCI) and New York University (NYU) study populations - NYU data,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,2|976|200643|171549|1853231|283168,Complete,NA
Study 212,"cross-sectional observational, not case-control",30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber (Q3 and Q4),low fiber (Q1 and Q2),lower quartiles (Q1 and Q2) of fiber intake vs control (Q3 and Q4),38,38,"no ""long term"" antibiotics use",16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body height,body mass index,body weight,race,sex,smoking behavior",NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2.,19 February 2020,Lora Kasselman,WikiWorks743,Table 2. Meta-analysis of the association between total fibre intake and genera and species in National Cancer Institute (NCI) and New York University (NYU) study populations - NYU data,decreased,NA,NA,Complete,NA
Study 213,meta-analysis,30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber (Q3 and Q4),low fiber (Q1 and Q2),lower quartiles (Q1 and Q2) of fiber intake vs control (Q3 and Q4),76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body height,body mass index,body weight,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2.,19 February 2020,Lora Kasselman,"WikiWorks743,Fatima",Figure 2 Forest plot of fold change of select genera (G) and species (S) in both the New York University and National Cancer Institute study populations with a significant or marginally significant association with higher total fibre intake and Table 2,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus",2|201174|1760|2037|2049|1654;2|976|200643|171549|815|816|820;2|976|200643|171549|1853231|283168;2|1239|526524|526525|128827|2749846|31971,Complete,NA
Study 213,meta-analysis,30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber (Q3 and Q4),low fiber (Q1 and Q2),lower quartiles (Q1 and Q2) of fiber intake vs control (Q3 and Q4),76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body height,body mass index,body weight,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2.,19 February 2020,Lora Kasselman,WikiWorks743,Figure 2 Forest plot of fold change of select genera (G) and species (S) in both the New York University and National Cancer Institute study populations with a significant or marginally significant association with higher total fibre intake and Table 2,decreased,NA,NA,Complete,NA
Study 213,meta-analysis,30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber from FRUITS/VEGETABLES (Q3 and Q4),low fiber from FRUITS/VEGETABLES (Q1 and Q2),lower quartiles (Q1 and Q2) of FRUIT/VEGETABLE fiber intake vs control (Q3 and Q4),76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body height,body mass index,body weight,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3.,19 February 2020,Lora Kasselman,WikiWorks743,"Fig. 3. Heat map representing colour-coded fold changes of select genera (G) and species (S), by total fibre and fibre from specific sources (fruits/vegetables, grains, and beans). * P <0·05 and ** P <0·001 in the meta-analysis of the National Cancer Institute and New York University study populations.",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",2|201174|1760|2037|2049|1654;2|976|200643|171549|1853231|283168;2|976|200643|171549|815|816|820,Complete,NA
Study 213,meta-analysis,30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber from BEANS (Q3 and Q4),low fiber from BEANS (Q1 and Q2),lower quartiles (Q1 and Q2) of BEAN fiber intake vs control (Q3 and Q4),76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body height,body mass index,body weight,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Figure 3.,19 February 2020,Lora Kasselman,"WikiWorks743,Fatima","Fig. 3. Heat map representing colour-coded fold changes of select genera (G) and species (S), by total fibre and fibre from specific sources (fruits/vegetables, grains, and beans). * P <0·05 and ** P <0·001 in the meta-analysis of the National Cancer Institute and New York University study populations.",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus|s__Amedibacillus dolichus",2|976|200643|171549|1853231|283168;2|1239|526524|526525|128827|2749846|31971,Complete,NA
Study 213,meta-analysis,30355393,10.1017/S0007114518002465,NA,"Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB , Ahn J",Association of dietary fibre intake and gut microbiota in adults,The British journal of nutrition,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high fiber from BEANS (Q3 and Q4),low fiber from BEANS (Q1 and Q2),lower quartiles (Q1 and Q2) of BEAN fiber intake vs control (Q3 and Q4),76,75,"no ""long term"" antibiotics use",16S,34,"Illumina,Roche454",DESeq2,0.05,TRUE,NA,NA,"age,body height,body mass index,body weight,race,sex,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,Figure 3.,19 February 2020,Lora Kasselman,WikiWorks743,"Fig. 3. Heat map representing colour-coded fold changes of select genera (G) and species (S), by total fibre and fibre from specific sources (fruits/vegetables, grains, and beans). * P <0·05 and ** P <0·001 in the meta-analysis of the National Cancer Institute and New York University study populations.",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1a,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|1224|1236|91347|543|590;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158851;2|976|200643;2|976;2|976|200643|171549,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1a,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes",2|1239|186801|186802|186804;2|1239|186801;2|1239|186801|186802|216572|1263;2|1239|186801|186802|31979;2|1239|186801|186802|186806|1730;2|976|200643|171549|171552;2|1239|186801|186802|186803|572511;2|1239,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|1224|1236|91347|543|590;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158851;2|976|200643;2|976;2|976|200643|171549,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes",2|1239|186801|186802|186804;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186806|1730;2|1239|186801|186802|31979;2|1239|186801|186802|186803|572511;2|1239|186801|186802;2|1239|186801;2|1239,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 5,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976|200643;2|976;2|976|200643|171549,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 6,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes",2|1239|186801|186802|186806|1730;2|1239|186801|186802|186804;2|1239,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 7,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella",2|1224|1236|91347|543|158851;2|1224|1236|91347|543|547;2|1224|1236|91347|543|590,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 8,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes",2|1239|186801|186802|186804;2|1239|186801|186802|31979;2|1239|186801|186802|186803|572511;2|1239,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 9,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|1224|1236|91347|543|547;2|1224|1236|91347|543|158851;2|976|200643;2|976;2|976|200643|171549,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 10,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes",2|1239|186801|186802|216572|1263;2|1239|186801|186802|31979;2|1239|186801|186802;2|1239|186801;2|1239,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 11,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|1224|1236|91347|543|590;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158851;2|976|200643;2|976;2|976|200643|171549,Complete,NA
Study 214,time series / longitudinal observational,27292825,10.1016/j.jaci.2016.03.041,NA,"Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S , Clemente JC",Early-life gut microbiome composition and milk allergy resolution,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,milk allergy resolution,children with milk allergy persistence,child with persistent milk allergy,128,98,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 12,Supplemental Figure E1,20 February 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa in children age 3 to 6 months with milk allergy persistence and milk allergy resolution at age 8,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes",2|1239|186801|186802|186804;2|1239|186801|186802|31979;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186803|572511;2|1239|186801|186802;2|1239|186801;2|1239,Complete,NA
Study 215,case-control,27812181,10.1371/journal.pone.0166026,NA,"Zheng H, Liang H, Wang Y, Miao M, Shi T, Yang F, Liu E, Yuan W, Ji ZS , Li DK",Altered Gut Microbiota Composition Associated with Eczema in Infants,PloS one,2016,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,infant with eczema,infant with eczema,51,50,NA,16S,34,Roche454,Metastats,1e-5,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 3, Supplemental Table S2, Supplemental Table S3",21 February 2020,Lucy Mellor,"WikiWorks743,Fatima",Differentially abdundant species in the gut of infants with and without eczema,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Archaea,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Rhizobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|626929;2|1224|28221|213118|213119;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|204475|745368;2|1239|186801|186802|186803;2|1239|186801|186802|541000;2|1239|91061|1385|186822;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171551;2|976|200643|171549|171552|838|28126;2|1224|28211|356|82115;2|74201|203494|48461|203557;2|1239|186801|186802|186803|2316020|33038;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|186803|207244;2157;2|1224|28221|213115|194924|35832;2|1239|186801|186802|186803|33042;2|1224|1236|91347|543|413496|28141;2|1224|28221|213115|194924|872;2|1224|1236|91347|543|547;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|946234;2|1239|186801|186802|204475;2|1239|91061|1385|186822|44249;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551|836;2|1224|28211|356|82115|379;2|1239|186801|186802|186803|841;2|1239|909932|1843489|31977|29465,Complete,NA
Study 215,case-control,27812181,10.1371/journal.pone.0166026,NA,"Zheng H, Liang H, Wang Y, Miao M, Shi T, Yang F, Liu E, Yuan W, Ji ZS , Li DK",Altered Gut Microbiota Composition Associated with Eczema in Infants,PloS one,2016,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,infant with eczema,infant with eczema,51,50,NA,16S,34,Roche454,Metastats,1e-5,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 3, Supplemental Table S2, Supplemental Table S3",21 February 2020,Lucy Mellor,"WikiWorks743,Fatima",Differentially abdundant species in the gut of infants with and without eczema,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|1843488|909930;2|1239|909932|1843488|909930|904;2|1239|909932|1843489|31977|209879;2|1239|909932|1843489|31977|156454;2|1239|186801|186802|216572|244127;2|976|200643|171549|815|816|817;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85019;2|201174|1760|85006|85019|1696;2|1239|186801|186802|31979|580596;2|1239|91061|186826|186828;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|1760|85006|85020;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|189330;2|1224|28216|206351|481|538;2|1239|526524|526525|128827;2|1239|526524;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1239|526524|526525|128827|1573535|1735;2|1224|1236|91347|543|570;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572|459786;2|1224|1236|135625|712;2|1239|186801|186802|186804;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|186802|216572|1263;2|1239|91061|1385|90964;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1304;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303;2|1239|909932|1843489|31977,Complete,NA
Study 216,"cross-sectional observational, not case-control",27362264,10.1371/journal.pone.0158498,NA,"Martin R, Makino H, Cetinyurek Yavuz A, Ben-Amor K, Roelofs M, Ishikawa E, Kubota H, Swinkels S, Sakai T, Oishi K, Kushiro A , Knol J","Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota",PloS one,2016,Experiment 1,Netherlands,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,NA,80,28,"use of antibiotics between 2 weeks prior to delivery and 2 weeks after delivery, for any reason except for prophylactic use (e.g. cesar- ean section).",16S,NA,RT-qPCR,NA,NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,23 February 2020,Shaimaa Elsafoury,WikiWorks743,Prevalence of different bacterial groups in infants born by vaginal delivery or C-section.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens",2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|909656|821;2|976|200643|171549|815|816|47678;2|201174|1760|85004|31953|1678|216816|1679;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678|1686;2|1239|91061|186826|81852|1350;2|1239|186801|186802|31979|1485|1502,Complete,NA
Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,child with eczema,19,15,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Table 2,26 February 2020,Lucy Mellor,"WikiWorks743,Fatima",Differences in microbiota of healthy and eczematous children at 18 months of age,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella nexilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] cellulosi",2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|186803|1506577|29361;2|1239|186801|186802|186803|2316020|46228;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|29343,Complete,NA
Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,child with eczema,19,15,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Table 2,26 February 2020,Lucy Mellor,WikiWorks743,Differences in microbiota of healthy and eczematous children at 18 months of age,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidetes",2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|820;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|1283313|76122;2|976,Complete,NA
Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Figure 1,27 February 2020,Lucy Mellor,WikiWorks743,Relative contribution of phylum-like bacterial groups to the total HITChip signals of infants at 6 and 18 months of age,increased,NA,NA,Complete,NA
Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Figure 1,27 February 2020,Lucy Mellor,WikiWorks743,Relative contribution of phylum-like bacterial groups to the total HITChip signals of infants at 6 and 18 months of age,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Bacilli",2|201174;2|1239|91061,Complete,NA
Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,Experiment 3,Finland,Homo sapiens,feces,UBERON:0001988,age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,Table 1,27 February 2020,Lucy Mellor,WikiWorks743,"Genus-like phylogenetic groups changing statistically significantly from 6 to 18 months of age as assessed by
HITChip analysis",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium faecium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio crossotus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Tenericutes|c__Mollicutes",2|1239|186801|186802|216572|1263|40518;2|1239|909932|1843488|909930|33024|33025;2|1239|186801|186802|186803|830|45851;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|140625|140626;2|1239|526524|526525|2810280|100883|100884;2|32066|203490|203491|203492|848;2|1224|1236|91347|1903414|583;2|1224|28216|80840|995019|40544|40545;2|544448|31969,Complete,NA
Study 217,prospective cohort,23339708,10.1186/1471-2180-13-12,NA,"Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S , de Vos WM",Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease,BMC microbiology,2013,Experiment 3,Finland,Homo sapiens,feces,UBERON:0001988,age,EFO:0000246,infant at 6 months,infant at 18 months,infant 18 months of age,34,34,NA,16S,NA,Human Intestinal Tract Chip,ANOVA,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 2,Table 1,27 February 2020,Lucy Mellor,WikiWorks743,"Genus-like phylogenetic groups changing statistically significantly from 6 to 18 months of age as assessed by
HITChip analysis",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum",2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|2767842|1590,Complete,NA
Study 218,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q, Li F, Zhuang Y, Xu J, Wang J, Mao X, Zhang Y , Liu X",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,hepatocellular carcinoma,EFO:0000182,healthy control,non-HBV non-HCV related HCC,patients underwent viral serologic testing (HBsAg and HCVAb),33,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 3,26 February 2020,Fatima Zohra,WikiWorks743,Genera strikingly different in gut microbiota associated with hepatits B and non-hepatitis virus related hepatocellular carcinoma,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,2|1239|186801|186802|216572|244127,Complete,NA
Study 218,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q, Li F, Zhuang Y, Xu J, Wang J, Mao X, Zhang Y , Liu X",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,hepatocellular carcinoma,EFO:0000182,healthy control,non-HBV non-HCV related HCC,patients underwent viral serologic testing (HBsAg and HCVAb),33,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 3,26 February 2020,Fatima Zohra,WikiWorks743,Genera strikingly different in gut microbiota associated with hepatits B and non-hepatitis virus related hepatocellular carcinoma,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|909932|909929|1843491|158846;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|186803,Complete,NA
Study 218,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q, Li F, Zhuang Y, Xu J, Wang J, Mao X, Zhang Y , Liu X",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,hepatocellular carcinoma,EFO:0000182,healthy control,HBV related HCC,patients underwent viral serologic testing (HBsAg and HCVAb),33,35,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,26 February 2020,Fatima Zohra,WikiWorks743,Genera strikingly different in gut microbiota associated with hepatits B and non-hepatitis virus related hepatocellular carcinoma,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",2|976|200643|171549|171552|838;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|216572|244127,Complete,NA
Study 218,"cross-sectional observational, not case-control",30675188,10.1186/s13099-018-0281-6,NA,"Liu Q, Li F, Zhuang Y, Xu J, Wang J, Mao X, Zhang Y , Liu X",Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma,Gut pathogens,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,hepatocellular carcinoma,EFO:0000182,HBV related HCC,non-HBV non-HCV,patients underwent viral serologic testing (HBsAg and HCVAb),22,35,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 3,26 February 2020,Fatima Zohra,WikiWorks743,Genera strikingly different in gut microbiota associated with hepatits B and non-hepatitis virus related hepatocellular carcinoma,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Buchnera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|1224|1236|91347|1903409|32199;2|1239|186801|186802|186803|28050;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|186806|1730|39496;2|976|200643|171549|171552|1283313,Complete,NA
Study 219,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J, Li Z , Ortiz RM",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,higher fiber (almonds) - interaction by time,lower fiber (cracker),students eating crackers,35,38,NA,16S,45,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,unchanged,NA,decreased,Signature 1,Table 1,28 February 2020,Lora Kasselman,WikiWorks743,ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline and 8 wk after the intervention,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,2|976|200643|171549|815|816|817,Complete,NA
Study 219,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J, Li Z , Ortiz RM",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,baseline,week 8,students eating crackers,35,38,NA,16S,45,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,28 February 2020,Lora Kasselman,"WikiWorks743,Lwaldron",ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline and 8 wk after the intervention,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Tenericutes|c__Mollicutes",2|1239|186801|186802|186803|28050;2|544448|31969,Complete,NA
Study 219,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J, Li Z , Ortiz RM",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,baseline,week 8,students eating crackers,35,38,NA,16S,45,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,28 February 2020,Lora Kasselman,"WikiWorks743,Lwaldron",ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline and 8 wk after the intervention,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|976|200643|171549|171550|239759;2|976|200643|171549|1853231|574697;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005473,Complete,NA
Study 219,randomized controlled trial,31528836,10.1093/cdn/nzz079,NA,"Dhillon J, Li Z , Ortiz RM",Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases <i>Bacteroides fragilis</i> Abundance Compared with an Isocaloric Snack in College Freshmen,Current developments in nutrition,2019,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,higher fiber (almonds),lower fiber (cracker),students eating crackers,35,38,NA,16S,45,Illumina,ANCOM,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,28 February 2020,Lora Kasselman,WikiWorks743,ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline and 8 wk after the intervention,decreased,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,2|1224|28216|80840|995019|40544,Complete,NA
Study 220,case-control,29791788,10.1111/jam.13929,NA,"Jugé R, Rouaud-Tinguely P, Breugnot J, Servaes K, Grimaldi C, Roth MP, Coppin H , Closs B",Shift in skin microbiota of Western European women across aging,Journal of applied microbiology,2018,Experiment 1,France,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,younger age,older age European women,aging,17,17,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 1,"Figure 4, Figure S1, Figure s2",1 March 2020,Rimsha Azhar,WikiWorks743,Taxonomic analysis of forehead microbiota using LEfSe between older and younger european women,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria",2|201174|1760|85006|1268|1663;2|32066|203490|203491|1129771|168808;2|1224|1236|2887326|468;2|1224|1236|72274;2|201174|1760|85007|1653|1716;2|1224|1236|135619|28256;2|1224|1236|135619|28256|2745;2|1224|1236|135619;2|1224|28216|206351|481;2|1224|28216|206351;2|1224|28216;2|1224,Complete,NA
Study 220,case-control,29791788,10.1111/jam.13929,NA,"Jugé R, Rouaud-Tinguely P, Breugnot J, Servaes K, Grimaldi C, Roth MP, Coppin H , Closs B",Shift in skin microbiota of Western European women across aging,Journal of applied microbiology,2018,Experiment 1,France,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,younger age,older age European women,aging,17,17,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,unchanged,NA,NA,unchanged,Signature 2,"Figure 4, Figure S1, Figure s2",1 March 2020,Rimsha Azhar,WikiWorks743,Taxonomic analysis of forehead microbiota using  LEfSe between older and younger european women,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales",2|201174|1760|85009|31957;2|201174|1760|85009|31957|1743;2|201174|1760|85009,Complete,NA
Study 221,case-control,30006660,10.1007/s10096-018-3322-7,NA,"Paalanne N, Husso A, Salo J, Pieviläinen O, Tejesvi MV, Koivusaari P, Pirttilä AM, Pokka T, Mattila S, Jyrkäs J, Turpeinen A, Uhari M, Renko M , Tapiainen T",Intestinal microbiome as a risk factor for urinary tract infections in children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2018,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,urinary tract infection,EFO:0003103,healthy controls,urinary tract infection,urinary tract infection,69,37,NA,16S,45,Ion Torrent,LEfSe,NA,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2,2 March 2020,Rimsha Azhar,WikiWorks743,Comaprison between UTI patients and Health controls using linear discriminant analysis,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania|s__Holdemania massiliensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia flexa,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus dispar,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia glucerasea",2|1224|1236|91347|543|547;2|1239|526524|526525|128827|61170|1468449;2|1239|91061|1385|186817|2800373|86664;2|1239|186801|186802|186803|2719313|333367;2|1239|91061|186826|81852|1350|44009;2|1239|186801|186802|186803|572511|536633,Complete,NA
Study 221,case-control,30006660,10.1007/s10096-018-3322-7,NA,"Paalanne N, Husso A, Salo J, Pieviläinen O, Tejesvi MV, Koivusaari P, Pirttilä AM, Pokka T, Mattila S, Jyrkäs J, Turpeinen A, Uhari M, Renko M , Tapiainen T",Intestinal microbiome as a risk factor for urinary tract infections in children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2018,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,urinary tract infection,EFO:0003103,healthy controls,urinary tract infection,urinary tract infection,69,37,NA,16S,45,Ion Torrent,LEfSe,NA,FALSE,3,"age,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2,2 March 2020,Rimsha Azhar,"WikiWorks743,Fatima",Comaprison between UTI patients and Health controls using linear discriminant analysis,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium tertium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia aurea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia lituseburensis",2|1239|186801|186802|31979|1485|1559;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|150022|1260;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1224|28216|80840|75682|149698;2|1224|28216|80840|75682;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|186802|186804;2|976|200643|171549|171552|838|386414;2|1224|28216|80840|75682|149698|373040;2|1239|186801|186802|186804|1501226|1537,Complete,NA
Study 222,case-control,26729566,10.1038/srep18594,NA,"Yang I, Woltemate S, Piazuelo MB, Bravo LE, Yepez MC, Romero-Gallo J, Delgado AG, Wilson KT, Peek RM, Correa P, Josenhans C, Fox JG , Suerbaum S",Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia,Scientific reports,2016,Experiment 1,Colombia,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,low gastric cancer risk patients,high gastric cancer risk,high gastric cancer risk,20,20,NA,16S,NA,Illumina,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,2 March 2020,Valentina Pineda,WikiWorks743,OTUs with significantly different occurrence among towns,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",2|32066|203490|203491|1129771|32067|157687;2|1239|909932|1843489|31977|29465|1926307,Complete,NA
Study 222,case-control,26729566,10.1038/srep18594,NA,"Yang I, Woltemate S, Piazuelo MB, Bravo LE, Yepez MC, Romero-Gallo J, Delgado AG, Wilson KT, Peek RM, Correa P, Josenhans C, Fox JG , Suerbaum S",Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia,Scientific reports,2016,Experiment 1,Colombia,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,low gastric cancer risk patients,high gastric cancer risk,high gastric cancer risk,20,20,NA,16S,NA,Illumina,Metastats,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,2 March 2020,Valentina Pineda,"WikiWorks743,Lwaldron",OTUs with significantly different occurrence among towns,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oris,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp.,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Haematobacter|s__uncultured Haematobacter sp.",2|201174|1760|2037|2049|1654|29317;2|976|117743|200644|49546|1016|1017;2|976|117743|200644|49546;2|976|117743|200644|49546|237|239;2|1224|28216|206351|481|482|484;2|1224|28216|206351|481|482|192066;2|976|200643|171549|171551;2|976|200643|171549|171551|836|1924944;2|976|200643|171549|171552|838|28135;2|201174|1760|85006|1268|32207|1885016;2|976|117747|200666|84566;2|1239|91061|1385|90964|1279|29387;2|1239|91061|186826|1300|1301|1303;2|1224|28211|204455|31989|366614|1310087,Complete,NA
Study 223,case-control,29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients,patients infected with HIV,35,33,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 5b,4 March 2020,Fatima Zohra,WikiWorks743,Alterations of gut microbiota of patients with acquired immune deficiency syndrome,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales",2|1239|91061|186826|1300|1301|1343;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186803|1506553;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|91061|186826;2|1239|91061;2|1224;2|1224|1236;2|1224|1236|91347|543;2|1224|1236|91347,Complete,NA
Study 223,case-control,29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected patients,patients infected with HIV,35,33,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 5b,4 March 2020,Fatima Zohra,WikiWorks743,Alterations of gut microbiota of patients with acquired immune deficiency syndrome,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|976;2|976|200643;2|976|200643|171549;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|541000;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|909932;2|1239|909932|909929;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838|165179;2|1239|186801|186802|186803;2|1239|909932|909929|1843491|158846;2|976|200643|171549|815|909656|821;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|216851;2|1239|909932|1843489|31977|39948;2|1239|909932|1843488|909930;2|1239|909932|1843488|909930|33024,Complete,NA
Study 223,case-control,29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected homosexual patients,homosexual patients infected with HIV,35,4,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,4 March 2020,Fatima Zohra,WikiWorks743,Effects of HIV transmission route of fecal microbiota in patients with HIV,increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__Erysipelatoclostridium ramosum",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|526524|526525|128827|1505663;2|1239|526524|526525|128827|1505663|1547,Complete,NA
Study 223,case-control,29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,HIV infected homosexual patients,homosexual patients infected with HIV,35,4,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6b,4 March 2020,Fatima Zohra,WikiWorks743,Effects of HIV transmission route of fecal microbiota in patients with HIV,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1239|186801|186802;2|1239|186801;2|976;2|976|200643|171549;2|976|200643;2|1239|186801|186802|541000;2|1239|909932|909929;2|1239|909932;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|976|200643|171549|171552|838|165179;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930;2|1239|909932|1843488|909930|33024,Complete,NA
Study 223,case-control,29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healthy controls,Intravenous drug abuse HIV patients,Intravenous drug abuse patients infected with HIV,35,3,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,4 March 2020,Fatima Zohra,WikiWorks743,Effects of HIV transmission route of fecal microbiota in patients with HIV,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus",2|1224|1236|91347|543;2|1224|1236|91347;2|1239|186801|186802|186803;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|2316020|33038,Complete,NA
Study 223,case-control,29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,hetersexual,homosexual,homosexual patients infected with HIV,26,4,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6d,4 March 2020,Fatima Zohra,WikiWorks743,relative abundance bacteria with significance between heterosexual and homosexual subjects,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|171552|838;2|1239|186801|186802|186803|1506553;2|1239|909932|1843488|909930|33024;2|976|200643|171549|2005525|375288,Complete,NA
Study 223,case-control,29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healty control,HAART,HIV infected patients treated with highly active antiretroviral therapy(HAART),35,14,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 7c,4 March 2020,Fatima Zohra,WikiWorks743,Effects of HAART on gut microbiota in patients with HIV,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|2316020|33038;2|976|200643|171549|815|816|817,Complete,NA
Study 223,case-control,29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healty control,HAART,HIV infected patients treated with highly active antiretroviral therapy(HAART),35,14,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 7c,4 March 2020,Fatima Zohra,WikiWorks743,Effects of HAART on gut microbiota in patients with HIV,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1239|186801;2|1239|186801|186802;2|976;2|976|200643;2|976|200643|171549;2|1239|186801|186802|541000;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|909932;2|1239|909932|909929;2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|216851;2|1239|909932|1843489|31977|39948;2|1239|909932|1843488|909930;2|1239|909932|1843488|909930|33024,Complete,NA
Study 223,case-control,29411528,10.1111/jcmm.13508,NA,"Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y , Nie Y",Alterations in the gut microbiota of patients with acquired immune deficiency syndrome,Journal of cellular and molecular medicine,2018,Experiment 6,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healthy control,HAART untreated,HIV infected patients not treated with HAART,35,19,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 7c,4 March 2020,Fatima Zohra,WikiWorks743,Effects of HAART on gut microbiota in patients with HIV,increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061;2|1224|1236|91347|543;2|1224|1236|91347;2|1239|91061|186826;2|1224|1236;2|1224;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,NA
Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,baseline,barley (WGB),baseline (before fiber supplementation),28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Table 2, text",4 March 2020,Lora Kasselman,"WikiWorks743,Fatima",Table 2 Abundance of dominant bacterial taxa (% of total microbiota) in fecal samples as determined by 454 pyrosequencing (values are presented as mean±s.d.),increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|572511|418240;2|1239;2|1239|186801|186802|186803|841|301302;2|1239|186801|186802|186803|841|166486;2|1239|186801|186802|186803|39491,Complete,NA
Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,baseline,barley (WGB),baseline (before fiber supplementation),28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Table 2, text",4 March 2020,Lora Kasselman,WikiWorks743,Table 2 Abundance of dominant bacterial taxa (% of total microbiota) in fecal samples as determined by 454 pyrosequencing (values are presented as mean±s.d.),decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|976|200643|171549|1853231|283168|28118;2|976;2|976|200643|171549|171551;2|976|200643|171549|1853231|283168,Complete,NA
Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,baseline,brown rice (BR),baseline (before fiber supplementation),28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Table 2, text",4 March 2020,Lora Kasselman,WikiWorks743,Table 2 Abundance of dominant bacterial taxa (% of total microbiota) in fecal samples as determined by 454 pyrosequencing (values are presented as mean±s.d.),increased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,baseline,brown rice (BR),baseline (before fiber supplementation),28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Table 2, text",4 March 2020,Lora Kasselman,WikiWorks743,Table 2 Abundance of dominant bacterial taxa (% of total microbiota) in fecal samples as determined by 454 pyrosequencing (values are presented as mean±s.d.),decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,NA
Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,baseline,brown rice + barley (BR + WGB),baseline (before fiber supplementation),28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,"Table 2, text",4 March 2020,Lora Kasselman,WikiWorks743,Table 2 Abundance of dominant bacterial taxa (% of total microbiota) in fecal samples as determined by 454 pyrosequencing (values are presented as mean±s.d.),increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes",2|1239|186801|186802|186803|572511;2|1239,Complete,NA
Study 224,randomized controlled trial,23038174,10.1038/ismej.2012.104,NA,"Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD , Walter J",Gut microbiome composition is linked to whole grain-induced immunological improvements,The ISME journal,2013,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,baseline,brown rice + barley (BR + WGB),baseline (before fiber supplementation),28,28,3 months,16S,123,Roche454,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,"Table 2, text",4 March 2020,Lora Kasselman,WikiWorks743,Table 2 Abundance of dominant bacterial taxa (% of total microbiota) in fecal samples as determined by 454 pyrosequencing (values are presented as mean±s.d.),decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,NA
Study 225,prospective cohort,22153774,10.1016/j.jaci.2011.10.025,NA,"Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L , Jenmalm MC",Low diversity of the gut microbiota in infants with atopic eczema,The Journal of allergy and clinical immunology,2012,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy infant,infant with atopic eczema,infant with atopic eczema,20,20,NA,16S,34,Roche454,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 3, text",4 March 2020,Lucy Mellor,WikiWorks743,Relative abundance of dominant taxa in stool samples obtained at 12 months from infants with and without atopic eczema during the first 2 years of life,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|1239|91061|186826|81852|1350;2|1239|186801|186802|186804,Complete,NA
Study 225,prospective cohort,22153774,10.1016/j.jaci.2011.10.025,NA,"Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L , Jenmalm MC",Low diversity of the gut microbiota in infants with atopic eczema,The Journal of allergy and clinical immunology,2012,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy infant,infant with atopic eczema,infant with atopic eczema,20,20,NA,16S,34,Roche454,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 3, text",4 March 2020,Lucy Mellor,WikiWorks743,Relative abundance of dominant taxa in stool samples obtained at 12 months from infants with and without atopic eczema during the first 2 years of life,decreased,k__Bacteria|p__Proteobacteria,2|1224,Complete,NA
Study 226,case-control,27477587,10.1038/srep30673,NA,"Ling Z, Jin C, Xie T, Cheng Y, Li L , Wu N",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healthy control,HIV-1 infected,HIV-1 diagnosed patients,16,67,1 month,16S,123,Roche454,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 2B,2C, 2D, 2E",4 March 2020,Fatima Zohra,WikiWorks743,Comparison of the relative abundance in healthy controls and HIV-1 positive individuals,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes",2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|909929|1843491|158846;2|1224;2|1239|186801|186802|216572|216851;2|1224|28216|80840;2|1224|28216;2|1224|28216|80840|995019;2|1224|28216|80840|995019|577310;2|1239|526524|526525;2|1239|526524|526525|128827;2|1239|526524;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|547;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|31979|580596;2|1239|186801|186802|186803|189330;2|1239,Complete,NA
Study 226,case-control,27477587,10.1038/srep30673,NA,"Ling Z, Jin C, Xie T, Cheng Y, Li L , Wu N",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,healthy control,HIV-1 infected,HIV-1 diagnosed patients,16,67,1 month,16S,123,Roche454,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 2B,2C, 2D, 2E",4 March 2020,Fatima Zohra,WikiWorks743,Comparison of the relative abundance in healthy controls and HIV-1 positive individuals,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|186803|33042;2|976|200643|171549|2005519|397864;2|1239|909932|1843489|31977|39948;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,NA
Study 226,case-control,27477587,10.1038/srep30673,NA,"Ling Z, Jin C, Xie T, Cheng Y, Li L , Wu N",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,untreated,HIV-1 treated,HIV-1 diagnosed patients,35,32,1 month,16S,123,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3B,4 March 2020,Fatima Zohra,WikiWorks743,Comparison of the relative abundance in healthy controls and HIV-1 positive individuals,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes",2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|186801|186802|186803|572511;2|201174|1760|2037;2|201174|1760|2037|2049|1654;2|1239|909932|1843489|31977|29465;2|201174|1760|2037|2049;2|1224;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977;2|1239|909932|909929;2|1239|909932;2|1239,Complete,NA
Study 226,case-control,27477587,10.1038/srep30673,NA,"Ling Z, Jin C, Xie T, Cheng Y, Li L , Wu N",Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population,Scientific reports,2016,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,untreated,HIV-1 treated,HIV-1 diagnosed patients,35,32,1 month,16S,123,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3B,4 March 2020,Fatima Zohra,WikiWorks743,Comparison of the relative abundance in healthy controls and HIV-1 positive individuals,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter,k__Bacteria|p__Synergistetes|c__Synergistia,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|976|200643|171549;2|976|200643;2|976;2|1239|186801|186802|216572|216851;2|1239|909932|1843489|31977|39948;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|508458|649775|649776|649777|638847;2|508458|649775;2|508458|649775|649776;2|508458|649775|649776|649777;2|508458|649775|649776|649777|2753;2|976|200643|171549|2005519|397864;2|1239|186801|186802|216572|459786;2|976|200643|171549|1853231|283168,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, Text",5 March 2020,Lucy Mellor,WikiWorks743,Phylum level relative abundance of gut microbiota in infants with transient atopic dermatitis (AD) and healthy controls,increased,k__Bacteria|p__Actinobacteria,2|201174,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Text",5 March 2020,Lucy Mellor,WikiWorks743,Genus level relative abundance of gut microbiota in infants with transient atopic dermatitis (AD) and healthy controls,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|201174|1760|85004|31953|1678;2|74201|203494|48461|1647988|239934,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2b, Text",5 March 2020,Lucy Mellor,WikiWorks743,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and healthy controls,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Text",5 March 2020,Lucy Mellor,WikiWorks743,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and healthy controls,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2b, Text",5 March 2020,Lucy Mellor,WikiWorks743,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and transient atopic dermatitis,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Text",5 March 2020,Lucy Mellor,WikiWorks743,Genus level relative abundance of gut microbiota in infants with persistent atopic dermatitis (AD) and transient atopic dermatitis,decreased,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,2|74201|203494|48461|1647988|239934,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 4,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S1a,5 March 2020,Lucy Mellor,WikiWorks743,LEfSe analysis of the infant gut microbiota in healthy controls and persistent AD subjects,increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|1239|91061;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|91061|186826;2|1239|186801|186802|186804|1505657;2|1239|186801|186802|216572|216851;2|976|200643|171549|171551;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186804|1505652;2|1239|186801|186802|186804|1501226;2|1239|91061|186826|186828|117563;2|1239|91061|186826|186827;2|1239|526524|526525|2810280|100883,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 4,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy controls,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,84,26,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure S1a,5 March 2020,Lucy Mellor,WikiWorks743,LEfSe analysis of the infant gut microbiota in healthy controls and persistent AD subjects,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pseudocitrobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|1224|1236|91347|543|1504576;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|543|160674;2|1224|1236|91347|543|1330547;2|1224|1236|91347|543|544;2|201174|1760|2037;2|1224|1236|91347|543|547;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|1239|526524|526525|2810280|100883,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 5,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S1b,5 March 2020,Lucy Mellor,WikiWorks743,LEfSe analysis of the infant gut microbiota in transient AD and persistent AD subjects,increased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes",2|1239|526524|526525|2810280|100883;2|1239|186801|186802|186803|189330;2|1224|1236|2887326|468|469;2|1224|1236|2887326|468;2|1224|1236|72274;2|1239|186801|186802|186804|1501226;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 5,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,transient atopic dermatitis,infants with persistent atopic dermatitis,infant with persistent atopic dermatitis,22,26,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure S1b,5 March 2020,Lucy Mellor,WikiWorks743,LEfSe analysis of the infant gut microbiota in transient AD and persistent AD subjects,decreased,"k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella",2|74201;2|74201|203494|48461;2|74201|203494;2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543|547;2|1224|1236|91347|543|1330547;2|1224|1236|91347|543|160674,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 6,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure S1c,5 March 2020,Lucy Mellor,"WikiWorks743,Fatima",LEfSe analysis of the infant gut microbiota in healthy controls and transient AD subjects,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria",2|201174|1760;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174,Complete,NA
Study 227,case-control,32009325,10.4168/aair.2020.12.2.322,NA,"Park YM, Lee SY, Kang MJ, Kim BS, Lee MJ, Jung SS, Yoon JS, Cho HJ, Lee E, Yang SI, Seo JH, Kim HB, Suh DI, Shin YH, Kim KW, Ahn K , Hong SJ","Imbalance of Gut <i>Streptococcus</i>, <i>Clostridium</i>, and <i>Akkermansia</i> Determines the Natural Course of Atopic Dermatitis in Infant","Allergy, asthma & immunology research",2020,Experiment 6,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,infant with transient atopic dermatitis,infant with transient atopic dermatitis,84,22,before sample collection,16S,123,Roche454,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure S1c,5 March 2020,Lucy Mellor,WikiWorks743,LEfSe analysis of the infant gut microbiota in healthy controls and transient AD subjects,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales",2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207;2|201174|1760|85006,Complete,NA
Study 228,randomized controlled trial,30139999,10.1038/s41598-018-30783-1,NA,"Gurry T, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z , Alm EJ",Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort,Scientific reports,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,day 6 of PECTIN spike-in,day 3 of PECTIN spike-in,before pectin spike-in,9,9,6 months,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1b and text,11 March 2020,Lora Kasselman,WikiWorks743,"OTUs that showed statistically significant (DESeq. 2, FDR < 0.1) differential abundance on day 6 compared to day 3 in response to particular spike-ins. Mean relative abundances are computed across all participants and then converted to Z-scores across timepoints, to illustrate relative changes through time. - PECTIN",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239|186801|186802|186803;2|1239|186801|186802|186803|841;2|976|200643|171549|815|816;2|1239|186801|186802|216572|44748;2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851|853,Complete,NA
Study 228,randomized controlled trial,30139999,10.1038/s41598-018-30783-1,NA,"Gurry T, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z , Alm EJ",Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort,Scientific reports,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,day 6 of INULIN spike-in,day 3 of INULIN spike-in,before pectin spike-in,9,9,6 months,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1b and text,11 March 2020,Lora Kasselman,WikiWorks743,"OTUs that showed statistically significant (DESeq. 2, FDR < 0.1) differential abundance on day 6 compared to day 3 in response to particular spike-ins. Mean relative abundances are computed across all participants and then converted to Z-scores across timepoints, to illustrate relative changes through time. - INULIN",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|1239|186801|186802|186803;2|976|200643|171549|815|816|820;2|1239|186801|186802|216572|216851|853,Complete,NA
Study 229,laboratory experiment,29909506,10.1186/s13568-018-0629-9,NA,"Bang SJ, Kim G, Lim MY, Song EJ, Jung DH, Kum JS, Nam YD, Park CS , Seo DH",The influence of in vitro pectin fermentation on the human fecal microbiome,AMB Express,2018,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,late pectin incubation time,early,before/early pectin incubation,3,3,6 months,16S,12,RT-qPCR,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 and text,12 March 2020,Lora Kasselman,WikiWorks743,Significantly changed taxa according to pectin incubation time (q value < 0.1),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|201174|1760|85004|31953|1678;2|201174|84998|84999|84107;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|186804;2|1224|28216|80840|75682|846;2|1239|186801|186802|990719;2|1239|186801|186802|31979;2|976|200643|171549|1853231|283168;2|1239|186801|186802|186803|33042;2|976|200643|171549|1853231|574697;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|572511;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|186803|841;2|976|200643|171549|171550;2|976|200643|171549|815|816,Complete,NA
Study 229,laboratory experiment,29909506,10.1186/s13568-018-0629-9,NA,"Bang SJ, Kim G, Lim MY, Song EJ, Jung DH, Kum JS, Nam YD, Park CS , Seo DH",The influence of in vitro pectin fermentation on the human fecal microbiome,AMB Express,2018,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,late pectin incubation time,early,before/early pectin incubation,3,3,6 months,16S,12,RT-qPCR,Linear Regression,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4 and text,12 March 2020,Lora Kasselman,WikiWorks743,Significantly changed taxa according to pectin incubation time (q value < 0.1),decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|1239|186801|186802|186803|28050;2|1224|28216|80840|995019|40544;2|1239|186801|186802|186803|189330;2|1239|186801|186802|31979|1485;2|1224|28216|80840;2|976|200643|171549,Complete,NA
Study 230,prospective cohort,28903469,10.1093/femsec/fix099,NA,"Tanaka M, Korenori Y, Washio M, Kobayashi T, Momoda R, Kiyohara C, Kuroda A, Saito Y, Sonomoto K , Nakayama J",Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood,FEMS microbiology ecology,2017,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,non-allergy,infant with food allergy,infant with food allergy,27,14,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, text",12 March 2020,Lucy Mellor,WikiWorks743,Relative abundance of gut microbiota of infants at 2 months of age in food allergy (FA) and non-allergy (NA) groups,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1243;2|1239|91061|186826|33958|46255;2|1239|909932|1843489|31977|29465,Complete,NA
Study 230,prospective cohort,28903469,10.1093/femsec/fix099,NA,"Tanaka M, Korenori Y, Washio M, Kobayashi T, Momoda R, Kiyohara C, Kuroda A, Saito Y, Sonomoto K , Nakayama J",Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood,FEMS microbiology ecology,2017,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,non-allergy,infant with food allergy,infant with food allergy,27,14,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 4c, text",12 March 2020,Lucy Mellor,WikiWorks743,Relative abundances of genera in infants at 1 year of age which were statistically signficant differences between the food allergy (FA) and non-allergy (NA) groups,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1224|1236|91347|543;2|1239|186801|186802|31979|1485,Complete,NA
Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,Experiment 1,United Kingdom,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,renatta canada apple - at 10 hr,cellulose,poorly fermentable fiber (cellulose),3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,"Figure 1, Table 2, and text",18 March 2020,Lora Kasselman,WikiWorks743,"Changes in bacterial taxa relative abundance (%) at 10 h and 24 h of in vitro batch culture fermentations inoculated with human feces (n = 3 healthy donors) and administrated with inulin, cellulose, Renetta Canada, Golden Delicious and Pink Lady as the substrates (treatments).",increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,NA
Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,Experiment 2,United Kingdom,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,golden delicious apple - at 10 hr,cellulose,poorly fermentable fiber (cellulose),3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,"Figure 1, Table 2, and text",18 March 2020,Lora Kasselman,WikiWorks743,"Changes in bacterial taxa relative abundance (%) at 10 h and 24 h of in vitro batch culture fermentations inoculated with human feces (n = 3 healthy donors) and administrated with inulin, cellulose, Renetta Canada, Golden Delicious and Pink Lady as the substrates (treatments).",increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,NA
Study 231,laboratory experiment,28538678,10.3390/nu9060533,NA,"Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA , Tuohy KM",Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model,Nutrients,2017,Experiment 3,United Kingdom,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,pink lady apple - at 10 hr,cellulose,poorly fermentable fiber (cellulose),3,3,3 months,16S,34,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,"Figure 1, Table 2, and text",18 March 2020,Lora Kasselman,WikiWorks743,"Changes in bacterial taxa relative abundance (%) at 10 h and 24 h of in vitro batch culture fermentations inoculated with human feces (n = 3 healthy donors) and administrated with inulin, cellulose, Renetta Canada, Golden Delicious and Pink Lady as the substrates (treatments).",increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,NA
Study 232,"cross-sectional observational, not case-control",24451087,10.1186/2049-2618-1-26,NA,"McHardy IH, Li X, Tong M, Ruegger P, Jacobs J, Borneman J, Anton P , Braun J",HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota,Microbiome,2013,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,HC,HIV infected cART negative,HIV infected patients not on combined anti-retroviral therapy,20,40,NA,16S,4,Illumina,Kruskall-Wallis,0.15,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Figure 3,18 March 2020,Fatima Zohra,WikiWorks743,Phylogenetic differences in HIV subjects not on combination anti-retroviral therpay,increased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|32066;2|32066|203490;2|1239|186801|186802|186804;2|32066|203490|203491|203492;2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|186804|1257;2|976|200643|171549|171551|836;2|32066|203490|203491|203492|848,Complete,NA
Study 232,"cross-sectional observational, not case-control",24451087,10.1186/2049-2618-1-26,NA,"McHardy IH, Li X, Tong M, Ruegger P, Jacobs J, Borneman J, Anton P , Braun J",HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota,Microbiome,2013,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,HC,HIV infected cART negative,HIV infected patients not on combined anti-retroviral therapy,20,40,NA,16S,4,Illumina,Kruskall-Wallis,0.15,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Figure 3,18 March 2020,Fatima Zohra,WikiWorks743,Phylogenetic differences in HIV subjects not on combination anti-retroviral therpay,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186803;2|1239|186801|186802|541000;2|976|200643|171549|171550;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|841;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|1263;2|976|200643|171549|171550|239759,Complete,NA
Study 233,"cross-sectional observational, not case-control",24399150,10.1038/mi.2013.116,NA,"Dillon SM, Lee EJ, Kotter CV, Austin GL, Dong Z, Hecht DK, Gianella S, Siewe B, Smith DM, Landay AL, Robertson CE, Frank DN , Wilson CC",An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia,Mucosal immunology,2014,Experiment 1,United States of America,Homo sapiens,colonic mucosa,UBERON:0000317,HIV infection,EFO:0000764,uninfected,HIV-infected,HIV-1 infected subjects,14,18,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Figure 1, Supplemental table S1",18 March 2020,Fatima Zohra,WikiWorks743,"Colonic muscosal dysbiosis in chronic, untreated HIV-1 infections",increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",2|1224;2|976|200643|171549|171552|838;2|1224|1236|2887326|468|469;2|976|200643|171549|171552;2|1224|28211|356|118882;2|1224|1236|135614|32033;2|1224|1236|2887326|468,Complete,NA
Study 233,"cross-sectional observational, not case-control",24399150,10.1038/mi.2013.116,NA,"Dillon SM, Lee EJ, Kotter CV, Austin GL, Dong Z, Hecht DK, Gianella S, Siewe B, Smith DM, Landay AL, Robertson CE, Frank DN , Wilson CC",An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia,Mucosal immunology,2014,Experiment 1,United States of America,Homo sapiens,colonic mucosa,UBERON:0000317,HIV infection,EFO:0000764,uninfected,HIV-infected,HIV-1 infected subjects,14,18,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Figure 1, Supplemental table S1",18 March 2020,Fatima Zohra,WikiWorks743,"Colonic muscosal dysbiosis in chronic, untreated HIV-1 infections",decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1239;2|976|200643|171549|815|816;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|33042;2|976|200643|171549|171551;2|976|200643|171549|171550,Complete,NA
Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,Experiment 1,"Finland,Germany,United Kingdom",Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,healthy control,adult with atopic dermatitis,adult with atopic dermatitis,115,82,2 weeks,16S,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1c, Supplemental Figure 3b",19 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,NA
Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,Experiment 1,"Finland,Germany,United Kingdom",Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,healthy control,adult with atopic dermatitis,adult with atopic dermatitis,115,82,2 weeks,16S,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1c, Supplemental Figure 3b",19 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant OTUs among adults with atopic dermatitis (AD) and healthy controls,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pelomonas|s__Pelomonas sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes",2|1224|28216|80840|119060|32008|36773;2|1239|1737404|1737405|1570339|150022|1981334;2|1239|91061|1385|90964|1279|29387;2|1239|91061|186826|33958|1578|1591;2|1224|28216|80840|80864|335058|1909303;2|201174|1760|85009|31957|1912216|1747,Complete,NA
Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,Experiment 2,"Finland,Germany,United Kingdom",Homo sapiens,skin of body,UBERON:0002097,psoriasis,EFO:0000676,healthy control,adult with psoriasis,adult with psoriasis,115,119,2 weeks,16S,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 1c, Supplemental Figure 3b",19 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.",2|201174|1760|85007|1653|1716|146827;2|1239|1737404|1737405|1570339|150022|1981334;2|1224|28216|206351|481;2|201174|1760|85007|1653|1716|161879;2|1239|1737404|1737405|1570339|165779|1872515,Complete,NA
Study 234,case-control,31619666,10.1038/s41467-019-12253-y,NA,"Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B , Alenius H",Microbe-host interplay in atopic dermatitis and psoriasis,Nature communications,2019,Experiment 2,"Finland,Germany,United Kingdom",Homo sapiens,skin of body,UBERON:0002097,psoriasis,EFO:0000676,healthy control,adult with psoriasis,adult with psoriasis,115,119,2 weeks,16S,NA,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 1c, Supplemental Figure 3b",19 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant OTUs among adults with psoriasis (PSO) and healthy controls,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pelomonas|s__Pelomonas sp.",2|1224|28216|80840|119060|32008|36773;2|1239|91061|186826|33958|1578|1591;2|1224|28216|80840|80864|335058|1909303,Complete,NA
Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy control,child with food allergy,child with food allergy,21,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Figure 4, Figure 5",20 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.",2|1239|186801|186802|216572|459786|351091;2|1239|186801|186802|216572|216851|1971605,Complete,NA
Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy control,child with food allergy,child with food allergy,21,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Figure 4, Figure 5",20 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and healthy controls,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,2|1239|186801|186802|186803|572511|1955243,Complete,NA
Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy sibling,child with food allergy,child with food allergy,25,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Figure 5",20 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings,increased,NA,NA,Complete,NA
Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy sibling,child with food allergy,child with food allergy,25,22,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Figure 5",20 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant operational taxonomic units (OTUs) obsereved between food-allergic children and their siblings,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.",2|976|200643|171549|171550|239759|28117;2|976|200643|171549|171550|239759|1872444,Complete,NA
Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy control,healthy sibling,sibling with no food allergy,21,25,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 3, Figure 4, Figure 5",20 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.",2|1239|186801|186802|216572|459786|351091;2|1239|186801|186802|216572|216851|1971605;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|171550|239759|1872444,Complete,NA
Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy control,healthy sibling,sibling with no food allergy,21,25,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 3, Figure 4, Figure 5",20 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant operational taxonomic units (OTUs) obsereved between non-food-allergic siblings and healthy controls,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,2|1239|186801|186802|186803|572511|1955243,Complete,NA
Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,age,EFO:0000246,<7 years,7-18 years,child age 7-18,26,42,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,20 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons in children <7 years compared to children 7-18 years,increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,NA
Study 235,case-control,29624747,10.1111/pai.12904,NA,"Kourosh A, Luna RA, Balderas M, Nance C, Anagnostou A, Devaraj S , Davis CM",Fecal microbiome signatures are different in food-allergic children compared to siblings and healthy children,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2018,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,age,EFO:0000246,<7 years,7-18 years,child age 7-18,26,42,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,20 March 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxons in children <7 years compared to children 7-18 years,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|1239;2|1224;2|1239|526524|526525|128827;2|1239|186801|186802|186803;2|1239|186801|186802|186804,Complete,NA
Study 236,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C, Rossmeier A, Lechner K, Wu L, Waldmann E, Fischer S, Stark RG, Altenhofer J, Henze K , Parhofer KG","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,after walnut diet,before walnut diet,before walnut consumption,135,135,"excluded those on ""antibiotic therapy""",16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,smoking behavior,triglycerides",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,"Figure 4b, 5a, and text",25 March 2020,Lora Kasselman,WikiWorks743,Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|572511,Complete,NA
Study 236,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C, Rossmeier A, Lechner K, Wu L, Waldmann E, Fischer S, Stark RG, Altenhofer J, Henze K , Parhofer KG","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,after walnut diet,before walnut diet,before walnut consumption,135,135,"excluded those on ""antibiotic therapy""",16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,smoking behavior,triglycerides",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,"Figure 4b, 5a, and text",25 March 2020,Lora Kasselman,WikiWorks743,Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|186801|186802|541000;2|201174|1760|85004|31953|1678,Complete,NA
Study 236,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C, Rossmeier A, Lechner K, Wu L, Waldmann E, Fischer S, Stark RG, Altenhofer J, Henze K , Parhofer KG","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,Experiment 2,Germany,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,replace both,carbohydrate replacement (with walnuts),before walnut consumption,135,135,"excluded those on ""antibiotic therapy""",16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,smoking behavior,triglycerides",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4b, 5a, and text",25 March 2020,Lora Kasselman,WikiWorks743,Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|204475;2|1239|186801|186802|186803|1407607;2|976|200643|171549|815|816,Complete,NA
Study 236,randomized controlled trial,29470389,10.3390/nu10020244,NA,"Bamberger C, Rossmeier A, Lechner K, Wu L, Waldmann E, Fischer S, Stark RG, Altenhofer J, Henze K , Parhofer KG","A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial",Nutrients,2018,Experiment 3,Germany,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,fat replacement (with walnuts),replace both,before walnut consumption,135,135,"excluded those on ""antibiotic therapy""",16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,"age,body mass index,smoking behavior,triglycerides",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4b, 5a, and text",25 March 2020,Lora Kasselman,WikiWorks743,Most abundant Operational Taxonomic Units for both walnut and control phase at genus level. Significant different OTUs are marked with by using * and p-values. pvalues were calculated using a pairwise Fisher test.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|204475;2|1239|186801|186802|186803|1407607;2|976|200643|171549|815|816,Complete,NA
Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,chronic hepatitis C virus infection,EFO:0004220,healthy controls,cirrhosis patients,heatitis C patients without cirrhosis,50,38,3 months,16S,12,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,decreased,decreased,NA,decreased,NA,NA,Signature 1,Table 3,25 March 2020,Fatima Zohra,WikiWorks743,Genera with distinct patterns and their mean abundance in predefinded groups,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|976|200643|171549|171552|1283313;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1224|1236|135625|712|724;2|201174|1760|85006|1268|1269;2|1239|91061|186826|33958|46255,Complete,NA
Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,Experiment 1,Germany,Homo sapiens,feces,UBERON:0001988,chronic hepatitis C virus infection,EFO:0004220,healthy controls,cirrhosis patients,heatitis C patients without cirrhosis,50,38,3 months,16S,12,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,decreased,decreased,NA,decreased,NA,NA,Signature 2,Table 3,25 March 2020,Fatima Zohra,WikiWorks743,Genera with distinct patterns and their mean abundance in predefinded groups,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Candidatus Melainabacteria|o__Vampirovibrionales|g__Vampirovibrio",2|976|200643|171549|1853231|574697;2|256845|1313211|278082|255528|172900;2|1224|28221|213115|194924|35832;2|1239|909932|909929|1843491|52225;2|1798710|2211217|213484,Complete,NA
Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,Experiment 2,Germany,Homo sapiens,feces,UBERON:0001988,chronic hepatitis C virus infection,EFO:0004220,no cirrhosis,cirrhosis patients,heatitis C patients with cirrhosis,38,57,3 months,16S,12,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,NA,Signature 1,Table 3,25 March 2020,Fatima Zohra,WikiWorks743,Genera with distinct patterns and their mean abundance in predefinded groups,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus",2|1224|1236|91347|543|544;2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1253,Complete,NA
Study 237,"cross-sectional observational, not case-control",28561276,10.1111/liv.13485,NA,"Heidrich B, Vital M, Plumeier I, Döscher N, Kahl S, Kirschner J, Ziegert S, Solbach P, Lenzen H, Potthoff A, Manns MP, Wedemeyer H , Pieper DH",Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls,Liver international : official journal of the International Association for the Study of the Liver,2018,Experiment 3,Germany,Homo sapiens,feces,UBERON:0001988,chronic hepatitis C virus infection,EFO:0004220,healthy controls,hepatitis C patients,hepatitic C patients,50,95,3 months,16S,12,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,25 March 2020,Fatima Zohra,WikiWorks743,Genera with distinct patterns and their mean abundance in predefinded groups,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio",2|1239|186801|186802|216572|946234;2|1239|909932|1843489|31977|906;2|1239|186801|186802|216572|1017280;2|1239|186801|186802|216572|35829,Complete,NA
Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4A,26 March 2020,Cynthia Anderson,WikiWorks743,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|1506553;2|1224|28216|80840|995019|40544;2|1239|526524|526525|128827|1505663;2|1239|186801|186802|186803|437755;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|459786;2|1239|91061|186826|1300|1301,Complete,Fatima Zohra
Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4A,26 March 2020,Cynthia Anderson,"WikiWorks743,Fatima",The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|207244;2|976|200643|171549|815|816;2|1239|186801|186802|186803|572511;2|1239|186801|186802|990719;2|1224|1236|91347|543|547;2|1224|1236|91347|543|561;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186804|1505657;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186804|1501226;2|1224|1236|91347|543|620;2|976|200643|171549|1853231|574697,Complete,Fatima Zohra
Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,age,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4B,26 March 2020,Cynthia Anderson,WikiWorks743,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for age,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella",2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|1506553;2|1239|526524|526525|128827|1505663;2|1239|186801|186802|216572|946234;2|1239|186801|186802|186803|437755,Complete,Fatima Zohra
Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,age,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4B,26 March 2020,Cynthia Anderson,WikiWorks743,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for age,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|572511;2|976|200643|171549|171550|239759,Complete,Fatima Zohra
Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,race,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4C,26 March 2020,Cynthia Anderson,WikiWorks743,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for race,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella",2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|1506553;2|1239|91061|186826|1300|1301;2|1239|526524|526525|128827|1505663;2|1239|186801|186802|186803|437755,Complete,Fatima Zohra
Study 238,case-control,31500892,10.1016/j.ygyno.2019.09.002,NA,"Sims TT, Colbert LE, Zheng J, Delgado Medrano AY, Hoffman KL, Ramondetta L, Jazaeri A, Jhingran A, Schmeler KM, Daniel CR , Klopp A",Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls,Gynecologic oncology,2019,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,cervical cancer,MONDO:0002974,healthy controls,cervical cancer patient,patients with biopsy-proven carcinoma of the cervix,46,42,1 month- controls only,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,race,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4C,26 March 2020,Cynthia Anderson,WikiWorks743,The fecal microbiota of individuals with cervical cancer statistically significantly different from that of healthy individuals after adjusting for race,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239|186801|186802|186804|1505657;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|207244;2|1224|1236|91347|543|547;2|976|200643|171549|171550|239759,Complete,Fatima Zohra
Study 239,case-control,29318631,10.1111/all.13389,NA,"Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, Jones SM, Leung DYM, Sampson HA, Sicherer SH , Bunyavanich S",Early-life gut microbiome and egg allergy,Allergy,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,egg allergy,EFO:0007248,healthy control,infant with egg allergy,infant with egg allergy,75,66,NA,16S,4,Illumina,"LEfSe,Logistic Regression",0.05,FALSE,2,NA,"age,antibiotic,atopic eczema,breast feeding",NA,increased,increased,NA,NA,increased,Signature 1,"Figure 2b, text",26 March 2020,Lucy Mellor,WikiWorks743,Bacterial genera significantly associated with egg allergy,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1357,Complete,NA
Study 239,case-control,29318631,10.1111/all.13389,NA,"Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, Jones SM, Leung DYM, Sampson HA, Sicherer SH , Bunyavanich S",Early-life gut microbiome and egg allergy,Allergy,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,egg allergy,EFO:0007248,healthy control,infant with egg allergy,infant with egg allergy,75,66,NA,16S,4,Illumina,"LEfSe,Logistic Regression",0.05,FALSE,2,NA,"age,antibiotic,atopic eczema,breast feeding",NA,increased,increased,NA,NA,increased,Signature 2,"Figure 2b, text",26 March 2020,Lucy Mellor,WikiWorks743,Bacterial genera significantly associated with egg allergy,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,2|1239|91061|186826|33958|1243,Complete,NA
Study 239,case-control,29318631,10.1111/all.13389,NA,"Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, Jones SM, Leung DYM, Sampson HA, Sicherer SH , Bunyavanich S",Early-life gut microbiome and egg allergy,Allergy,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,egg allergy,EFO:0007248,healthy control,infant with egg sensitization,infant with egg sensitization,40,101,NA,16S,4,Illumina,"LEfSe,Logistic Regression",0.05,FALSE,2,NA,"age,race",NA,increased,increased,NA,NA,increased,Signature 1,"Figure 5b, text",27 March 2020,Lucy Mellor,WikiWorks743,Bacterial genera significantly associated with egg sensitization,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|841,Complete,NA
Study 240,case-control,25599982,10.1111/cea.12487,NA,"Azad MB, Konya T, Guttman DS, Field CJ, Sears MR, HayGlass KT, Mandhane PJ, Turvey SE, Subbarao P, Becker AB, Scott JA , Kozyrskyj AL",Infant gut microbiota and food sensitization: associations in the first year of life,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy control,infant with food sensitization,infant with food sensitization,154,12,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,decreased,Signature 1,"Table 3, text",27 March 2020,Lucy Mellor,WikiWorks743,Relative abundance of dominant phyla and families in fecal microbiota of infants at 3 months according to food sensitization at 1 year,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224;2|1224|1236|91347|543,Complete,NA
Study 240,case-control,25599982,10.1111/cea.12487,NA,"Azad MB, Konya T, Guttman DS, Field CJ, Sears MR, HayGlass KT, Mandhane PJ, Turvey SE, Subbarao P, Becker AB, Scott JA , Kozyrskyj AL",Infant gut microbiota and food sensitization: associations in the first year of life,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,Experiment 2,Canada,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy control,infant with food sensitization,infant with food sensitization,154,12,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 3, text",27 March 2020,Lucy Mellor,WikiWorks743,Relative abundance of dominant phyla and families in fecal microbiota of infants at 1 year according to food sensitization at 1 year,increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,NA
Study 240,case-control,25599982,10.1111/cea.12487,NA,"Azad MB, Konya T, Guttman DS, Field CJ, Sears MR, HayGlass KT, Mandhane PJ, Turvey SE, Subbarao P, Becker AB, Scott JA , Kozyrskyj AL",Infant gut microbiota and food sensitization: associations in the first year of life,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,Experiment 2,Canada,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,healthy control,infant with food sensitization,infant with food sensitization,154,12,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Table 3, text",27 March 2020,Lucy Mellor,WikiWorks743,Relative abundance of dominant phyla and families in fecal microbiota of infants at 1 year according to food sensitization at 1 year,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|976;2|976|200643|171549|815,Complete,NA
Study 241,case-control,30418043,10.1556/030.65.2018.045,NA,"Muleviciene A, D'Amico F, Turroni S, Candela M , Jankauskiene A",Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study,Acta microbiologica et immunologica Hungarica,2018,Experiment 1,Lithuania,Homo sapiens,feces,UBERON:0001988,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,infants and young children with iron deficiency anemia,10,10,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,29 March 2020,Rimsha Azhar,WikiWorks743,Discriminant species-level taxa between iron deficiency anemia (IDA) infants and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale",2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|39778;2|1239|186801|186802|31979|1485|137838,Complete,NA
Study 241,case-control,30418043,10.1556/030.65.2018.045,NA,"Muleviciene A, D'Amico F, Turroni S, Candela M , Jankauskiene A",Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study,Acta microbiologica et immunologica Hungarica,2018,Experiment 1,Lithuania,Homo sapiens,feces,UBERON:0001988,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,infants and young children with iron deficiency anemia,10,10,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3,29 March 2020,Rimsha Azhar,WikiWorks743,Discriminant species-level taxa between iron deficiency anemia (IDA) infants and healthy controls,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|186803|189330|39486;2|201174|1760|85004|31953|1678|1681;2|1239|909932|1843489|31977|39948,Complete,NA
Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,Experiment 1,China,Homo sapiens,dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,iron defiency anemia,24,24,2 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,"Figure 3b, 4b, Table S2",29 March 2020,Rimsha Azhar,WikiWorks743,Comparison of bacterial taxonomy (>1% relative abundance) of samples between healthy controls and iron deficiency anemia (IDA) patients,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239;2|1224|1236|2887326|468|475;2|1239|91061|186826|1300|1357;2|1224|1236|72274|135621|286;2|1239|91061|186826|81852|1350;2|201174|1760|85006|1268|57493;2|1239|91061|186826|33958|1578,Complete,NA
Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,Experiment 1,China,Homo sapiens,dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,iron defiency anemia,24,24,2 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,"Figure 3b, 4b, Table S2",29 March 2020,Rimsha Azhar,WikiWorks743,Comparison of bacterial taxonomy (>1% relative abundance) of samples between healthy controls and iron deficiency anemia (IDA) patients,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium",2|201174;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|482;2|1224|1236|135625|712|416916;2|1224|1236|135615|868|2717,Complete,NA
Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,Experiment 2,China,Homo sapiens,dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,iron defiency anemia,24,24,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure 5b,29 March 2020,Rimsha Azhar,WikiWorks743,LEfSe analysis of samples between healthy controls and iron deficiency anemia (IDA) patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria",2|1239|91061;2|1239|91061|186826;2|1239;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300;2|1224|1236|72274;2|201174|1760|85010|2070;2|1224|1236|72274|135621|286;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1224|1236|2887326|468;2|1224|1236|2887326|468|475;2|1239|186801|186802|186804;2|201174|1760|85006|1268|57493,Complete,NA
Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,Experiment 2,China,Homo sapiens,dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,healthy control,iron deficiency anemia,iron defiency anemia,24,24,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure 5b,29 March 2020,Rimsha Azhar,WikiWorks743,LEfSe analysis of samples between healthy controls and iron deficiency anemia (IDA) patients,decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Schlegelella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia",2|1224|29547;2|1224|29547|213849;2|1224|29547|213849|72294;2|1224|29547|213849|72294|194;2|1224|1236|135615|868;2|1224|1236|135615;2|1224|1236|135615|868|2717;2|201174|1760|85006|1268|32207;2|1224|1236|135625|712|416916;2|1224|28216|80840|80864|215579;2|1224|28216|80840;2|976|117743|200644|49546|1016;2|976|117743;2|976|117743|200644|49546;2|976|117743|200644;2|1224|1236|135625|712;2|1224|1236|135625;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1224|28216;2|201174|1760|85007;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174;2|201174|1760,Complete,NA
Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,Experiment 3,China,Homo sapiens,dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,iron deficiency anemia moderate,iron deficiency anemia severe,iron defiency anemia,16,8,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5d,29 March 2020,Rimsha Azhar,WikiWorks743,LEfSe analysis of samples between iron deficiency anemia moderate (IDA_m) and iron deficiency anemia severe (IDA_s) patients,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Erythrobacteraceae|g__Porphyrobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales",2|201174|1760|85006|1268|57493;2|1224|28211|204457|335929|1111;2|201174|1760|85004|31953;2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964;2|1224|1236|2887326|468|475;2|1224|1236|2887326|468;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|351;2|1239;2|1224|1236;2|1239|91061|186826|1300|1357;2|1224|1236|72274,Complete,NA
Study 242,"cross-sectional observational, not case-control",31752810,10.1186/s12903-019-0947-6,NA,"Xi R, Wang R, Wang Y, Xiang Z, Su Z, Cao Z, Xu X, Zheng X , Li J",Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing,BMC oral health,2019,Experiment 3,China,Homo sapiens,dental plaque,UBERON:0016482,Iron deficiency anemia,HP:0001891,iron deficiency anemia moderate,iron deficiency anemia severe,iron defiency anemia,16,8,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5d,29 March 2020,Rimsha Azhar,WikiWorks743,LEfSe analysis of samples between iron deficiency anemia moderate (IDA_m) and iron deficiency anemia severe (IDA_s) patients,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",2|1224|1236|135625;2|1224|1236|135625|712;2|1224|28216|206351;2|1224|28216|206351|481,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,non-current H.pylori infection,current H.pyloriI infection,H.pylori infection,23,24,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2D,1 April 2020,Fatima Zohra,"WikiWorks743,Fatima",association of fecal microbiota and current or non-current H.Pylori infection,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|91061|1385|1378;2|1239|526524|526525|128827,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,non-current H.pylori infection,current H.pyloriI infection,H.pylori infection,23,24,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure S2D,1 April 2020,Fatima Zohra,WikiWorks743,association of fecal microbiota and current or non-current H.Pylori infection,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax facilis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus erythropolis",2|201174|1760|85007|85025;2|1224|28216|80840|80864|12916;2|201174|1760|85007|85025|1827;2|1224|28216|80840|80864|12916|12917;2|201174|1760|85007|85025|1827|1833,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,past H.pylori infection,current H.pyloriI infection,H.pylori infection,8,24,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2D,1 April 2020,Fatima Zohra,"WikiWorks743,Fatima",association between helicobacter pylori infection and fecal microbiota,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",2|1224|28216|80840|506;2|976|200643|171549;2|976;2|976|200643;2|1224|28216;2|1224|28216|80840;2|976|200643|171549|171552|838|165179;2|976|200643|171549|171552;2|1224|28216|80840|995019|40544;2|976|200643|171549|171552|838;2|976|200643|171549|815|816|820,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,H.pylori negative,past H.pylori infection,H.pylori infection,15,8,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2D,1 April 2020,Fatima Zohra,WikiWorks743,association between helicobacter pylori infection and fecal microbiota,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",2|976;2|976|200643;2|976|200643|171549;2|976|200643|171549|171551;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656|310298;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|820,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,normal,gastritis,gastritis,7,18,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,8 April 2020,Fatima Zohra,WikiWorks743,cladogram of differentially distributed taxa among different gastric lesion groups,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",2|1239;2|1239|186801;2|1239|186801|186802;2|1239|91061;2|1239|526524;2|1224|1236;2|1239|91061|186826;2|1239|526524|526525;2|1224|1236|91347;2|1239|186801|186802|186803;2|1239|186801|186802|541000;2|1239|526524|526525|128827;2|1224|1236|91347|543;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|244127;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1224|1236|91347|543|561|562,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,normal,gastritis,gastritis,7,18,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,8 April 2020,Fatima Zohra,WikiWorks743,cladogram of differentially distributed taxa among different gastric lesion groups,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976;2|976|200643;2|976|200643|171549,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,normal,metaplasia,metasplasia,7,22,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,8 April 2020,Fatima Zohra,WikiWorks743,cladogram of differentially distributed taxa among different gastric lesion groups,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239;2|1224;2|1239|186801;2|1239|526524;2|1224|1236;2|1239|186801|186802;2|1239|526524|526525;2|1224|1236|91347;2|1239|186801|186802|186803;2|1239|186801|186802|186804;2|1239|526524|526525|128827;2|1224|1236|91347|543;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186804|1501226;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|2810281|191303,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,normal,metaplasia,metasplasia,7,22,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,8 April 2020,Fatima Zohra,WikiWorks743,cladogram of differentially distributed taxa among different gastric lesion groups,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976;2|976|200643;2|976|200643|171549,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 6,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,gastritis,metaplasia,metasplasia,18,22,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,8 April 2020,Fatima Zohra,WikiWorks743,cladogram of differentially distributed taxa among different gastric lesion groups,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224;2|1224|1236;2|1224|1236|91347;2|1224|1236|91347|543,Complete,NA
Study 243,"cross-sectional observational, not case-control",29971220,10.3389/fcimb.2018.00202,NA,"Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC , Pan KF",Association Between Gut Microbiota and <i>Helicobacter pylori</i>-Related Gastric Lesions in a High-Risk Population of Gastric Cancer,Frontiers in cellular and infection microbiology,2018,Experiment 6,China,Homo sapiens,feces,UBERON:0001988,gastric cancer,MONDO:0001056,gastritis,metaplasia,metasplasia,18,22,NA,16S,4,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,8 April 2020,Fatima Zohra,WikiWorks743,cladogram of differentially distributed taxa among different gastric lesion groups,decreased,NA,NA,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1b, text",3 April 2020,Lucy Mellor,WikiWorks743,Skin microorganisms differ with age in the healthy skin,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",2|201174|1760|85007|1653|1716|1720;2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 1b, text",3 April 2020,Lucy Mellor,WikiWorks743,Skin microorganisms differ with age in the healthy skin,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,2|1239|91061|186826|1300|1301|1306,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 3,"Supplemental Table E2, Figure 2b, text",3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic compositions of the healthy skin microbiome at the genus level,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",2|201174|1760|85009|31957|1743;2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|165779,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 4,"Supplemental Table E2, Figure 2b, text",3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic compositions of the healthy skin microbiome at the genus level,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|91061|186826|186828|117563;2|1239|91061|1385|1378;2|1224|1236|135625|712|724,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 2,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,59,59,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Supplemental Table E4, Figure 2b",3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among children,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 2,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,59,59,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Supplemental Table E4, Figure 2b",3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among children,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|201174|1760|85007|1653|1716;2|201174|1760|2037|2049|1654;2|1239|91061|186826|1300|1301;2|1239|91061|1385|1378;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171551|836;2|32066|203490|203491|203492|848,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 3,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,13-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E4,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with lesional skin,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85009|31957|1743;2|201174|1760|85007|1653|1716;2|1239|91061|186826|33958|1578,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 3,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,13-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Table E4,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with lesional skin,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|91061|186826|1300|1301;2|1239|91061|186826|186828|117563;2|1239|91061|1385|1378;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 3,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,13-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 3,Supplemental Table E4,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with non-lesional skin,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85009|31957|1743;2|201174|1760|85007|1653|1716;2|1239|91061|186826|33958|1578,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 3,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,13-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 4,Supplemental Table E4,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the genus level among those with non-lesional skin,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|91061|186826|186828|117563;2|1239|91061|1385|1378;2|1239|909932|1843489|31977|29465;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 4,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,18-62 years,adult age 18-62,13,45,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E3,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic compositions of the healthy skin microbiome at the species level,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282;2|1239|91061|186826|33958|1578|147802,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 5,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,69,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E5,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the species level among adults-teenagers,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 6,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,non-lesional skin,lesional skin,atopic dermatitis lesional skin,59,59,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E5,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the species level among children,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 7,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,18-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplemental Table E5,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with lesional skin,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|33958|1578|147802,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 7,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,18-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplemental Table E5,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with lesional skin,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,2|1239|91061|186826|1300|1301|45634,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 7,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,18-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 3,Supplemental Table E5,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with non-lesional skin,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282;2|1239|91061|186826|33958|1578|147802,Complete,NA
Study 244,case-control,27474122,10.1016/j.jaci.2016.04.053,NA,"Shi B, Bangayan NJ, Curd E, Taylor PA, Gallo RL, Leung DYM , Li H",The skin microbiome is different in pediatric versus adult atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 7,United States of America,Homo sapiens,skin of body,UBERON:0002097,age,EFO:0000246,2-12 years,18-62 years,teenager/adult age 13-62,59,69,1 week (oral antibiotics),16S,123,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 4,Supplemental Table E5,3 April 2020,Lucy Mellor,WikiWorks743,Taxonomic composition of the atopic dermatitis skin microbiome at the species level among those with non-lesional skin,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus",2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|45634,Complete,NA
Study 245,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, Wang Q, Yao Z , Mo Z",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,"nephrolithiasis,urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,kidney stones,13,13,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,6 April 2020,Rimsha Azhar,WikiWorks743,LEfSe analysis based on OTU characterizes microbiome between the Kidney Stone group and HC group.,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea|s__Bosea thiooxidans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1224|1236|72274;2|1224|1236|2887326|468;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|286|287;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|620;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|2316020|33038;2|976|200643|171549|171552|1283313;2|1239|909932|909929|1843491|158846;2|1239|526524|526525|128827|1573534;2|1224|28211|356|2831100|85413;2|1224|28211|356|2831100|85413|53254;2|1239|186801|186802|186806|1730;2|1224|1236|91347|543|561,Complete,NA
Study 245,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, Wang Q, Yao Z , Mo Z",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,"nephrolithiasis,urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,kidney stones,13,13,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,3,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,6 April 2020,Rimsha Azhar,WikiWorks743,LEfSe analysis based on OTU characterizes microbiome between the Kidney Stone group and HC group.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Thalassospiraceae|g__Thalassospira,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",2|1239|186801|186802|216572|1508657;2|1239|186801|186802|990719;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827|61170;2|1224|28211|204441|2844866|168934;2|1224|28211|204441|41295;2|1224|28211|204441;2|1224|28211;2|508458|649775|649776|649777|638847;2|508458|649775|649776|649777|638847|638849;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|186803|841;2|976|200643|171549|171550|239759|328814;2|1239|186801|186802|186803;2|976|200643|171549|171550|239759|328813;2|1224|28216|80840|995019|577310;2|976|200643|171549|815|909656|310297;2|1224|1236|91347|543|547,Complete,NA
Study 245,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, Wang Q, Yao Z , Mo Z",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,"nephrolithiasis,urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,kidney stones,13,13,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table 2, Figure 2",6 April 2020,Rimsha Azhar,WikiWorks743,List of genera that were significantly different between Kidney Stone group and HC group,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales",2|976|200643|171549|171552|1283313;2|1239|526524|526525|128827|1505663;2|1239|186801|186802|186803;2|1239|909932|1843488|909930|33024;2|1239|909932|909929|1843491|158846;2|1224|1236|2887326|468|469;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1224|28216|80840|995019|40544;2|1239|526524|526525|128827;2|1224|1236|2887326|468;2|1224|1236|72274;2|1239|526524|526525,Complete,NA
Study 245,case-control,29353409,10.1007/s00240-018-1037-y,NA,"Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, Wang Q, Yao Z , Mo Z",16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones,Urolithiasis,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,"nephrolithiasis,urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone group,kidney stones,13,13,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,race",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table 2, Figure 2",6 April 2020,Rimsha Azhar,WikiWorks743,List of genera that were significantly different between Kidney Stone group and HC group,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|216572|292632;2|1239|186801|186802|186806|1730|42322;2|1239|526524|526525|128827|1573535;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|577310;2|1224|28221|213115|194924|35832,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,maternal prenatal asthma/male caucasian infant,392,36,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1a,8 April 2020,Lucy Mellor,WikiWorks743,Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to male caucasian infants,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas",2|1239|91061|186826|1300|1357;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|1239|909932|909929|1843491|158846,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,maternal prenatal asthma/male caucasian infant,392,36,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1a,8 April 2020,Lucy Mellor,WikiWorks743,Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to male caucasian infants,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,2|1224|1236|91347|543|158851,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 2,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,maternal prenatal asthma/female caucasian infant,329,38,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1b,8 April 2020,Lucy Mellor,WikiWorks743,Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to female caucasian infants,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976|200643|171549|815|816|817;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|351;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643;2|976;2|976|200643|171549,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 2,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,maternal prenatal asthma/female caucasian infant,329,38,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1b,8 April 2020,Lucy Mellor,WikiWorks743,Linear discriminant analysis (LDA) plots for maternal prenatal atopic asthma for those who gave birth to female caucasian infants,decreased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,2|1239|909932|1843489|31977|906,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 3,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,maternal prenatal asthma,934,87,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 1,9 April 2020,Lucy Mellor,WikiWorks743,Distribution of maternal prenatal asthma status and infant faecal Lactobacillus abundance according to study covariates,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 4,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,maternal prenatal asthma/caucasian infant,721,74,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,9 April 2020,Lucy Mellor,WikiWorks743,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian infants",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 5,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,"maternal prenatal asthma/female infant, vaginally delivered, breastfed, not exposed to maternal antibiotics",186,21,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S2,9 April 2020,Lucy Mellor,WikiWorks743,"Median relative abundance of dominant bacterial taxa in infant gut microbiota according to material prenatal asthma in female infants, vaginally delivered, breastfed, not exposed to materal antibiotics during birth",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea",2|976|200643|171549|815;2|976|200643|171549|815|816;2|976;2|1239|186801|186802|186803|189330,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 5,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,"maternal prenatal asthma/female infant, vaginally delivered, breastfed, not exposed to maternal antibiotics",186,21,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S2,9 April 2020,Lucy Mellor,WikiWorks743,"Median relative abundance of dominant bacterial taxa in infant gut microbiota according to material prenatal asthma in female infants, vaginally delivered, breastfed, not exposed to materal antibiotics during birth",decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239;2|1224;2|1224|1236|91347|543,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 6,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,"maternal prenatal asthma/caucasian infant, allergies during pregnancy",429,64,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S3,9 April 2020,Lucy Mellor,WikiWorks743,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian mothers with allergies during pregnancy",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|1224|1236|91347|543,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 7,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,"maternal prenatal asthma/caucasian infant, no allergies during pregnancy",278,10,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S3,9 April 2020,Lucy Mellor,WikiWorks743,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian mothers with no allergies during pregnancy",increased,"k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|74201;2|74201|203494|48461|203557;2|74201|203494|48461|1647988|239934,Complete,NA
Study 246,prospective cohort,29167295,10.1183/13993003.00280-2017,NA,"Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA , Kozyrskyj AL",Sex-specific impact of asthma during pregnancy on infant gut microbiota,The European respiratory journal,2017,Experiment 7,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma,maternal asthma,"maternal prenatal asthma/caucasian infant, no allergies during pregnancy",278,10,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S3,9 April 2020,Lucy Mellor,WikiWorks743,"Median relative abundance of dominant bacterial taxa at the phylum, family and genus levels in infant gut microbiota according to material prenatal asthma in caucasian mothers with no allergies during pregnancy",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654,Complete,NA
Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,Experiment 1,New Zealand,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,prebiotic (inulin-type fructan),placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,ANOVA,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",15 April 2020,Lora Kasselman,WikiWorks743,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|119852;2|1239|186801|186802|186803,Complete,NA
Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,Experiment 1,New Zealand,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,prebiotic (inulin-type fructan),placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,ANOVA,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Text, Table 4, Figure 5, and Figure 7",15 April 2020,Lora Kasselman,WikiWorks743,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|201174|1760|85004|31953|1678,Complete,NA
Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,Experiment 2,New Zealand,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,prebiotic (inulin-type fructan) - in participants with low dietary fiber,placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,ANOVA,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",15 April 2020,Lora Kasselman,WikiWorks743,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,Experiment 3,New Zealand,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,prebiotic (inulin-type fructan) - in participants with high dietary fiber,placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,ANOVA,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",15 April 2020,Lora Kasselman,WikiWorks743,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea",2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|189330,Complete,NA
Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,Experiment 3,New Zealand,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,prebiotic (inulin-type fructan) - in participants with high dietary fiber,placebo,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,ANOVA,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Text, Table 4, Figure 5, and Figure 7",15 April 2020,Lora Kasselman,WikiWorks743,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
Study 247,randomized controlled trial,29307330,10.1017/S0007114517003440,NA,"Healey G, Murphy R, Butts C, Brough L, Whelan K , Coad J","Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study",The British journal of nutrition,2018,Experiment 4,New Zealand,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,high dietary fiber,low dietary fiber,placebo (control for prebiotic intake - representing lower fiber group),34,33,6 months,16S,34,Illumina,ANOVA,0.05,FALSE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Text, Table 4, Figure 5, and Figure 7",15 April 2020,Lora Kasselman,WikiWorks743,Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,NA
Study 248,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D , Meiring TL",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,Experiment 1,South Africa,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,low risk hpv,high risk hpv,High risk HPV infection confirmed through HPV genotyping test,57,30,NA,16S,34,Illumina,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,figure 4,15 April 2020,Cynthia Anderson,WikiWorks743,Potential biomarkers for high-risk HPV by LefSe,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Coriobacterium,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria",2|1224|1236|72274|135621|351;2|1239|91061|186826|186827;2|201174|84998|84999;2|201174|84998|84999|84107|33870;2|201174;2|201174|1760|85004|31953;2|201174|1760|85004;2|32066|203490|203491;2|32066,Complete,Fatima Zohra
Study 248,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D , Meiring TL",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,Experiment 1,South Africa,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,low risk hpv,high risk hpv,High risk HPV infection confirmed through HPV genotyping test,57,30,NA,16S,34,Illumina,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,figure 4,15 April 2020,Cynthia Anderson,WikiWorks743,Potential biomarkers for high-risk HPV by LefSe,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae",2|1224|1236|135625;2|1224|1236|135625|712;2|1224|1236|135625|712|724;2|1224|28211;2|1224|1236;2|1224|1236|72274;2|1224|28211|356|69277|28100;2|1224|28211|356;2|1224|28211|356|69277,Complete,Fatima Zohra
Study 248,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D , Meiring TL",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,Experiment 2,South Africa,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,no HPV,HPV,HPV infection confirmed through HPV genotyping test,50,37,NA,16S,34,Illumina,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,supplemental figure 2,17 April 2020,Cynthia Anderson,WikiWorks743,Potential biomarkers for HPV by LefSe.,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|1224|28211;2|1224|28211|766;2|201174|1760;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|2701,Complete,Fatima Zohra
Study 248,"cross-sectional observational, not case-control",30986570,10.1016/j.pvr.2019.04.006,NA,"Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D , Meiring TL",The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection,"Papillomavirus research (Amsterdam, Netherlands)",2019,Experiment 2,South Africa,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,no HPV,HPV,HPV infection confirmed through HPV genotyping test,50,37,NA,16S,34,Illumina,LEfSe,0.2,TRUE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,supplemental figure 2,17 April 2020,Cynthia Anderson,WikiWorks743,Potential biomarkers for HPV by LefSe.,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas veronii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales",2|1224|1236;2|1224|1236|135625;2|1224|1236|135625|712;2|1224|1236|72274;2|1224|29547|213849;2|1224|29547;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|76761;2|1224|1236|72274|135621|351;2|1224|28211|356;2|1224|28211|356|69277;2|1224|28211|356|69277|28100;2|1224|28211|204458|76892;2|1224|28211|204458,Complete,Fatima Zohra
Study 249,case-control,29083504,10.1002/hep.29623,NA,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,Experiment 1,United States of America,Homo sapiens,blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,"NAC",alcoholics,alcoholic hepatitis,20,56,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 2B,15 April 2020,Fatima Zohra,WikiWorks743,Differential group taxonomic features for non-alcohol consuming controls (NAC) and combined alcoholic group,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerocolumna,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae|g__Bradyrhizobium",2|201174|1760|85006|85023|33882;2|1239|186801|186802|186803|1843210;2|1224|28211|356|41294|374,Complete,NA
Study 249,case-control,29083504,10.1002/hep.29623,NA,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,Experiment 1,United States of America,Homo sapiens,blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,"NAC",alcoholics,alcoholic hepatitis,20,56,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 2B,15 April 2020,Fatima Zohra,WikiWorks743,Differential group taxonomic features for non-alcohol consuming controls (NAC) and combined alcoholic group,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis|g__Thermicanus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Hydrogenophaga,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Schlegelella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas",2|201174|1760|85007|85026|2053;2|201174|1760|85009|85015|1839;2|201174|1760|85009|85015|53387;2|201174|1760|85004|31953|1678;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838;2|976|200643|171549|171550|239759;2|976|117743|200644|49546|237;2|1239|91061|1385|186817|182709;2|1239|91061|1385|539003|94008;2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|1263;2|1224|28211|356|119045|186650;2|1224|28211|204455|31989|265;2|1224|28211|766|775|780;2|1224|28216|80840|114248;2|1224|28216|80840|80864|12916;2|1224|28216|80840|80864|47420;2|1224|28216|80840|80864|215579;2|1224|28216|80840|75682|29580;2|1224|2008785|119069|206349|70774;2|1224|1236|135624|84642|642,Complete,NA
Study 249,case-control,29083504,10.1002/hep.29623,NA,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,Experiment 2,United States of America,Homo sapiens,blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,"NAC",HDC,alcoholic hepatitis,20,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 3C,15 April 2020,Fatima Zohra,WikiWorks743,differential group taxonomic features for non-alcohol consuming controls (NAC) and heavy drinking control (HDC),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae|g__Bradyrhizobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Rhodobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|201174|1760|85006|85023|33882;2|201174|1760|85006|1268|57493;2|201174|1760|85011|2062|1883;2|976|117743|200644|2762318|59732;2|1239|1737404|1737405|1570339|165779;2|32066|203490|203491|1129771;2|1224|28211|204458|76892|20;2|1224|28211|356|41294|374;2|1224|28211|204455|31989|1060;2|1224|28216|206351|481|482;2|1224|1236|2887326|468|469,Complete,NA
Study 249,case-control,29083504,10.1002/hep.29623,NA,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,Experiment 2,United States of America,Homo sapiens,blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,"NAC",HDC,alcoholic hepatitis,20,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 3C,15 April 2020,Fatima Zohra,WikiWorks743,differential group taxonomic features for non-alcohol consuming controls (NAC) and heavy drinking control (HDC),decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",2|201174|1760|85007|85026|2053;2|201174|1760|85009|85015|1839;2|201174|1760|85004|31953|1678;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|976|200643|171549|171551;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|976|117743|200644|49546|237;2|1239|91061|186826|1300|1301;2|1239|186801|186802|31979|1485;2|1224|28216|80840|114248;2|1224|28216|80840|80864|12916;2|1224|2008785|119069|206349|70774;2|1224|1236|72274|135621|351,Complete,NA
Study 249,case-control,29083504,10.1002/hep.29623,NA,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,Experiment 3,United States of America,Homo sapiens,blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,"NAC",MAH,alcoholic hepatitis,20,18,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 3C,15 April 2020,Fatima Zohra,WikiWorks743,differential group taxonomic features for non-alcohol consuming controls (NAC) and moderate alcoholic hepatitis(MAH),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae|g__Bradyrhizobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Curvibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|201174|1760|2037|2049|1654;2|976|117743|200644|2762318|501783;2|1239|91061|186826|186828;2|1239|91061|186826|186828|117563;2|1239|1737404|1737405|1570339|165779;2|1224|28211|356|41294|374;2|1224|28211|356|119045|407;2|1224|28216|80840|80864|281915;2|1224|1236|2887326|468|469,Complete,NA
Study 249,case-control,29083504,10.1002/hep.29623,NA,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,Experiment 3,United States of America,Homo sapiens,blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,"NAC",MAH,alcoholic hepatitis,20,18,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 3C,15 April 2020,Fatima Zohra,WikiWorks743,differential group taxonomic features for non-alcohol consuming controls (NAC) and moderate alcoholic hepatitis(MAH),decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Friedmanniella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",2|201174|1760|85009|85015|1839;2|201174|1760|85009|85015|53387;2|201174|1760|2037;2|976|200643|171549;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|976|117743|200644|49546|237;2|1239|91061|1385|186817|1386;2|1239|186801|186802|31979|1485;2|1224|28211|204457|41297;2|1224|28216|80840|75682|29580;2|1224|28216|80840;2|1224|2008785|119069|206349|70774;2|1224|1236|135624|84642;2|1224|1236|72274|135621|351,Complete,NA
Study 249,case-control,29083504,10.1002/hep.29623,NA,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,Experiment 4,United States of America,Homo sapiens,blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,"NAC",SAH,alcoholic hepatitis,20,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,figure 3C,15 April 2020,Fatima Zohra,WikiWorks743,differential group taxonomic features for non-alcohol consuming controls (NAC) and severe alcoholic hepatitis(SAH),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Gillisia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus",2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653|1716;2|201174|1760|85006|85020|43668;2|201174|1760|85006|85023|33882;2|201174|1760|85008|28056;2|976|117743|200644|49546|244698;2|1239|91061|186826|186828|1651,Complete,NA
Study 249,case-control,29083504,10.1002/hep.29623,NA,"Puri P, Liangpunsakul S, Christensen JE, Shah VH, Kamath PS, Gores GJ, Walker S, Comerford M, Katz B, Borst A, Yu Q, Kumar DP, Mirshahi F, Radaeva S, Chalasani NP, Crabb DW , Sanyal AJ",The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis,"Hepatology (Baltimore, Md.)",2018,Experiment 4,United States of America,Homo sapiens,blood,UBERON:0000178,"Hepatitis, Alcoholic",EFO:1001345,"NAC",SAH,alcoholic hepatitis,20,19,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,figure 3C,15 April 2020,Fatima Zohra,WikiWorks743,differential group taxonomic features for non-alcohol consuming controls (NAC) and severe alcoholic hepatitis(SAH),decreased,"k__Bacteria|p__Actinobacteria|c__Acidimicrobiia|o__Acidimicrobiales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Cytophagaceae",2|201174|84992|84993;2|201174|1760|85006|85023;2|201174|1760|85009|85015|1839;2|201174|1760|2037;2|201174|1760|85004|31953|1678;2|976|200643|171549;2|976|200643|171549|2005519|397864;2|976|200643|171549|171551;2|976|200643|171549|171552;2|976|200643|171549|171550|239759;2|976|117743|200644|49546|237;2|976|1853228|1853229|563835;2|976|768503|768507|89373,Complete,NA
Study 250,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL , Wallen GR",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,Experiment 1,United States of America,Homo sapiens,tongue,UBERON:0001723,severe aplastic anemia,EFO:0006927,baseline,hematopoietic stem cell transplantation engraftment,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,2345678,Ion Torrent,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,15 April 2020,Shaimaa Elsafoury,WikiWorks743,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola",2|201174|1760|85006|1268|32207|43675;2|976|200643|171549|171552|838|28129,Complete,NA
Study 250,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL , Wallen GR",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,Experiment 2,United States of America,Homo sapiens,tongue,UBERON:0001723,severe aplastic anemia,EFO:0006927,baseline,hematopoietic stem cell transplantation engraftment,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,3456789,Ion Torrent,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,15 April 2020,Shaimaa Elsafoury,WikiWorks743,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis",2|1224|1236|135625|712|724|729;2|201174|1760|2037|2049|1654|114702;2|1239|91061|1385|1378|84135;2|1239|186801|186802|186803|265975|237576;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838|425941,Complete,NA
Study 250,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL , Wallen GR",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,Experiment 3,United States of America,Homo sapiens,tongue,UBERON:0001723,severe aplastic anemia,EFO:0006927,engraftment,hematopoietic stem cell transplantation 100 days after the transplant,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,2345678,Ion Torrent,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,15 April 2020,Shaimaa Elsafoury,WikiWorks743,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella sanguinis",2|1224|1236|135625|712|724|729;2|1239|91061|1385|1378|84135,Complete,NA
Study 250,time series / longitudinal observational,30919073,10.1007/s00277-019-03599-w,NA,"Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL , Wallen GR",The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study,Annals of hematology,2019,Experiment 4,United States of America,Homo sapiens,tongue,UBERON:0001723,severe aplastic anemia,EFO:0006927,engraftment,hematopoietic stem cell transplantation 100 days after the transplant,"In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.",4,4,NA,16S,3456789,Ion Torrent,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 8&7,15 April 2020,Shaimaa Elsafoury,WikiWorks743,Statistically significant bacteria as determined by Lefse analysis for (a) hematopoietic stem cell transplantation and (b) immunosuppressive therapy group.,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,2|201174|1760|85006|1268|32207|43675,Complete,NA
Study 251,laboratory experiment,30643289,10.1038/s41591-018-0324-z,NA,"Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E, Belda-Ferre P, Campbell E, Aitoro R, Nocerino R, Paparo L, Andrade J, Antonopoulos DA, Berni Canani R , Nagler CR",Healthy infants harbor intestinal bacteria that protect against food allergy,Nature medicine,2019,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,healthy control,cows milk allergy,cows milk allergy,8,9,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Figure 2e,16 April 2020,Lucy Mellor,WikiWorks743,LEfSe analysis of genera that are significantly enriched in healthy-colonized mice or cow milk allergy-colonized mice,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239|91061|186826|81852|1350;2|976|200643|171549|2005519;2|1239|186801|186802|216572|1263;2|1239|186801|186802|541000;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|31979;2|1239|186801|186802;2|1239|186801|186802|186803|572511;2|976|200643|171549|2005525|375288,Complete,NA
Study 251,laboratory experiment,30643289,10.1038/s41591-018-0324-z,NA,"Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E, Belda-Ferre P, Campbell E, Aitoro R, Nocerino R, Paparo L, Andrade J, Antonopoulos DA, Berni Canani R , Nagler CR",Healthy infants harbor intestinal bacteria that protect against food allergy,Nature medicine,2019,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,healthy control,cows milk allergy,cows milk allergy,8,9,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,Figure 2e,16 April 2020,Lucy Mellor,WikiWorks743,LEfSe analysis of genera that are significantly enriched in healthy-colonized mice or cow milk allergy-colonized mice,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella",2|1239|186801|186802|186803;2|1239|526524|526525|128827;2|1224|1236|91347|543;2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|590,Complete,NA
Study 252,case-control,31211854,10.1111/sji.12799,NA,"Huang S, Mao J, Zhou L, Xiong X , Deng Y",The imbalance of gut microbiota and its correlation with plasma inflammatory cytokines in pemphigus vulgaris patients,Scandinavian journal of immunology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,pemphigus vulgaris,EFO:0004719,healthy control,pemphigus vulgaris,pemphigus vulgaris,14,18,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 2b,17 April 2020,Lucy Mellor,"WikiWorks743,Chloe",Bacterial taxa difference between pemphigus vulgaris (PV) patients and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827;2|1239|91061;2|1239|91061|186826|186828;2|1239|526524|526525|2810280|100883;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|186801|186802|216572|946234;2|1224|1236;2|1239|91061|186826|186828|117563;2|1239|91061|186826;2|1239|91061|186826|1300;2|1224|1236|91347|543|1940338,Complete,Chloe
Study 252,case-control,31211854,10.1111/sji.12799,NA,"Huang S, Mao J, Zhou L, Xiong X , Deng Y",The imbalance of gut microbiota and its correlation with plasma inflammatory cytokines in pemphigus vulgaris patients,Scandinavian journal of immunology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,pemphigus vulgaris,EFO:0004719,healthy control,pemphigus vulgaris,pemphigus vulgaris,14,18,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 2b,17 April 2020,Lucy Mellor,WikiWorks743,Bacterial taxa difference between pemphigus vulgaris (PV) patients and healthy controls,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales",2|201174|84998|84999|84107|102106;2|1239|186801|186802|186803|33042;2|1224|28211;2|1224|28216;2|1224|28216|80840,Complete,Chloe
Study 253,case-control,29052232,10.1111/all.13331,NA,"Kim BS, Lee E, Lee MJ, Kang MJ, Yoon J, Cho HJ, Park J, Won S, Lee SY , Hong SJ",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,Experiment 1,South Korea,Homo sapiens,nasopharynx,UBERON:0001728,asthma,MONDO:0004979,healthy control,asthma,asthma,31,31,3 months,16S,123,Roche454,Dunn's test,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2,17 April 2020,Lucy Mellor,WikiWorks743,Relative abundance of bacterial genera in patients with asthma and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|91061|1385|90964|1279;2|976|200643|171549|171552|838,Complete,NA
Study 253,case-control,29052232,10.1111/all.13331,NA,"Kim BS, Lee E, Lee MJ, Kang MJ, Yoon J, Cho HJ, Park J, Won S, Lee SY , Hong SJ",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,Experiment 1,South Korea,Homo sapiens,nasopharynx,UBERON:0001728,asthma,MONDO:0004979,healthy control,asthma,asthma,31,31,3 months,16S,123,Roche454,Dunn's test,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,17 April 2020,Lucy Mellor,WikiWorks743,Relative abundance of bacterial genera in patients with asthma and healthy controls,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,NA
Study 253,case-control,29052232,10.1111/all.13331,NA,"Kim BS, Lee E, Lee MJ, Kang MJ, Yoon J, Cho HJ, Park J, Won S, Lee SY , Hong SJ",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,Experiment 2,South Korea,Homo sapiens,nasopharynx,UBERON:0001728,asthma,MONDO:0004979,healthy control,asthma remission,asthma remission,31,30,3 months,16S,123,Roche454,Dunn's test,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2,17 April 2020,Lucy Mellor,WikiWorks743,Relative abundance of bacterial genera in patients with asthma remission and healthy controls,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|543311,Complete,NA
Study 253,case-control,29052232,10.1111/all.13331,NA,"Kim BS, Lee E, Lee MJ, Kang MJ, Yoon J, Cho HJ, Park J, Won S, Lee SY , Hong SJ",Different functional genes of upper airway microbiome associated with natural course of childhood asthma,Allergy,2018,Experiment 2,South Korea,Homo sapiens,nasopharynx,UBERON:0001728,asthma,MONDO:0004979,healthy control,asthma remission,asthma remission,31,30,3 months,16S,123,Roche454,Dunn's test,0.1,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,17 April 2020,Lucy Mellor,WikiWorks743,Relative abundance of bacterial genera in patients with asthma remission and healthy controls,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,NA
Study 254,case-control,27115405,10.1007/s00240-016-0882-9,NA,"Stern JM, Moazami S, Qiu Y, Kurland I, Chen Z, Agalliu I, Burk R , Davies KP",Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers,Urolithiasis,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,"nephrolithiasis,urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone patient,kidney stone,6,23,2 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b,17 April 2020,Rimsha Azhar,WikiWorks743,The composition of the microbiota between kidney stone formers and non-stone forming controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|976|200643|171549|815|816;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550|239759,Complete,NA
Study 254,case-control,27115405,10.1007/s00240-016-0882-9,NA,"Stern JM, Moazami S, Qiu Y, Kurland I, Chen Z, Agalliu I, Burk R , Davies KP",Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers,Urolithiasis,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,"nephrolithiasis,urolithiasis","EFO:0004253,MONDO:0024647",healthy control,kidney stone patient,kidney stone,6,23,2 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2b,17 April 2020,Rimsha Azhar,WikiWorks743,The composition of the microbiota between kidney stone formers and non-stone forming controls,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|201174|1760|2037|2049|184869;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289,Complete,NA
Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,Experiment 1,United Republic of Tanzania,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,23,45,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,figure 6a,21 April 2020,Cynthia Anderson,WikiWorks743,LEfSe linear discriminant analysis (LDA) scores between unmatched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Tenericutes,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1224|1236|72274|135621|351;2|1239|91061|1385|90964|1279;2|1224|1236|72274;2|544448;2|544448|31969|2085;2|1239|91061|1385|90964,Complete,Fatima Zohra
Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,Experiment 1,United Republic of Tanzania,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,23,45,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,figure 6a,21 April 2020,Cynthia Anderson,WikiWorks743,LEfSe linear discriminant analysis (LDA) scores between unmatched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",2|1224|1236;2|1239|1737404|1737405|1570339|150022,Complete,Fatima Zohra
Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,Experiment 2,United Republic of Tanzania,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,4,4,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,figure 6b,1 May 2020,Cynthia Anderson,WikiWorks743,LEfSe linear discriminant analysis (LDA) scores between matched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Tenericutes,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales",2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|543311;2|544448;2|544448|31969;2|544448|31969|2085,Complete,Fatima Zohra
Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,Experiment 2,United Republic of Tanzania,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,negative for intraepithelial lesion or malignancy,high-grade squamous intraepithelial lesions,high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear,4,4,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,age,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,figure 6b,1 May 2020,Cynthia Anderson,WikiWorks743,LEfSe linear discriminant analysis (LDA) scores between matched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM),decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578|147802;2|1239|91061;2|1239|91061|186826;2|1239|1737404|1737405|1570339|150022,Complete,Fatima Zohra
Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,Experiment 3,United Republic of Tanzania,Homo sapiens,uterine cervix,UBERON:0000002,HIV infection,EFO:0000764,HIV-,HIV+,HIV+ comfirmed by Standard Diagnostics HIV-1/2 3.0 detection kit,95,39,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,figure 6c,3 May 2020,Cynthia Anderson,WikiWorks743,LEfSe linear discriminant analysis (LDA) scores.,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Tenericutes,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae",2|1239;2|1239|91061|1385|186817|1386;2|1224|1236|135625|712|724|727;2|1239|186801;2|1239|186801|186802|186804;2|1239|186801|186802|186804|1257;2|1239|186801|186802|186804|1257|1261;2|1239|91061|1385|1378;2|1239|91061|186826|186827|1375;2|1239|91061|186826|186828|117563;2|1239|91061|186826|186828;2|544448;2|544448|31969;2|544448|31969|2085|2092;2|544448|31969|2085;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301;2|1239|91061|1385|90964|1279;2|1224|28211|356|82115;2|201174|1760|2037;2|201174|1760|2037|2049;2|1239|909932|1843488|909930|904;2|1239|186801|186802|186803|437755;2|1224|28211;2|201174|1760|85004|31953,Complete,Fatima Zohra
Study 255,case-control,30782659,10.1128/mBio.02785-18,NA,"Klein C, Gonzalez D, Samwel K, Kahesa C, Mwaiselage J, Aluthge N, Fernando S, West JT, Wood C , Angeletti PC","Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions",mBio,2019,Experiment 3,United Republic of Tanzania,Homo sapiens,uterine cervix,UBERON:0000002,HIV infection,EFO:0000764,HIV-,HIV+,HIV+ comfirmed by Standard Diagnostics HIV-1/2 3.0 detection kit,95,39,NA,16S,4,Illumina,LEfSe,0.1,TRUE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 2,figure 6c,3 May 2020,Cynthia Anderson,WikiWorks743,LEfSe linear discriminant analysis (LDA) scores.,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|2037|2049|28263;2|544448|31969|2085|2092|2129;2|1239|91061|186826|33958|2742598|1598;2|201174|1760;2|201174|1760|85004;2|201174|1760|85004|31953|1678,Complete,Fatima Zohra
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal tissues,peritumoral tissues,gastric cancer,230,247,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 1,"Figure 2a, 2c, 2f",20 April 2020,Rimsha Azhar,WikiWorks743,Comparison of the relative abundance of dominant bacterial taxa at different levels,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Hyphomicrobiaceae|g__Aquabacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|1224;2|1224|29547|213849|72293;2|1224|1236|135619|28256;2|1239|91061|186826|1300;2|1239|909932|1843489|31977;2|1224|1236|135622|267890;2|1239|91061|186826|33958;2|1239|186801|186802|186804;2|1224|29547|213849|72293|209;2|1224|1236|135619|28256|2745;2|1239|91061|186826|1300|1301;2|1224|1236|135622|267890|22;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|29465;2|1224|28211|356|119045|407;2|1239|186801|186802|186804|1257;2|1239|909932|909929|1843491|970;2|1224|28211|356|45401|45402;2|976|200643|171549|815|816|817;2|74201|203494|48461|1647988|239934|239935,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal tissues,peritumoral tissues,gastric cancer,230,247,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 2,"Figure 2a, 2c, 2f",20 April 2020,Rimsha Azhar,WikiWorks743,Comparison of the relative abundance of dominant bacterial taxa at different levels,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Acidobacteria,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Chloroflexi,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus",2|1239;2|976;2|57723;2|32066;2|200795;2|1239|186801|186802|541000;2|1224|1236|91347|543;2|976|200643|171549|171552;2|1224|28211|204457|41297;2|976|200643|171549|815;2|1239|91061|1385|186817;2|976|200643|171549|171551;2|976|200643|171549|171552|838;2|1224|28211|204457|41297|13687;2|1239|186801|186802|216572|216851;2|1224|1236|72274|135621|286;2|976|200643|171549|815|816;2|1239|91061|1385|186817|1386;2|32066|203490|203491|203492|848;2|201174|1760|85009|31957|1743;2|201174|1760|85007|1653|1716;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838|165179;2|1239|91061|1385|186817|1386|1396,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 2,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,peritumoral tissues,tumoral tissues,gastric cancer,247,229,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,increased,NA,unchanged,Signature 1,"Figure 2a, 2c, 2f",20 April 2020,Rimsha Azhar,WikiWorks743,Comparison of the relative abundance of dominant bacterial taxa at different levels,increased,"k__Bacteria|p__Acidobacteria,k__Bacteria|p__Chloroflexi,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus",2|57723;2|200795;2|1224|1236|91347|543;2|976|200643|171549|171552;2|1239|186801|186802|186803;2|1224|1236|72274|135621|351;2|976|200643|171549|171552|838;2|1224|1236|72274|135621|286;2|1239|91061|1385|186817|1386;2|976|200643|171549|171552|838|28132;2|1239|91061|186826|1300|1301|1328;2|201174|1760|85009|31957|1743;2|1239|91061|1385|186817|1386|1396,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 2,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,peritumoral tissues,tumoral tissues,gastric cancer,247,229,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,increased,decreased,increased,NA,unchanged,Signature 2,"Figure 2a, 2c, 2f",20 April 2020,Rimsha Azhar,WikiWorks743,Comparison of the relative abundance of dominant bacterial taxa at different levels,decreased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori",2|1224;2|1224|1236|135619|28256;2|1239|186801|186802|541000;2|976|117747|200666|84566;2|1224|1236|135622|267890;2|976|200643|171549|171551;2|1224|1236|135619|28256|2745;2|1224|1236|135622|267890|22;2|1224|28211|204457|41297|13687;2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1224|29547|213849|72293|209|210,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 3,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal tissues,tumoral tissues,gastric cancer,230,229,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 1,"Figure 2a, 2c, 2f",20 April 2020,Rimsha Azhar,WikiWorks743,Comparison of the relative abundance of dominant bacterial taxa at different levels,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|1239;2|201174;2|32066;2|1239|909932|1843489|31977;2|1239|186801|186802|186803;2|1224|1236|135622|267890;2|1239|186801|186802|186804;2|1224|1236|135619|28256|2745;2|1239|91061|186826|1300|1301;2|1224|1236|135622|267890|22;2|1239|91061|186826|33958|1578;2|1239|91061|1385|186817|1386;2|1239|909932|909929|1843491|970;2|32066|203490|203491|203492|848;2|201174|1760|85009|31957|1743;2|201174|1760|85007|1653|1716;2|976|200643|171549|171552|838|28132;2|1239|91061|186826|1300|1301|1328;2|201174|1760|85009|31957|1912216|1747;2|74201|203494|48461|1647988|239934|239935,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 3,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal tissues,tumoral tissues,gastric cancer,230,229,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,decreased,Signature 2,"Figure 2a, 2c, 2f",20 April 2020,Rimsha Azhar,WikiWorks743,Comparison of the relative abundance of dominant bacterial taxa at different levels,decreased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter pylori,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis",2|1224;2|1224|29547|213849|72293;2|1224|1236|72274|135621|351;2|976|200643|171549|815;2|1224|29547|213849|72293|209;2|1224|28211|204457|41297|13687;2|1224|1236|72274|135621|286;2|976|200643|171549|815|816;2|1224|29547|213849|72293|209|210;2|976|200643|171549|171552|838|165179;2|976|200643|171549|815|816|820,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 4,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,early stage normal,early stage tumor,gastric cancer,112,116,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",15 May 2020,Rimsha Azhar,WikiWorks743,Early-stage and late-stage gastric microbiota in the three stomach microhabitats,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|1300|1301|1328,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 4,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,early stage normal,early stage tumor,gastric cancer,112,116,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,unchanged,decreased,unchanged,NA,NA,Signature 2,"Figure 4k, 4l, 4m, 4n",15 May 2020,Rimsha Azhar,WikiWorks743,Early-stage and late-stage gastric microbiota in the three stomach microhabitats,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae",2|976|200643|171549|171552|838|165179;2|1224|28211|204457|41297|13687|172044,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 5,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,early stage normal,early stage peritumor,gastric cancer,112,118,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",15 May 2020,Rimsha Azhar,WikiWorks743,Early-stage and late-stage gastric microbiota in the three stomach microhabitats,decreased,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae,2|1224|28211|204457|41297|13687|172044,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 6,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,late stage normal,late stage tumor,gastric cancer,118,113,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",15 May 2020,Rimsha Azhar,WikiWorks743,Early-stage and late-stage gastric microbiota in the three stomach microhabitats,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|186826|1300|1301|1328,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 7,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,late stage normal,late stage tumor,gastric cancer,118,118,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,unchanged,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",15 May 2020,Rimsha Azhar,WikiWorks743,Early-stage and late-stage gastric microbiota in the three stomach microhabitats,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae",2|976|200643|171549|171552|838|165179;2|1224|28211|204457|41297|13687|172044,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 8,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,late stage normal,late stage peritumor,gastric cancer,118,129,1 month,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,"age,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 4k, 4l, 4m, 4n",15 May 2020,Rimsha Azhar,WikiWorks743,Early-stage and late-stage gastric microbiota in the three stomach microhabitats,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,2|976|200643|171549|171552|838|165179,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 9,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal HP-,normal HP+,gastric cancer,NA,NA,1 month,16S,34,Illumina,LEfSe,NA,TRUE,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,NA,Signature 1,"Figure 5l, Supp FigS9",15 May 2020,Rimsha Azhar,WikiWorks743,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria",2|1224|28216|80840;2|1224|28216|80840|75682|149698;2|1224|28216|80840|75682;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85007|1653|1716;2|201174|1760|85007|1653;2|201174|1760|2037|2049;2|201174|1760|2037|2049|1654;2|1224|28211|356|119045|407;2|1224|28211|356|119045;2|1239|186801|186802|186803;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|1224|28211|204457|41297;2|1224|28211;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|29547|213849|72293;2|1224|29547|213849|72293|209;2|1224|29547|213849;2|1224|29547;2|1224,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 9,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,normal HP-,normal HP+,gastric cancer,NA,NA,1 month,16S,34,Illumina,LEfSe,NA,TRUE,2,NA,"age,sex",NA,decreased,decreased,decreased,NA,NA,Signature 2,"Figure 5l, Supp FigS9",15 May 2020,Rimsha Azhar,WikiWorks743,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales",2|1239;2|1239|186801;2|1239|186801|186802|216572|1263;2|1239|909932|1843489|31977|39948;2|1239|186801|186802;2|1239|186801|186802|204475;2|1239|186801|186802|541000;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|216851;2|1224|1236|135619;2|1224|1236|135619|28256|2745;2|1224|1236|135619|28256;2|1224|28216;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|909932|1843488|909930;2|1239|909932|1843488|909930|33024;2|1224|1236|135622|267890;2|1224|1236|135622|267890|22;2|1224|1236|135622,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 10,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,peritumor HP-,peritumor HP+,gastric cancer,NA,NA,1 month,16S,34,Illumina,LEfSe,NA,TRUE,2,NA,"age,sex",NA,decreased,unchanged,decreased,NA,NA,Signature 1,Figure S10,15 May 2020,Rimsha Azhar,WikiWorks743,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria",2|1239|91061|1385|1378;2|1239|91061|1385;2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1224;2|1224|29547|213849|72293;2|1224|29547|213849|72293|209;2|1224|29547|213849;2|1224|29547,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 10,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,peritumor HP-,peritumor HP+,gastric cancer,NA,NA,1 month,16S,34,Illumina,LEfSe,NA,TRUE,2,NA,"age,sex",NA,decreased,unchanged,decreased,NA,NA,Signature 2,Figure S10,15 May 2020,Rimsha Azhar,WikiWorks743,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239|186801;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930;2|1239|186801|186802;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|216851;2|976|200643|171549|171550|239759;2|976|200643|171549|171550;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|541000;2|1239|186801|186802|204475;2|1239|909932|909929|1843491|158846;2|1239|91061|1385|186817|1386;2|1239|91061|186826;2|976|200643|171549|2005525|375288,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 11,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,tumor HP-,tumor HP+,gastric cancer,NA,NA,1 month,16S,34,Illumina,LEfSe,NA,TRUE,2,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure S11,29 May 2020,Rimsha Azhar,WikiWorks743,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Novosphingobium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria",2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224|28211|204458;2|1224|28211|204458|76892;2|1224|28211|204458|76892|41275;2|1224|28211|356;2|1224|28211;2|1239|186801|186802|186803|572511;2|1224|28216|80840;2|1224|28216|80840|75682|149698;2|1224|28211|204457;2|976|117747|200666|84566;2|1224|28211|204457|41297|165696;2|1224|29547|213849|72293;2|1224|29547|213849|72293|209;2|1224|29547|213849;2|1224|29547,Complete,NA
Study 256,case-control,30584008,10.1016/j.ebiom.2018.12.034,NA,"Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L , Ling Z",Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer,EBioMedicine,2019,Experiment 11,China,Homo sapiens,stomach,UBERON:0000945,gastric cancer,MONDO:0001056,tumor HP-,tumor HP+,gastric cancer,NA,NA,1 month,16S,34,Illumina,LEfSe,NA,TRUE,2,NA,"age,sex",NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure S11,29 May 2020,Rimsha Azhar,WikiWorks743,Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Proteobacteria",2|1224|1236|2887326|468|469;2|1224|1236|2887326|468;2|1239|186801|186802|216572|1263;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|351;2|1224|1236|72274;2|1224|28216;2|1224|28211|356|118882;2|1224|28211|204457|41297|13687;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953;2|1224,Complete,NA
Study 257,case-control,29687353,10.1007/s00430-018-0542-5,NA,"Allali I, Boukhatem N, Bouguenouch L, Hardi H, Boudouaya HA, Cadenas MB, Ouldim K, Amzazi S, Azcarate-Peril MA , Ghazal H",Gut microbiome of Moroccan colorectal cancer patients,Medical microbiology and immunology,2018,Experiment 1,Morocco,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy control,colorectal cancer,colorectal cancer,12,11,3 months,16S,12,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region","body mass index,family history of cancer,sex",NA,NA,NA,NA,NA,unchanged,Signature 1,Table 2 and text,21 April 2020,Lora Kasselman,WikiWorks743,"Comparison of bacterial genera significantly (Steel Dwass All Pairs, p values < 0.05) over- or underrepresented in CRC versus controls",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|976|200643|171549|1853231|574697;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551|836;2|1239|186801|186802|990719|990721;2|1239|186801|186802|990719;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979;2|1239|186801|186802|186807|51514;2|1239|186801|186802|186803;2|1239|186801|186802|186804|1257;2|1239|186801|186802|541000;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263;2|1239|909932|909929|1843491|970;2|32066|203490|203491|203492|848;2|1224|28216|80840|75682|846;2|1224|28221|213115|194924;2|1224|28221|213115|194924|35832;2|74201|203494|48461|1647988|239934,Complete,NA
Study 257,case-control,29687353,10.1007/s00430-018-0542-5,NA,"Allali I, Boukhatem N, Bouguenouch L, Hardi H, Boudouaya HA, Cadenas MB, Ouldim K, Amzazi S, Azcarate-Peril MA , Ghazal H",Gut microbiome of Moroccan colorectal cancer patients,Medical microbiology and immunology,2018,Experiment 1,Morocco,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy control,colorectal cancer,colorectal cancer,12,11,3 months,16S,12,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region","body mass index,family history of cancer,sex",NA,NA,NA,NA,NA,unchanged,Signature 2,Table 2 and text,21 April 2020,Lora Kasselman,WikiWorks743,"Comparison of bacterial genera significantly (Steel Dwass All Pairs, p values < 0.05) over- or underrepresented in CRC versus controls",decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae",2|1239|909932|909929|1843491|158846;2|1224|28211|356|41294,Complete,NA
Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,Experiment 1,"Canada,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy control,carcinoma,carcinoma,30,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Figure 2 and text,21 April 2020,Lora Kasselman,WikiWorks743,LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836;2|1239|186801|186802|186803;2|1224|1236|91347|543,Complete,NA
Study 258,case-control,25104642,10.1158/1940-6207.CAPR-14-0129,NA,"Zackular JP, Rogers MA, Ruffin MT , Schloss PD",The human gut microbiome as a screening tool for colorectal cancer,"Cancer prevention research (Philadelphia, Pa.)",2014,Experiment 1,"Canada,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy control,carcinoma,carcinoma,30,30,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2.5,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 2 and text,21 April 2020,Lora Kasselman,WikiWorks743,LeFSe analysis for healthy vs. carcinoma clinical groups. LDA values are represented for OTUs enriched in healthy and carcinoma clinical groups.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales",2|976|200643|171549|815|816;2|1239|186801|186802|186803;2|1239|186801|186802,Complete,NA
Study 259,randomized controlled trial,29489859,10.1371/journal.pone.0192443,NA,"Glatz M, Jo JH, Kennedy EA, Polley EC, Segre JA, Simpson EL , Kong HH",Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis,PloS one,2018,Experiment 1,United States of America,Homo sapiens,skin of cheek,UBERON:0008803,atopic eczema,EFO:0000274,no emollient use,emollient use,infant randomized to emollient therapy,9,10,during study,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 3b,23 April 2020,Lucy Mellor,WikiWorks743,Relative abundance of Streptococcus salivarius in infants randomized to emollient and control in cheek sample,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,2|1239|91061|186826|1300|1301|1304,Complete,NA
Study 259,randomized controlled trial,29489859,10.1371/journal.pone.0192443,NA,"Glatz M, Jo JH, Kennedy EA, Polley EC, Segre JA, Simpson EL , Kong HH",Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis,PloS one,2018,Experiment 2,United States of America,Homo sapiens,skin of forearm,UBERON:0003403,atopic eczema,EFO:0000274,no emollient use,emollient use,infant randomized to emollient therapy,9,10,during study,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 3b,23 April 2020,Lucy Mellor,WikiWorks743,Relative abundance of Streptococcus salivarius in infants randomized to emollient and control in dorsal forearm sample,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,2|1239|91061|186826|1300|1301|1304,Complete,NA
Study 259,randomized controlled trial,29489859,10.1371/journal.pone.0192443,NA,"Glatz M, Jo JH, Kennedy EA, Polley EC, Segre JA, Simpson EL , Kong HH",Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis,PloS one,2018,Experiment 2,United States of America,Homo sapiens,skin of forearm,UBERON:0003403,atopic eczema,EFO:0000274,no emollient use,emollient use,infant randomized to emollient therapy,9,10,during study,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 3b,23 April 2020,Lucy Mellor,WikiWorks743,Relative abundance of Streptococcus salivarius in infants randomized to emollient and control in volar forearm sample,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,2|1239|91061|186826|1300|1301|1304,Complete,NA
Study 260,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B, Naaber P, Sepp E , Mikelsaar M",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,Experiment 1,"Estonia,Sweden",Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,nonallergic,allergic,child with allergy,35,27,NA,NA,NA,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, text",24 April 2020,Lucy Mellor,WikiWorks743,Relative amounts of aerobic and anaerobic microorganisms in allergic and nonallergic 2-year old children,increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,2|1224|1236|91347,Complete,NA
Study 260,prospective cohort,10202341,10.1046/j.1365-2222.1999.00560.x,NA,"Björkstén B, Naaber P, Sepp E , Mikelsaar M",The intestinal microflora in allergic Estonian and Swedish 2-year-old children,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,1999,Experiment 1,"Estonia,Sweden",Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,nonallergic,allergic,child with allergy,35,27,NA,NA,NA,NA,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, text",24 April 2020,Lucy Mellor,WikiWorks743,Relative amounts of aerobic and anaerobic microorganisms in allergic and nonallergic 2-year old children,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 261,case-control,29434076,10.1620/tjem.244.113,NA,"Hamada S, Masamune A, Nabeshima T , Shimosegawa T",Differences in Gut Microbiota Profiles between Autoimmune Pancreatitis and Chronic Pancreatitis,The Tohoku journal of experimental medicine,2018,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,chronic pancreatitis,EFO:0000342,autoimmune pancreatitis type 1,chronic pancreatitis,autoimmune pancreatitis type 1,8,12,NA,16S,45,Illumina,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",25 April 2020,Rimsha Azhar,WikiWorks743,Proportions of bacterial species in gut microbiota were determined in patients with type 1 autoimmune pancreatitis (AIP) and chronic pancretitis (CP),increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium lacusfryxellense,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis",2|976|200643|171549|815|816|28116;2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|1302;2|1239|186801|186802|31979|1485|205328;2|1239|186801|186802|186803|2719313|460384,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 1,United States of America,Homo sapiens,"bronchus,nose","UBERON:0002185,UBERON:0000004",atopic asthma,EFO:0010638,bronchial brush specimen type,nasal brush,nasal brush specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired bronchial brush (BB) and nasal brush (NB) specimen types,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279;2|1239|91061|186826|186828|1651;2|1224|1236|2887326|468|475,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 1,United States of America,Homo sapiens,"bronchus,nose","UBERON:0002185,UBERON:0000004",atopic asthma,EFO:0010638,bronchial brush specimen type,nasal brush,nasal brush specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired bronchial brush (BB) and nasal brush (NB) specimen types,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|201174|1760|2037|2049|1654;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|32066|203490|203491|1129771|32067,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 2,United States of America,Homo sapiens,"bronchus,mouth","UBERON:0002185,UBERON:0000165",atopic asthma,EFO:0010638,bronchial brush specimen type,oral wash,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 1,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired bronchial brush (BB) and oral wash (OW) specimen types,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|201174|1760|2037|2049|1654;2|1239|91061|186826|1300|1301;2|32066|203490|203491|1129771|32067,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 2,United States of America,Homo sapiens,"bronchus,mouth","UBERON:0002185,UBERON:0000165",atopic asthma,EFO:0010638,bronchial brush specimen type,oral wash,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 2,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired bronchial brush (BB) and oral wash (OW) specimen types,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85007|1653|1716;2|976|200643|171549|171552|838;2|1224|1236|2887326|468|475;2|1239|91061|1385|90964|1279,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 3,United States of America,Homo sapiens,"nose,sputum","UBERON:0000004,UBERON:0007311",atopic asthma,EFO:0010638,nasal brush specimen type,induced sputum,induced sputum specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired nasal brush (NB) and induced sputum (IS) specimen types,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|201174|1760|2037|2049|1654;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|32066|203490|203491|1129771|32067,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 3,United States of America,Homo sapiens,"nose,sputum","UBERON:0000004,UBERON:0007311",atopic asthma,EFO:0010638,nasal brush specimen type,induced sputum,induced sputum specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired nasal brush (NB) and induced sputum (IS) specimen types,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279;2|1239|91061|186826|186828|1651;2|1224|1236|2887326|468|475,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 4,United States of America,Homo sapiens,"nose,mouth","UBERON:0000004,UBERON:0000165",atopic asthma,EFO:0010638,nasal brush specimen type,oral wash,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 1,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired nasal brush (NB) and oral wash (OW) specimen types,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|201174|1760|2037|2049|1654;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|32066|203490|203491|1129771|32067,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 4,United States of America,Homo sapiens,"nose,mouth","UBERON:0000004,UBERON:0000165",atopic asthma,EFO:0010638,nasal brush specimen type,oral wash,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,increased,increased,NA,NA,NA,increased,Signature 2,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired nasal brush (NB) and oral wash (OW) specimen types,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279;2|1239|91061|186826|186828|1651;2|1224|1236|2887326|468|475,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 5,United States of America,Homo sapiens,"sputum,mouth","UBERON:0007311,UBERON:0000165",atopic asthma,EFO:0010638,induced sputum specimen type,oral wash,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired induced sputum (IS) and oral wash (OW) specimen types,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,2|201174|1760|2037|2049|1654,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 5,United States of America,Homo sapiens,"sputum,mouth","UBERON:0007311,UBERON:0000165",atopic asthma,EFO:0010638,induced sputum specimen type,oral wash,oral wash specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired induced sputum (IS) and oral wash (OW) specimen types,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85007|1653|1716;2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 6,United States of America,Homo sapiens,"bronchus,sputum","UBERON:0002185,UBERON:0007311",atopic asthma,EFO:0010638,bronchial brush specimen type,induced sputum,induced sputum specimen type,27,27,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,increased,NA,NA,NA,increased,Signature 1,Figure 3,30 April 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in paired bronchial brush (BB) and induced sputum (IS) specimen types,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1239|91061|186826|1300|1301;2|32066|203490|203491|1129771|32067,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 7,United States of America,Homo sapiens,"bronchus,sputum","UBERON:0002185,UBERON:0007311",atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma,11,22,3 months,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4d, Text",14 May 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in bronchial brush (BB) and induced sputum (IS) specimen types distinct in atopic asthmatics and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1224|28216|206351|481|482;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1224|1236|135625|712|724,Complete,NA
Study 262,prospective cohort,29885665,10.1186/s40168-018-0487-3,NA,"Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV , Boushey HA",Bacterial biogeography of adult airways in atopic asthma,Microbiome,2018,Experiment 7,United States of America,Homo sapiens,"bronchus,sputum","UBERON:0002185,UBERON:0007311",atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma,11,22,3 months,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 4d, Text",14 May 2020,Lucy Mellor,WikiWorks743,Distribution of the relative abundance for most prevalent genera in bronchial brush (BB) and induced sputum (IS) specimen types distinct in atopic asthmatics and healthy controls,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 263,"cross-sectional observational, not case-control",30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,chron's disease,patients with immune-mediated inflammatory disease (IMID),23,20,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,3 May 2020,Fatima Zohra,WikiWorks743,Abundant taxa in IMID microbiota relative to HC,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|84111;2|201174|1760|85006|1268|32207;2|1239;2|1239|186801|186802|186803|572511;2|1239|91061|186826|186828;2|1239|526524|526525|128827|1573536;2|1239|91061|1385|1378;2|1239|186801|186802|186804|1505657;2|1239|91061|186826|1300|1301,Complete,NA
Study 263,"cross-sectional observational, not case-control",30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy controls,chron's disease,patients with immune-mediated inflammatory disease (IMID),23,20,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,3 May 2020,Fatima Zohra,WikiWorks743,Abundant taxa in IMID microbiota relative to HC,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|201174|84998|1643822|1643826|553372;2|201174|84998|84999|84107;2|1239|186801;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803|33042;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|186802|186803|28050;2|1239|186801|186802|543314|86331;2|1239|186801|186802|216572|459786;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186803;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748;2|1239|186801|186802|216572|292632;2|1239|526524|526525|2810281|191303,Complete,NA
Study 263,"cross-sectional observational, not case-control",30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,Experiment 2,Canada,Homo sapiens,feces,UBERON:0001988,ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis,patients with immune-mediated inflammatory disease (IMID),23,19,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,6 May 2020,Fatima Zohra,WikiWorks743,Abundant taxa in IMID microbiota relative to HC,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|1678;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|186806|264995;2|1239|526524|526525|128827|1573536;2|1239|91061|1385|1378;2|1239|91061|186826|1300|1301,Complete,NA
Study 263,"cross-sectional observational, not case-control",30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,Experiment 2,Canada,Homo sapiens,feces,UBERON:0001988,ulcerative colitis,EFO:0000729,healthy controls,ulcerative colitis,patients with immune-mediated inflammatory disease (IMID),23,19,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,6 May 2020,Fatima Zohra,WikiWorks743,Abundant taxa in IMID microbiota relative to HC,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|201174|84998|1643822|1643826|644652;2|1239|186801|186802|204475;2|1239|186801|186802|186803|28050;2|1239|186801|186802|543314|86331;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748,Complete,NA
Study 263,"cross-sectional observational, not case-control",30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,Experiment 3,Canada,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,healthy controls,multiple sceloris,patients with immune-mediated inflammatory disease (IMID),23,19,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,6 May 2020,Fatima Zohra,WikiWorks743,Abundant taxa in IMID microbiota relative to HC,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|186806|264995;2|1239|186801|186802|31979|1485;2|1239|526524|526525|128827|1573536;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303,Complete,NA
Study 263,"cross-sectional observational, not case-control",30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,Experiment 3,Canada,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,healthy controls,multiple sceloris,patients with immune-mediated inflammatory disease (IMID),23,19,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,6 May 2020,Fatima Zohra,WikiWorks743,Abundant taxa in IMID microbiota relative to HC,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Sporobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|186801|186802|31979|580596;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|100132;2|1239|186801|186802|216572|292632,Complete,NA
Study 263,"cross-sectional observational, not case-control",30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,Experiment 4,Canada,Homo sapiens,feces,UBERON:0001988,rheumatoid arthritis,EFO:0000685,healthy controls,arthiritis,patients with immune-mediated inflammatory disease (IMID),23,21,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Table 2,6 May 2020,Fatima Zohra,WikiWorks743,Abundant taxa in IMID microbiota relative to HC,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|1760|2037|2049|1654;2|201174|84998|1643822|1643826|84111;2|201174|1760|85006|1268|32207;2|1239;2|1239|526524|526525|128827|1573536;2|1239|91061|1385|1378;2|1239|91061|186826|1300|1301,Complete,NA
Study 263,"cross-sectional observational, not case-control",30545401,10.1186/s40168-018-0603-4,NA,"Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN , Van Domselaar G",A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?,Microbiome,2018,Experiment 4,Canada,Homo sapiens,feces,UBERON:0001988,rheumatoid arthritis,EFO:0000685,healthy controls,arthiritis,patients with immune-mediated inflammatory disease (IMID),23,21,8 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Table 2,6 May 2020,Fatima Zohra,WikiWorks743,Abundant taxa in IMID microbiota relative to HC,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|186801|186802|186806|264995;2|1239|186801|186802|31979|580596;2|1239|186801|186802|31979|1485;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|204475;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|44748;2|1239|186801|186802|216572|292632,Complete,NA
Study 264,"cross-sectional observational, not case-control",26062721,10.1017/S0950268815000965,NA,"Dareng EO, Ma B, Famooto AO, Adebamowo SN, Offiong RA, Olaniyan O, Dakum PS, Wheeler CM, Fadrosh D, Yang H, Gajer P, Brotman RM, Ravel J , Adebamowo CA",Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women,Epidemiology and infection,2016,Experiment 1,Nigeria,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-/HIV-,HPV+/HIV-,HR-HPV+ confirmed by medical records and HPV genotyping test,99,12,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Fig. 4b,3 May 2020,Cynthia Anderson,WikiWorks743,Identified phylotype biomarkers ranked by effect size in HIV–women,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium|s__Arcanobacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus asaccharolyticus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales",2|1239|1737404|1737405|1570339|165779|1872515;2|1239|909932|1843489|31977|906|2023260;2|201174|1760|2037|2049|28263;2|1239|186801|186802|186804|1257|1261;2|1239|909932|1843489|31977|39948|309120;2|201174|1760|2037|2049|28263|72409;2|1239|186801|186802|186804;2|1239|186801|186802|186804|1257;2|1239|1737404|1737405|1570339|162289|1971214;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|162289|1258;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171552|838|59823;2|1239|909932|1843489|31977|906;2|1239|186801|186802|31979;2|976;2|976|200643;2|976|200643|171549;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|32066;2|32066|203490|203491,Complete,Fatima Zohra
Study 264,"cross-sectional observational, not case-control",26062721,10.1017/S0950268815000965,NA,"Dareng EO, Ma B, Famooto AO, Adebamowo SN, Offiong RA, Olaniyan O, Dakum PS, Wheeler CM, Fadrosh D, Yang H, Gajer P, Brotman RM, Ravel J , Adebamowo CA",Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women,Epidemiology and infection,2016,Experiment 1,Nigeria,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-/HIV-,HPV+/HIV-,HR-HPV+ confirmed by medical records and HPV genotyping test,99,12,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Fig. 4b,3 May 2020,Cynthia Anderson,WikiWorks743,Identified phylotype biomarkers ranked by effect size in HIV–women,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Haloferacales|f__Halorubraceae|g__Halorubrum,k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Haloferacales|f__Halorubraceae|g__Halorubrum|s__Halorubrum sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales",2|1239|91061|186826|33958|1578|147802;2|1224|28211;2|1224|28211|356;2157|28890|183963|1644055|1963271|56688;2157|28890|183963|1644055|1963271|56688|1879286;2|1224|1236|135614,Complete,Fatima Zohra
Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,Experiment 1,Finland,Homo sapiens,mouth,UBERON:0000165,human papilloma virus infection,EFO:0001668,at birth,two months,HPV infection,13,22,NA,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Figure 2D,6 May 2020,Fatima Zohra,WikiWorks743,The effect of age on infant oral microbiota,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268;2|1239|91061|186826|1300;2|1239|909932|1843489|31977|29465|39778;2|201174|1760|85006|1268|32207|43675,Complete,NA
Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,Experiment 1,Finland,Homo sapiens,mouth,UBERON:0000165,human papilloma virus infection,EFO:0001668,at birth,two months,HPV infection,13,22,NA,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Figure 2D,6 May 2020,Fatima Zohra,WikiWorks743,The effect of age on infant oral microbiota,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae",2|1239|91061|186826|33958|1578;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|906;2|1239|91061|1385|90964|1279;2|201174|1760|85009|31957|1743;2|1224|28211|356|82115|357;2|1224|28216|80840|80864|80865;2|1224|1236|72274|135621|286;2|1239|1737404|1737405|1737406,Complete,NA
Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,Experiment 2,Finland,Homo sapiens,mouth,UBERON:0000165,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV infection,21,14,NA,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 5F,6 May 2020,Fatima Zohra,WikiWorks743,Infant oral HPV infection and bacterial microbiota,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma",2|1239|91061|1385|186817|400634;2|544448|31969|2085|2092|2129,Complete,NA
Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,Experiment 2,Finland,Homo sapiens,mouth,UBERON:0000165,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV infection,21,14,NA,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 5F,6 May 2020,Fatima Zohra,WikiWorks743,Infant oral HPV infection and bacterial microbiota,decreased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,NA
Study 265,time series / longitudinal observational,30395655,10.1371/journal.pone.0207016,NA,"Tuominen H, Rautava S, Collado MC, Syrjänen S , Rautava J",HPV infection and bacterial microbiota in breast milk and infant oral mucosa,PloS one,2018,Experiment 3,Finland,Homo sapiens,mouth,UBERON:0000165,human papilloma virus infection,EFO:0001668,HPV- at two months,HPV+,HPV infection,17,5,NA,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,text,6 May 2020,Fatima Zohra,WikiWorks743,effect of age on infant oral HPV infection and bacterial microbiota,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|29465|39778,Complete,NA
Study 266,case-control,27381339,10.4014/jmb.1603.03057,NA,"Ruengsomwong S, La-Ongkham O, Jiang J, Wannissorn B, Nakayama J , Nitisinprasert S","Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk",Journal of microbiology and biotechnology,2016,Experiment 1,Thailand,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,healthy non-vegetarian,healthy vegetarian,healthy vegetarians,36,36,1 month,16S,678,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Fig. 3 and Table1,6 May 2020,Valentina Pineda,WikiWorks743,"Abundance of gut microbiota at the family, genus and species levels detected in both vegetarian and non-vegetarian groups.",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1224|1236|91347|543|570,Complete,NA
Study 266,case-control,27381339,10.4014/jmb.1603.03057,NA,"Ruengsomwong S, La-Ongkham O, Jiang J, Wannissorn B, Nakayama J , Nitisinprasert S","Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk",Journal of microbiology and biotechnology,2016,Experiment 1,Thailand,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,healthy non-vegetarian,healthy vegetarian,healthy vegetarians,36,36,1 month,16S,678,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Fig. 3 and Table1,6 May 2020,Valentina Pineda,WikiWorks743,"Abundance of gut microbiota at the family, genus and species levels detected in both vegetarian and non-vegetarian groups.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia",2|976|200643|171549|171551;2|74201|203494|48461|203557;2|976|200643|171549|171550;2|976|200643|171549|815;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|816;2|976|200643|171549|171550|239759;2|74201|203494|48461|1647988|239934,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 1,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma,21,42,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2a, Supplemental Table S4",25 June 2020,Lucy Mellor,WikiWorks743,Bacterial taxa significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC),increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis|s__Sphingopyxis alaskensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|838;2|203691|203692|136|2845253|157;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|543314|109326;2|976|200643|171549|171551|836;2|1224|29547|213849|72294|194;2|1224|28216|206351|481|32257;2|1224|28211|204457|41297|165697;2|976|200643|171549|171552|1283313|76122;2|1239|909932|1843489|31977|29465|39778;2|203691|203692|136|2845253|157|59892;2|1224|28211|204457|41297|165697|117207;2|976|200643|171549|171552|838|165179;2|1224|28216|206351|481|482|28449;2|1239|91061|186826|33958|1578|147802,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 1,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma,21,42,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2a, Supplemental Table S4",25 June 2020,Lucy Mellor,WikiWorks743,Bacterial taxa significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC),decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria|s__Kocuria palustris,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae",2|1224|28211|356|119045|407;2|1239|186801|186802|186804|1257;2|1239|91061|186826|33958|1578;2|1224|1236|135625|712|713;2|32066|203490|203491|1129771|32067;2|201174|1760|85006|1268|57493|71999;2|1239|91061|186826|33958|2759736|57037,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 2,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic no asthma,21,21,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2b, Supplemental Table S5",25 June 2020,Lucy Mellor,WikiWorks743,Bacterial taxa significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis|s__Sphingopyxis alaskensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae",2|1224|1236|135625|712|416916;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|201174|1760|85007|1653|1716;2|201174|1760|2037|2049|1654;2|1239|909932|909929|1843491|970;2|1224|29547|213849|72293|2353;2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|29465;2|1224|1236|2887326|468|475;2|1239|526524|526525|2810280|519427;2|1224|28211|204457|41297|165697;2|1224|1236|135625|712|416916|739;2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|29465|39778;2|1224|28211|204457|41297|165697|117207;2|976|200643|171549|171552|838|425941;2|203691|203692|136|2845253|157|59892;2|1224|1236|135625|712|724|727,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 2,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic no asthma,21,21,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2b, Supplemental Table S5",25 June 2020,Lucy Mellor,WikiWorks743,Bacterial taxa significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae",2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1224|1236|72274|135621|286;2|1224|29547|213849|72293|209;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|33958|2759736|57037,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 3,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma,21,42,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2c, Supplemental Table S6",25 June 2020,Lucy Mellor,WikiWorks743,Bacterial taxa significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA),increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",2|32066|203490|203491|1129771|32067;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838;2|1239|909932|909929|1843491|970;2|1224|1236|135625|712|724;2|544448|31969|2085|2092|2093;2|1239|909932|1843489|31977|39948;2|1224|28216|206351|481|482|28449;2|976|200643|171549|171552|838|28131,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 3,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma,21,42,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2c, Supplemental Table S6",25 June 2020,Lucy Mellor,WikiWorks743,Bacterial taxa significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA),decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Sharpea,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Flexispira,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium columnare,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingopyxis|s__Sphingopyxis alaskensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae",2|1224|28211|204457|41297|165697;2|1239|526524|526525|2810280|519427;2|1239|91061|186826|33958|1578;2|1239|526524|526525|128827|174708;2|1239|91061|186826|1300|1301;2|976|200643|171549|171551|836;2|1224|29547|213849|72293|2353;2|201174|1760|85007|1653|1716;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|416916|739;2|976|117743|200644|49546|237|996;2|976|200643|171549|171552|838|425941;2|976|200643|171549|815|816|817;2|203691|203692|136|2845253|157|59892;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|724|729;2|976|200643|171549|171552|838|165179;2|976|117743|200644|49546|1016|1018;2|1239|186801|186802|186803|2316020|33038;2|1224|28211|204457|41297|165697|117207;2|1239|91061|186826|33958|2759736|57037,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 4,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,nonresponder,inhaled corticosteroid responder,inhaled corticosteroid (ICS) responder,10,15,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6b,8 May 2020,Lucy Mellor,WikiWorks743,Taxa significantly enriched or depleted in relative abundance in inhaled corticosteroid (ICS) responders verses nonresponders among those with atopic asthma,increased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|526524|526525|128827;2|1224|28216|206351|481;2|1239|909932|1843489|31977;2|1239|186801|186802|186803;2|1224|28211|204457|41297;2|1224|1236|2887326|468;2|1239|186801|186802|186804;2|32066|203490|203491|203492;2|1239|91061|186826|1300,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 4,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,nonresponder,inhaled corticosteroid responder,inhaled corticosteroid (ICS) responder,10,15,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 6b,8 May 2020,Lucy Mellor,WikiWorks743,Taxa significantly enriched or depleted in relative abundance in inhaled corticosteroid (ICS) responders verses nonresponders among those with atopic asthma,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group",2|201174|1760|85006|85023;2|1224|1236|135625|712;2|976|200643|171549|171551;2|203691|203692|136|137;2|976|200643|171549|171552;2|976|117743|200644|49546;2|1239|91061|186826|33958;2|544448|31969|2085|2092;2|1239|91061|186826|186827;2|201174|1760|2037|2049;2|1224|1236|72274|135621|351,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 5,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,baseline,post inhaled corticosteroid treatment,inhaled corticosteroid treatment,8,8,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure 6d",8 May 2020,Lucy Mellor,WikiWorks743,Taxa differentially expressed in asthmatic subjects who responded to treatment after inhaled corticosteroid (ICS) treatment,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae",2|201174|1760|85006|85023;2|1224|28216|206351|481|482;2|1224|1236|2887326|468|475;2|203691|203692|136|137;2|201174|1760|2037|2049;2|544448|31969|2085|2092,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 5,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,baseline,post inhaled corticosteroid treatment,inhaled corticosteroid treatment,8,8,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 6d",8 May 2020,Lucy Mellor,WikiWorks743,Taxa differentially expressed in asthmatic subjects who responded to treatment after inhaled corticosteroid (ICS) treatment,decreased,"k__Bacteria|p__Tenericutes|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|544448|31969|186329|2146;2|1239|91061|186826|33958;2|976|200643|171549|171552;2|1239|186801|186802|186803;2|1239|186801|186802|186804;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|39948,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 6,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,baseline,post placebo treatment,placebo treatment,8,8,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure 6d",8 May 2020,Lucy Mellor,WikiWorks743,Taxa differentially expressed in asthmatic subjects after placebo treatment,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae",2|1224|28216|206351|481|538;2|203691|203692|136|137;2|544448|31969|2085|2092,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 6,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,baseline,post placebo treatment,placebo treatment,8,8,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 6d",8 May 2020,Lucy Mellor,WikiWorks743,Taxa differentially expressed in asthmatic subjects after placebo treatment,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|1224|1236|2887326|468|469;2|201174|1760|2037|2049;2|976|200643|171549|171552;2|1239|186801|186802|186804,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 7,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma,21,42,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure E4a,8 May 2020,Lucy Mellor,WikiWorks743,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC),increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Spirochaetes",2|201174;2|976;2|32066;2|1224;2|203691,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 7,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,healthy control,atopic asthma,atopic asthma,21,42,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure E4a,8 May 2020,Lucy Mellor,WikiWorks743,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC),decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 8,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic no asthma,21,21,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure E4b,8 May 2020,Lucy Mellor,WikiWorks743,Bacterial phylum significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria",2|201174;2|1239;2|1224,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 8,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,healthy control,atopic no asthma,atopic no asthma,21,21,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure E4b,8 May 2020,Lucy Mellor,WikiWorks743,Bacterial phylum significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC),decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Spirochaetes",2|976;2|32066;2|203691,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 9,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma,21,42,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Figure E4c,8 May 2020,Lucy Mellor,WikiWorks743,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA),increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria",2|976;2|32066,Complete,NA
Study 267,prospective cohort,27838347,10.1016/j.jaci.2016.08.055,NA,"Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA , Huang YJ","Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment",The Journal of allergy and clinical immunology,2017,Experiment 9,United States of America,Homo sapiens,bronchus,UBERON:0002185,atopic asthma,EFO:0010638,atopic no asthma,atopic asthma,atopic asthma,21,42,3 months,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Supplemental Figure E4c,8 May 2020,Lucy Mellor,WikiWorks743,Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA),decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Spirochaetes",2|201174;2|1239;2|1224;2|203691,Complete,NA
Study 268,time series / longitudinal observational,29563617,10.1038/s41598-018-23389-0,NA,"Zhang H, Lu J, Lu Y, Cai Q, Liu H , Xu C",Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in china,Scientific reports,2018,Experiment 1,China,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,after loop electrosurgical excision procedure,before,Cervical intraepithelial neoplasia 2/3 patients who underwent Loop electrosurgical excision procedure(LEEP),26,26,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,unchanged,increased,Signature 1,Figure 4,9 May 2020,Cynthia Anderson,WikiWorks743,Histogram of the LDA scores was used to features differentially abundant between LEEP and no LEEP state.,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|201174|1760;2|201174|1760|85004;2|201174|1760|85004|31953;2|976|200643|171549|171552|838|419005;2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|168808;2|201174|1760|85004|31953|2701|2702;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186803;2|201174|1760|85007|1653;2|201174|1760|85007;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186804;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|31979|1485;2|1239|186801|186802|541000;2|1224|28216|80840|119060;2|1239|91061|186826|33958|1578|33959;2|201174|84998|84999|84107|102106,Complete,Fatima Zohra
Study 268,time series / longitudinal observational,29563617,10.1038/s41598-018-23389-0,NA,"Zhang H, Lu J, Lu Y, Cai Q, Liu H , Xu C",Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in china,Scientific reports,2018,Experiment 1,China,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,after loop electrosurgical excision procedure,before,Cervical intraepithelial neoplasia 2/3 patients who underwent Loop electrosurgical excision procedure(LEEP),26,26,6 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,unchanged,increased,Signature 2,Figure 4,9 May 2020,Cynthia Anderson,WikiWorks743,Histogram of the LDA scores was used to features differentially abundant between LEEP and no LEEP state.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli",2|1239|91061|1385|90964|1279;2|1224|1236|2887326|468;2|1239|526524|526525;2|1239|526524;2|1239|526524|526525|128827;2|1224|28216|80840|119060|48736;2|201174|84998|84999;2|201174|84998|84999|84107;2|1239;2|1239|91061,Complete,Fatima Zohra
Study 269,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua LL, Rajasuriar R, Lim YAL, Woo YL, Loke P , Ariffin H","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,Experiment 1,Malaysia,Homo sapiens,feces,UBERON:0001988,leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,10 May 2020,William Lam,WikiWorks743,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients pre-chemotherapy and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",2|976|200643|171549|815|816;2|976|200643|171549|815|816|820;2|976|200643|171549|815|816|817,Complete,NA
Study 269,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua LL, Rajasuriar R, Lim YAL, Woo YL, Loke P , Ariffin H","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,Experiment 1,Malaysia,Homo sapiens,feces,UBERON:0001988,leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,10 May 2020,William Lam,WikiWorks743,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients pre-chemotherapy and healthy controls,decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|1224|29547|213849|72294|194;2|1239|909932|1843489|31977;2|201174|1760|85007|1653|1716;2|201174|1760|85004|31953|1678;2|201174|84998|84999|1643824|1380;2|1239|1737404|1737405|1570339|162289;2|1239|91061|1385|90964|1279;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|165779;2|976|200643|171549|171551|836,Complete,NA
Study 269,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua LL, Rajasuriar R, Lim YAL, Woo YL, Loke P , Ariffin H","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,Experiment 1,Malaysia,Homo sapiens,feces,UBERON:0001988,leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 3b,10 May 2020,William Lam,WikiWorks743,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients post-chemotherapy and healthy controls,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
Study 269,time series / longitudinal observational,32093640,10.1186/s12885-020-6654-5,NA,"Chua LL, Rajasuriar R, Lim YAL, Woo YL, Loke P , Ariffin H","Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy",BMC cancer,2020,Experiment 1,Malaysia,Homo sapiens,feces,UBERON:0001988,leukemia,EFO:0000565,healthy control,Acute Lymphoblastic Leukemia diagnosis and Pre- Chemotherapy treatment,children (ages 2-6 years old) diagnosed with and treated for Acute Lymphoblastic Leukemia,7,7,NA,16S,4,Illumina,DESeq2,0.1,TRUE,NA,ethnic group,NA,NA,NA,NA,NA,NA,NA,Signature 4,Figure 3b,10 May 2020,William Lam,WikiWorks743,Differentially abundant bacteria were identified between Acute Lymphoblastic Leukemia (ALL) patients post-chemotherapy and healthy controls,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|201174|84998|84999|1643824|1380;2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|32066|203490|203491|203492|848;2|201174|1760|85007|1653|1716,Complete,NA
Study 270,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C , Torcia MG",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,Experiment 1,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+  determined through HR-HC2 assay,17,55,3 days,16S,345,Roche454,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,figure 6a,10 May 2020,Cynthia Anderson,WikiWorks743,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|32066|203490|203491|1129771|168808;2|1239|909932|1843489|31977|906;2|1239|91061|186826|33958|1253;2|201174|1760|85006|85019|1696;2|1224|1236|72274|135621|286,Complete,Fatima Zohra
Study 270,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C , Torcia MG",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,Experiment 1,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+  determined through HR-HC2 assay,17,55,3 days,16S,345,Roche454,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,figure 6a,10 May 2020,Cynthia Anderson,WikiWorks743,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Pseudoxanthomonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Candidatus Melainabacteria|o__Vampirovibrionales|g__Vampirovibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges",2|1224|1236|135614|32033|83618;2|201174|1760|2037|2049|1654;2|1798710|2211217|213484;2|1224|1236|2887326|468|222991,Complete,Fatima Zohra
Study 270,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C , Torcia MG",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,Experiment 2,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,human papilloma virus infection,EFO:0001668,HPV+ (clearance),HPV+ (persistance),HR-HPV+ persistence confirmed by HPV genotyping after 1 year,27,28,3 days,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,figure 6b,10 May 2020,Cynthia Anderson,WikiWorks743,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ (clearance) and HPV+ (persistence),increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|201174|84998|84999|1643824|1380;2|1239|186801|186802|216572|216851,Complete,Fatima Zohra
Study 270,prospective cohort,28860468,10.1038/s41598-017-09842-6,NA,"Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C , Torcia MG",Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection,Scientific reports,2017,Experiment 2,Italy,Homo sapiens,Vaginal fluid,UBERON:0036243,human papilloma virus infection,EFO:0001668,HPV+ (clearance),HPV+ (persistance),HR-HPV+ persistence confirmed by HPV genotyping after 1 year,27,28,3 days,16S,345,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,figure 6b,10 May 2020,Cynthia Anderson,WikiWorks743,Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ (clearance) and HPV+ (persistence),decreased,NA,NA,Complete,Fatima Zohra
Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease- (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 1a,16 May 2020,William Lam,WikiWorks743,Linear discriminant analysis (LDA) effect size analysis of microbiota differentially associated with MRD status with subclass of autologous stem cell transplantation (ASCT),increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens|s__Ethanoligenens harbinense,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ethanoligenens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter|s__Sporobacter termitidis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|216572|253238|253239;2|1239|186801|186802|216572|253238;2|1239|186801|186802|216572|44748|44749;2|1239|186801|186802|216572|44748,Complete,NA
Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease- (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,unchanged,NA,Signature 2,Figure 1a,16 May 2020,William Lam,WikiWorks743,Linear discriminant analysis (LDA) effect size analysis of microbiota differentially associated with MRD status with subclass of autologous stem cell transplantation (ASCT),decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces israelii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella nexilis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus equinus",2|201174|1760|2037|2049|1654|1659;2|201174|1760|2037|2049|1654|1655;2|201174|1760|85006;2|201174|1760|85006|1268;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|2047;2|201174|1760|85006|1268|32207|43675;2|1239|186801|186802|186803|1506577|29361;2|1239|91061|186826|1300|1301|1335,Complete,NA
Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease- (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1b,16 May 2020,William Lam,WikiWorks743,Relative abundance of genera Eubacterium and Faecalibacterium by MRD status,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,2|1239|186801|186802|186806|1730,Complete,NA
Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease- (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Figure 1b,16 May 2020,William Lam,WikiWorks743,Relative abundance of genera Eubacterium and Faecalibacterium by MRD status,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,NA
Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease- (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,16 May 2020,William Lam,WikiWorks743,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,NA
Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,female,males,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,16 May 2020,William Lam,WikiWorks743,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,NA
Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,Experiment 5,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,Minimal Residual Disease- (positivity) with Allogenic Stem Cell Transplant,Minimal Residual Disease- (negativity) with Allogenic Stem Cell Transplant,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,16 May 2020,William Lam,WikiWorks743,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,2|1239|186801|186802|186803|2569097|39488,Complete,NA
Study 271,case-control,31289031,10.1182/bloodadvances.2019032276,NA,"Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O , Lesokhin AM",Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition,Blood advances,2019,Experiment 6,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,Age greater than 65 years old,Age less than 65 years old,Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity (MRD-) after upfront treatment,18,16,NA,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Figure 1c,16 May 2020,William Lam,WikiWorks743,Forest plots showing effect of covariates on relative abundance of E hallii and F prausnitzii,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,2|1239|186801|186802|186803|2569097|39488,Complete,NA
Study 272,case-control,30153231,10.1097/INF.0000000000002174,NA,"Kelly MS, Surette MG, Smieja M, Rossi L, Luinstra K, Steenhoff AP, Goldfarb DM, Pernica JM, Arscott-Mills T, Boiditswe S, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Feemster KA , Seed PC",Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana,The Pediatric infectious disease journal,2018,Experiment 1,Botswana,Homo sapiens,nasopharynx,UBERON:0001728,pneumonia,EFO:0003106,negative,S.pneumoniae positive,clinical pneumonnia,74,96,NA,16S,3,Illumina,Logistic Regression,0.05,FALSE,NA,"date,primary care clinic",age,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,13 May 2020,Fatima Zohra,WikiWorks743,Relative abundance of highly abundant genera by S. pneumoniae colonization,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|2887326|468|475;2|1239|91061|186826|1300|1301,Complete,NA
Study 272,case-control,30153231,10.1097/INF.0000000000002174,NA,"Kelly MS, Surette MG, Smieja M, Rossi L, Luinstra K, Steenhoff AP, Goldfarb DM, Pernica JM, Arscott-Mills T, Boiditswe S, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Feemster KA , Seed PC",Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana,The Pediatric infectious disease journal,2018,Experiment 1,Botswana,Homo sapiens,nasopharynx,UBERON:0001728,pneumonia,EFO:0003106,negative,S.pneumoniae positive,clinical pneumonnia,74,96,NA,16S,3,Illumina,Logistic Regression,0.05,FALSE,NA,"date,primary care clinic",age,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,13 May 2020,Fatima Zohra,WikiWorks743,Relative abundance of highly abundant genera by S. pneumoniae colonization,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279,Complete,NA
Study 273,case-control,30838178,10.3389/fcimb.2019.00028,NA,"Nearing JT, Connors J, Whitehouse S, Van Limbergen J, Macdonald T, Kulkarni K , Langille MGI",Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia,Frontiers in cellular and infection microbiology,2019,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,non-infectious complications (NIC),Infectious complications (IC),Infectious complications (IC) in the past 6 months of Acute Lymphoblastic Leukemia treatment,7,9,"Prophylactic Septra which was prescribed ubiquitously to patients throughout the study, as per standard of care.",WMS,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 3a,17 May 2020,William Lam,WikiWorks743,Six species were found to be significantly different in relative abundance between samples from not immune compromised and immune compromised patients: Fecalibacterium prausnitzii,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,NA
Study 273,case-control,30838178,10.3389/fcimb.2019.00028,NA,"Nearing JT, Connors J, Whitehouse S, Van Limbergen J, Macdonald T, Kulkarni K , Langille MGI",Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia,Frontiers in cellular and infection microbiology,2019,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,non-infectious complications (NIC),Infectious complications (IC),Infectious complications (IC) in the past 6 months of Acute Lymphoblastic Leukemia treatment,7,9,"Prophylactic Septra which was prescribed ubiquitously to patients throughout the study, as per standard of care.",WMS,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 3a,17 May 2020,William Lam,WikiWorks743,Six species were found to be significantly different in relative abundance between samples from not immune compromised and immune compromised patients: Fecalibacterium prausnitzii,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,NA
Study 273,case-control,30838178,10.3389/fcimb.2019.00028,NA,"Nearing JT, Connors J, Whitehouse S, Van Limbergen J, Macdonald T, Kulkarni K , Langille MGI",Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia,Frontiers in cellular and infection microbiology,2019,Experiment 2,Canada,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,non-infectious complications (NIC),Infectious complications (IC),Infectious complications (IC) in the past 6 months of Acute Lymphoblastic Leukemia treatment,7,9,"Prophylactic Septra which was prescribed ubiquitously to patients throughout the study, as per standard of care.",WMS,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 3b,17 May 2020,William Lam,WikiWorks743,Six species were found to be significantly different in relative abundance between samples from not immune compromised and immune compromised patients: Brevundimonas diminuta,decreased,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,2|1224|28211|204458|76892|41275|293,Complete,NA
Study 273,case-control,30838178,10.3389/fcimb.2019.00028,NA,"Nearing JT, Connors J, Whitehouse S, Van Limbergen J, Macdonald T, Kulkarni K , Langille MGI",Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia,Frontiers in cellular and infection microbiology,2019,Experiment 2,Canada,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,non-infectious complications (NIC),Infectious complications (IC),Infectious complications (IC) in the past 6 months of Acute Lymphoblastic Leukemia treatment,7,9,"Prophylactic Septra which was prescribed ubiquitously to patients throughout the study, as per standard of care.",WMS,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 3c,17 May 2020,William Lam,WikiWorks743,Six species were found to be significantly different in relative abundance between samples from not immune compromised and immune compromised patients: Agrobacterium tumefaciens,decreased,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium|s__Agrobacterium tumefaciens,2|1224|28211|356|82115|357|358,Complete,NA
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 1,United States of America,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,17 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|32066|203490|203491|1129771|168808|40543;2|976|200643|171549|171552|838,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 1,United States of America,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,17 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|201174|1760|85004|31953|2701;2|1239|1737404|1737405|1570339|162289|1465756;2|1239|186801|186802|1686313|938288;2|201174|1760|2037|2049|2050|2052;2|201174|1760|85004|31953|1678;2|32066|203490|203491|203492|848|851;2|1239|1737404|1737405|1570339|165779|33032;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|39948;2|201174|1760|2037|2049|1654;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|33958|1578|1596,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 2,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,17 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella asaccharolytica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae",2|32066|203490|203491|1129771|168808|40543;2|1239|1737404|1737405|1570339|543311;2|1239|91061|1385|1378|502393;2|201174|1760|2037|2049|2050|2052;2|201174|1760|2037|2049|2767327|82135,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 2,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,17 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus coxii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus",2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|165779|1287640;2|1224|1236|91347|543|561;2|1224|1236|91347|1903410|71655;2|1224|1236|91347|543|620;2|1224|29547|213849|72294|194|827;2|1239|1737404|1737405|1570339|162289|1465756;2|1239|1737404|1737405|1570339|150022|1260;2|32066|203490|203491|203492|848|851;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|162289|755172;2|1239|1737404|1737405|1570339|162289|507750;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|1578|47770,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 3,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,17 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccalis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia",2|32066|203490|203491|1129771|168808|40543;2|201174|1760|85004|31953|2701;2|1239|186801|186802|31979|1485;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838|419005;2|976|200643|171549|171552|838|28127;2|32066|203490|203491|1129771|168808;2|201174|1760|2037|2049|2767327|82135;2|201174|84998|84999|1643824|1380;2|1239|91061|186826|1300|1301|1311;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803|177971,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 3,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,7 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting,decreased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus coxii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|1239|1737404|1737405|1570339|162289|1465756;2|201174|1760|85004|31953|1678;2|976|200643|171549|171552|838|28125;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|1737404|1737405|1570339|162289|33031;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|162289|755172;2|1239|1737404|1737405|1570339|165779|33032;2|1239|1737404|1737405|1570339|162289|507750;2|1239|186801|186802|1686313|938288;2|544448|31969|2085|2092|2129;2|1239|909932|1843489|31977|39948|308994;2|976|200643|171549|171552|838|28130;2|1239|909932|1843489|31977|39948;2|976|200643|171549|171551|836;2|1239|1737404|1737405|1570339|150022|1260;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838|28128;2|1239|91061|186826|33958|1578|1596,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 4,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical cancer,MONDO:0002974,HPV-,invasive cervical carcinoma,invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,20,10,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,17 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting,increased,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,2|32066|203490|203491|1129771|168808|40543,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 4,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical cancer,MONDO:0002974,HPV-,invasive cervical carcinoma,invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,20,10,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,17 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii|s__Winkia neuii subsp. anitrata,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus coxii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister propionicifaciens,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus",2|1239|91061|186826|33958|1578;2|1239|1737404|1737405|1570339|162289|1465756;2|976|200643|171549|171552|838|28125;2|1239|91061|186826|1300|1301;2|544448|31969|2085|2092|2129;2|1224|1236|91347|543|561;2|1224|1236|91347|1903410|71655;2|1224|1236|91347|543|620;2|1239|186801|186802|404402;2|201174|1760|85004|31953|1678;2|201174|1760|2037|2049|2692118|33007|29318;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|1686313|938288;2|1239|91061|186826|1300|1301|1328;2|201174|1760|85007|1653|1716;2|1239|1737404|1737405|1570339|165779|33032;2|1239|1737404|1737405|1570339|162289|507750;2|1239|1737404|1737405|1570339|162289|755172;2|976|200643|171549|171552|838|28128;2|1239|909932|1843489|31977|39948|308994;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|33958|1578|47770,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 5,United States of America,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,18 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting,increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186803|177971;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838;2|1239|186801|186802|186804|1257|1261;2|1239|909932|1843489|31977|906,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 5,United States of America,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ determined by the Linear Array HPV Genotyping Tests,20,31,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,18 May 2020,Cynthia Anderson,WikiWorks743,"Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|91061|186826|186827|1375;2|976|200643|171549|171552|838|386414;2|976|200643|171549|171552|838|28125;2|1239|1737404|1737405|1570339|162289|1465756;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|1737404|1737405|1570339|165779;2|201174|1760|85004|31953|2701;2|201174|1760|85004|31953|1678,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 6,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,18 May 2020,Cynthia Anderson,WikiWorks743,"Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity",increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella asaccharolytica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii|s__Winkia neuii subsp. anitrata,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccalis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|32066|203490|203491|1129771|168808|40543;2|32066|203490|203491|1129771|168808;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|28130;2|976|200643|171549|171552|838;2|201174|1760|85004|31953|1678;2|1239|1737404|1737405|1570339|165779|33032;2|1239|91061|1385|1378|502393;2|201174|1760|2037|2049|2692118|33007|29318;2|201174|1760|2037|2049|2050|2052;2|1239|91061|186826|33958|1578|147802;2|1239|186801|186802|186804|1257|1261;2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838|28127;2|1239|909932|1843489|31977|39948;2|976|200643|171549|171552|838|419005;2|1239|91061|186826|33958|1578|1596,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 6,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,low grade dysplasia,low grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,12,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,18 May 2020,Cynthia Anderson,WikiWorks743,"Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus coxii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus",2|1239|91061|186826|33958|1578;2|1239|1737404|1737405|1570339|162289|755172;2|1239|91061|186826|33958|1578|47770,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 7,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,18 May 2020,Cynthia Anderson,WikiWorks743,"Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia",2|976|200643|171549|171552|838|419005;2|1239|91061|186826|33958|1578|147802;2|1239|186801|186802|31979|1485;2|201174|1760|85004|31953|2701;2|1239|909932|1843489|31977|906;2|32066|203490|203491|1129771|168808|40543;2|1239|1737404|1737405|1570339|543311;2|32066|203490|203491|1129771|168808;2|1239|186801|186802|186803|177971,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 7,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,high grade dysplasia,high grade dysplasia confirmed by histology of colonoscopy-directed biopsy,20,27,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,18 May 2020,Cynthia Anderson,"WikiWorks743,Fatima","Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus lactolyticus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium coyleae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus coxii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus duerdenii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella|s__Ezakiella coagulans,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii",2|1239|91061|186826|186827|1375;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|165779|33032;2|1239|1737404|1737405|1570339|165779|1287640;2|201174|1760|85004|31953|1678;2|1224|29547|213849|72294|194|827;2|201174|1760|85007|1653|1716|53374;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|1686313|938288;2|1239|1737404|1737405|1570339|162290;2|201174|1760|85004|31953|2701;2|1239|186801|186802|404402;2|1239|1737404|1737405|1570339|162289|755172;2|1239|1737404|1737405|1570339|162289|507750;2|1239|1737404|1737405|1570339|162289|1465756;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552|838|28127;2|976|200643|171549|171552|838|386414;2|1239|1737404|1582879|46507;2|201174|1760|2037|2049|1653174|59505,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 8,United States of America,Homo sapiens,vagina,UBERON:0000996,cervical cancer,MONDO:0002974,HPV-,invasive cervical carcinoma,invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,20,10,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,body mass index,ethnic group",NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,23 May 2020,Cynthia Anderson,"WikiWorks743,Cynthia Anderson,Lwaldron","Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity",decreased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus grossensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia",2|1239|1737404|1737405|1570339|165779;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|2701;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|1578|47770;2|1239|186801|186802|186803|437755;2|1239|1737404|1737405|1570339|162289|1465756;2|976|200643|171549|171552|838|28125,Complete,Fatima
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 9,United States of America,Homo sapiens,vagina,UBERON:0000996,"human papilloma virus infection,cervical cancer","EFO:0001668,MONDO:0002974",abnormal pH,normal pH,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",20,74,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,23 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH and Hispanic vs. non-Hispanic,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae",2|976|200643|171549|171552|838|419005;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465|187328;2|544448|2790996|2895623|2895509|2098;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|31979|1485;2|32066|203490|203491|203492|848|851;2|1239|186801|186802|186804|1257;2|1239|91061|186826|81852|1350;2|1239|1737404|1737405|1570339|543311;2|1239|91061|1385|90964|1279;2|32066|203490|203491|1129771|168808;2|1239|91061|1385|1378;2|201174|1760|85004|31953|2701;2|32066|203490|203491|1129771|168808|40543;2|1239|186801|186802|186803|437755;2|201174|1760|2037|2049|2050|2052;2|976|200643|171549|171552|838|28130;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803|177971;2|201174|1760|85004|31953|1678;2|1239|91061|186826|1300|1301|1311,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 9,United States of America,Homo sapiens,vagina,UBERON:0000996,"human papilloma virus infection,cervical cancer","EFO:0001668,MONDO:0002974",abnormal pH,normal pH,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",20,74,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,23 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH and Hispanic vs. non-Hispanic,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae|g__Brenneria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|1239|91061|186826|33958|1578;2|1224|1236|91347|543|561;2|1224|1236|91347|1903410|71655;2|1224|1236|91347|543|620;2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1578|1596,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 10,United States of America,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,non-Hispanic,Hispanic,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",53,47,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,23 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH and Hispanic vs. non-Hispanic,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus mulieris,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus",2|1239|909932|1843489|31977|29465|187328;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|2050|2052;2|1239|91061|186826|186827|1375;2|201174|1760|85004|31953|2701;2|1239|91061|186826|81852|1350;2|1239|186801|186802|186803|437755;2|32066|203490|203491|1129771|168808|40543;2|201174|1760|2037|2049|2767327|82135;2|1239|909932|1843489|31977|906;2|32066|203490|203491|1129771|168808;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|186803|177971;2|976|200643|171549|171551|836;2|1239|91061|186826|1300|1301|1328,Complete,Fatima Zohra
Study 274,"cross-sectional observational, not case-control",29765068,10.1038/s41598-018-25879-7,NA,"Łaniewski P, Barnes D, Goulder A, Cui H, Roe DJ, Chase DM , Herbst-Kralovetz MM","Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women",Scientific reports,2018,Experiment 10,United States of America,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,non-Hispanic,Hispanic,"HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,",53,47,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,23 May 2020,Cynthia Anderson,WikiWorks743,Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH and Hispanic vs. non-Hispanic,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccalis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri",2|1239|91061|186826|33958|1578;2|976|200643|171549|171552|838|28127;2|1239|1737404|1737405|1570339|165779|33037;2|1239|91061|186826|33958|1578|1596,Complete,Fatima Zohra
Study 275,case-control,27527070,10.1186/s12864-016-2965-y,NA,"Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L , Nelson KE",Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis,BMC genomics,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,healthy sibling control,ALL patient,before chemotherapy adminstration in pediatric and adolescent Acute Lymphoblastic Leukemia at time of disease diagnosis,23,28,NA,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1,18 May 2020,William Lam,WikiWorks743,Mean microbial taxon abundances in Acute Lymphoblastic Leukemia Patient and Control groups (prior to chemotherapy treatment-  visit 1),increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|31979|1485;2|976|200643|171549|2005519|397864;2|1239|186801|186802|216572|459786;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|207244;2|1224|28216|80840|995019|40544;2|976|200643|171549|171552|577309;2|1239|186801|186802|216572|1263;2|1239|186801|186802|204475;2|201174|1760|85004|31953|1678;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|572511;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|838;2|976|200643|171549|815|816,Complete,NA
Study 275,case-control,27527070,10.1186/s12864-016-2965-y,NA,"Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L , Nelson KE",Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis,BMC genomics,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,healthy sibling control,ALL patient,before chemotherapy adminstration in pediatric and adolescent Acute Lymphoblastic Leukemia at time of disease diagnosis,23,28,NA,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1,18 May 2020,William Lam,WikiWorks743,Mean microbial taxon abundances in Acute Lymphoblastic Leukemia  Patient and Control groups (prior to chemotherapy treatment-  visit 1),decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|31979|1485;2|976|200643|171549|2005519|397864;2|1239|186801|186802|216572|459786;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|207244;2|1224|28216|80840|995019|40544;2|976|200643|171549|171552|577309;2|1239|186801|186802|216572|1263;2|1239|186801|186802|204475;2|201174|1760|85004|31953|1678;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|572511;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|838;2|976|200643|171549|815|816,Complete,NA
Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2b & Table 6 & text,21 May 2020,William Lam,WikiWorks743,Comparison of Intestinal Microbial between the Multiple Myeloma group and healthy control at the phylum level,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Verrucomicrobia",2|976;2|1239;2|1224;2|32066;2|74201,Complete,NA
Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2b & Table 6 & text,21 May 2020,William Lam,WikiWorks743,Comparison of Intestinal Microbial between the Multiple Myeloma group and healthy control at the phylum level,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Tenericutes",2|976;2|1239;2|201174;2|544448,Complete,NA
Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 1,Figure 3a,21 May 2020,William Lam,WikiWorks743,Intestinal Microbial taxonomic differences were detected based on Operational Taxonomic Unit between Multiple Myeloma group and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1224;2|1239|526524|526525|2810281|191303;2|1224|1236|91347|543|413496;2|1224|1236|91347|543|413496|28141,Complete,NA
Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,unchanged,NA,NA,NA,Signature 2,Figure 3a,21 May 2020,William Lam,WikiWorks743,Intestinal Microbial taxonomic differences were detected based on Operational Taxonomic Unit between Multiple Myeloma group and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",2|1239|186801|186802|216572|1508657;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186806|1730;2|201174|84998;2|201174|84998|84999;2|201174|84998|84999|84107;2|1239|186801|186802|186803|207244;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|2810280|135858;2|1224|28211|204441|41295;2|1224|28211;2|1224|28211|204441;2|1239|909932|1843488|909930|904,Complete,NA
Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,healthy control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",17,40,3 months,16S,34,Illumina,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 7 and text,21 May 2020,William Lam,WikiWorks743,"Genus with significant difference between Multiple Myeloma group and healthy control group was selected, followed by ordering according to the abundance in the intestinal tract of MM patients",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptoclostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma",2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|841;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|186804|1481960;2|1239|909932|1843488|909930|904;2|1239|526524|526525|128827|1472649,Complete,NA
Study 276,case-control,31678982,10.12659/MSM.919988,NA,"Zhang B, Gu J, Liu J, Huang B , Li J",Fecal Microbiota Taxonomic Shifts in Chinese Multiple Myeloma Patients Analyzed by Quantitative Polimerase Chain Reaction (QPCR) and 16S rRNA High-Throughput Sequencing,Medical science monitor : international medical journal of experimental and clinical research,2019,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,healthy relatives control,Multiple Myeloma patient,"patient diagnosis with multiple myeloma and no other disease validated to affect intestinal microbial including digestive disease like liver cirrhosis, liver cancer, inflammatory bowel disease, and irritable bowel syndrome; systemic disease like diabetes and hypertension and thyroid disease; no treatment including antibiotics, chemotherapy, plasma exchange or bone marrow transplant; no cold, fever or other infections within 3 months before sampling with administrated antibacterial drugs, gastrointestinal motility drugs or micro-ecological conditioning agents like eating and living habit change 1 week before sampling",21,21,3 months,16S,34,RT-qPCR,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 8 and text,21 May 2020,William Lam,WikiWorks743,Intestinal Microbial detection in Multiple Myeloma patients and their family members using Quantitative Reverse Transcription Polymerase Chain Reaction,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium leptum CAG:27,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1239|186801|186802|31979|1485|1263068;2|1224|1236|72274|135621|286|287,Complete,NA
Study 277,case-control,29522532,10.1371/journal.pone.0194060,NA,"Carmody LA, Caverly LJ, Foster BK, Rogers MAM, Kalikin LM, Simon RH, VanDevanter DR , LiPuma JJ",Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis,PloS one,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,Crohn's disease,EFO:0000384,healthy control,crohn's disease,new-onset adult crohn's disease (CD) patients,16,13,10 weeks,16S,123,Illumina,NA,0.05,FALSE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"figure 2, 3, 4",20 May 2020,Fatima Zohra,WikiWorks743,Significant difference between control group and crohn's disease,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfohalobiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Entomoplasmatales|f__Entomoplasmataceae|g__Mesoplasma,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfohalobiaceae|g__Desulfonauticus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio",2|1239|186801;2|1239|186801|186802|541000;2|1239|186801|186802|186803;2|1239|186801|186802|186806;2|976|200643|171549|171550;2|544448|31969|186328|33925;2|1224|28221|213115|213117;2|201174|1760|85007|1653;2|544448|31969|2085|2092;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|186806|1730;2|544448|31969|186328|33925|46239;2|1224|28221|213115|213117|206664;2|976|200643|171549|171551|836;2|976|200643|171549|171550|28138;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186803|830,Complete,NA
Study 278,"cross-sectional observational, not case-control",29362454,10.1038/s41598-018-19753-9,NA,"Da Silva HE, Teterina A, Comelli EM, Taibi A, Arendt BM, Fischer SE, Lou W , Allard JP",Nonalcoholic fatty liver disease is associated with dysbiosis independent of body mass index and insulin resistance,Scientific reports,2018,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,healthy control,non alcoholic fatty liver disease,biopsy proved steatosis and non alcoholic steatohepatitis,28,39,6 monts,16S,NA,RT-qPCR,Metastats,0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 1,table 2,20 May 2020,Fatima Zohra,WikiWorks743,Taxa identified as differentially abundant in patients with nonalocholic fatty liver disease (NAFLD) compared to HC,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958,Complete,NA
Study 278,"cross-sectional observational, not case-control",29362454,10.1038/s41598-018-19753-9,NA,"Da Silva HE, Teterina A, Comelli EM, Taibi A, Arendt BM, Fischer SE, Lou W , Allard JP",Nonalcoholic fatty liver disease is associated with dysbiosis independent of body mass index and insulin resistance,Scientific reports,2018,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,healthy control,non alcoholic fatty liver disease,biopsy proved steatosis and non alcoholic steatohepatitis,28,39,6 monts,16S,NA,RT-qPCR,Metastats,0.05,TRUE,NA,NA,NA,NA,NA,NA,unchanged,NA,NA,Signature 2,table 2,20 May 2020,Fatima Zohra,WikiWorks743,Taxa identified as differentially abundant in patients with nonalocholic fatty liver disease (NAFLD) compared to HC,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes",2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|207244;2|976|200643|171549|815|816;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|216851;2|976|200643|171549|815;2|1239|186801|186802|186803;2|976|200643|171549|171551;2|976|200643|171549|171550;2|1239|186801|186802|541000;2|976;2|1239,Complete,NA
Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,acute myeloid leukemia,EFO:0000222,Low Intensity Chemotherapy,High Intensity Chemotherapy,Acute Myeloid Leukemia patients with receiving low- intensity remission induction chemotherapy,11,28,NA,16S,4,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure S1 and text, Table S1, Figure 4",22 May 2020,William Lam,WikiWorks743,Mycobiome characteristics correlate with chemotherapy intensity at later point of sample collection (T6),increased,NA,NA,Complete,NA
Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,acute myeloid leukemia,EFO:0000222,Low Intensity Chemotherapy,High Intensity Chemotherapy,Acute Myeloid Leukemia patients with receiving low- intensity remission induction chemotherapy,11,28,NA,16S,4,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure S1 and text, Table S1, Figure 4",22 May 2020,William Lam,WikiWorks743,Mycobiome characteristics correlate with chemotherapy intensity at later point of sample collection (T6),decreased,NA,NA,Complete,NA
Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,acute myeloid leukemia,EFO:0000222,No bacterial infections,bacterial infections,Acute Myeloid Leukemia patients that experience microbiologically defined bacterial infections during remission induction chemotherapy,30,9,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 6 and text, Table S2 and S3",22 May 2020,William Lam,WikiWorks743,Relative abundance differences of taxa at individual time points among Acute Myeloid Leukemia patients who did and did not experience bacterial infection during remission induction chemotherapy at midpoint time point (T3) prior to neutrophil recovery,increased,NA,NA,Complete,NA
Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,acute myeloid leukemia,EFO:0000222,No bacterial infections,bacterial infections,Acute Myeloid Leukemia patients that experience microbiologically defined bacterial infections during remission induction chemotherapy,30,9,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 6 and text, Table S2 and S3",22 May 2020,William Lam,WikiWorks743,Relative abundance differences of taxa at individual time points among Acute Myeloid Leukemia patients who did and did not experience bacterial infection during remission induction chemotherapy at midpoint time point (T3) prior to neutrophil recovery,decreased,NA,NA,Complete,NA
Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,acute myeloid leukemia,EFO:0000222,No bacterial infections,bacterial infections,Acute Myeloid Leukemia patients that experience microbiologically defined bacterial infections during remission induction chemotherapy,30,9,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 3,"Figure 6 and text, Table S2 and S3",22 May 2020,William Lam,WikiWorks743,Relative abundance differences of taxa at individual time points among Acute Myeloid Leukemia patients who did and did not experience bacterial infection during remission induction chemotherapy at later time point (T6) prior to neutrophil recovery,increased,NA,NA,Complete,NA
Study 279,time series / longitudinal observational,32295867,10.1128/mSphere.00048-20,NA,"Robinson S, Peterson CB, Sahasrabhojane P, Ajami NJ, Shelburne SA, Kontoyiannis DP , Galloway-Peña JR",Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia,mSphere,2020,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,acute myeloid leukemia,EFO:0000222,No bacterial infections,bacterial infections,Acute Myeloid Leukemia patients that experience microbiologically defined bacterial infections during remission induction chemotherapy,30,9,NA,16S,4,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 4,"Figure 6 and text, Table S2 and S3",22 May 2020,William Lam,WikiWorks743,Relative abundance differences of taxa at individual time points among Acute Myeloid Leukemia patients who did and did not experience bacterial infection during remission induction chemotherapy at later time point (T6) prior to neutrophil recovery,decreased,NA,NA,Complete,NA
Study 280,"cross-sectional observational, not case-control",26574055,10.1038/srep16865,NA,"Mitra A, MacIntyre DA, Lee YS, Smith A, Marchesi JR, Lehne B, Bhatia R, Lyons D, Paraskevaidis E, Li JV, Holmes E, Nicholson JK, Bennett PR , Kyrgiou M",Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity,Scientific reports,2015,Experiment 1,United Kingdom,Homo sapiens,posterior fornix of vagina,UBERON:0016486,cervical glandular intraepithelial neoplasia,EFO:1000165,low grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion confirmed by histology or cytology,52,92,14 days,16S,12,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,figure 5,23 May 2020,Cynthia Anderson,WikiWorks743,Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia sanguinegens,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae",2|1239|186801|186802|186804|1257|1261;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|165779|33036;2|32066|203490|203491|1129771|168808;2|32066|203490|203491;2|32066|203490|203491|1129771|168808|40543;2|32066;2|32066|203490|203491|1129771,Complete,Fatima Zohra
Study 280,"cross-sectional observational, not case-control",26574055,10.1038/srep16865,NA,"Mitra A, MacIntyre DA, Lee YS, Smith A, Marchesi JR, Lehne B, Bhatia R, Lyons D, Paraskevaidis E, Li JV, Holmes E, Nicholson JK, Bennett PR , Kyrgiou M",Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity,Scientific reports,2015,Experiment 1,United Kingdom,Homo sapiens,posterior fornix of vagina,UBERON:0016486,cervical glandular intraepithelial neoplasia,EFO:1000165,low grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion,high grade squamus intraepithelial lesion confirmed by histology or cytology,52,92,14 days,16S,12,Illumina,LEfSe,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,figure 5,23 May 2020,Cynthia Anderson,WikiWorks743,Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus coleohominis",2|1239|91061|186826|33958|1578|109790;2|1239|91061|186826|33958|2742598|181675,Complete,Fatima Zohra
Study 281,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y , Gyarmati P",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,Experiment 1,United States of America,Mus musculus,small intestine,UBERON:0002108,acute lymphoblastic leukemia,EFO:0000220,Fecal bacterial composition in small intestines of control mice,Fecal bacterial composition in small intestines of leukemia mice,three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 4a, 4b and text",24 May 2020,William Lam,WikiWorks743,Relative abundances and the ratio of relative abundances of the bacterial microbiota between the fecal compositions in the small intestine of control and leukemic mice model,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium|s__Dehalobacterium formicoaceticum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|216572|119852;2|544448|31969|186332|186333|2086;2|1239|186801|186802|186803|830;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186807|51514|51515;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|207244;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|186803|572511,Complete,NA
Study 281,laboratory experiment,31884727,10.1002/mbo3.982,NA,"Song Y , Gyarmati P",Microbiota changes in a pediatric acute lymphocytic leukemia mouse model,MicrobiologyOpen,2020,Experiment 1,United States of America,Mus musculus,small intestine,UBERON:0002108,acute lymphoblastic leukemia,EFO:0000220,Fecal bacterial composition in small intestines of control mice,Fecal bacterial composition in small intestines of leukemia mice,three-week old female mice induced leukemia using lymphomblasts from pediatric acture lymphocytic leukemia patients from ATCC,8,8,NA,16S,4,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 4a, 4b and text",24 May 2020,William Lam,WikiWorks743,Relative abundances and the ratio of relative abundances of the bacterial microbiota between the fecal compositions in the small intestine of control and leukemic mice model,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia",2|1239|91061|186826|33958|1578;2|201174|84998|1643822|1643826|447020;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|186803|207244;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|186803|572511,Complete,NA
Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,Grades 0-I (non-acute graft-host disease),Grades II-IV (acute graft-host-disease),patients diagnoised with acute graft-versus-host disease (aGVHD),49,32,NA,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,"Figure 3a, b and text",26 May 2020,William Lam,WikiWorks743,Differences of intestinal microbiota at engraftment between acute graft-verse-house disease (aGVHD) and non-acute graft-versus host disease (non-aGVHD) patients,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria",2|976|200643|171549|171551;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236;2|1224,Complete,NA
Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,Grades 0-I (non-acute graft-host disease),Grades II-IV (acute graft-host-disease),patients diagnoised with acute graft-versus-host disease (aGVHD),49,32,NA,16S,4,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,"Figure 3a, b and text",26 May 2020,William Lam,WikiWorks743,Differences of intestinal microbiota at engraftment between acute graft-verse-house disease (aGVHD) and non-acute graft-versus host disease (non-aGVHD) patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|186806;2|1239|186801|186802|186803;2|1239|186801|186802|186804;2|1239|186801|186802|541000;2|1239|186801|186802;2|1239|186801;2|1239|526524|526525|128827;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|572511,Complete,NA
Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,standard conditioning,intensified conditioning,patients diagnoised with grade II to IV acute graft-versus-host disease (aGVHD) undergoing intense conditioning,19,13,NA,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,increased,NA,Signature 1,"Figure 5a, b, c, d",26 May 2020,William Lam,WikiWorks743,Differences in the intestinal microbiota (diversity and composition) are associated with conditioning intensity in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|186802|186803;2|1239|186801|186802|541000,Complete,NA
Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,no b-lactum antibiotics,b-lactum antibiotics,"patients diagnoised with grade II to IV acute graft-versus-host disease (aGVHD) undergoing intense conditioning treated with b-lactum (include carbapenem, cephalosporin, and b-lactam-b-lactamase combinations.)",48,31,NA,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 4 a, b, d",26 May 2020,William Lam,WikiWorks743,Differences in the intestinal microbiota (diversity and composition) are associated with Beta-Lactum antibiotic in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,2|1239|186801|186802|186803,Complete,NA
Study 282,prospective cohort,29740427,10.3389/fimmu.2018.00669,NA,"Han L, Jin H, Zhou L, Zhang X, Fan Z, Dai M, Lin Q, Huang F, Xuan L, Zhang H , Liu Q",Intestinal Microbiota at Engraftment Influence Acute Graft-Versus-Host Disease <i>via</i> the Treg/Th17 Balance in Allo-HSCT Recipients,Frontiers in immunology,2018,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,no vancomycin antibiotics,vancomycin antibiotics,patients diagnoised with grade II to IV acute graft-versus-host disease (aGVHD) undergoing intense conditioning treated with vancomycin,59,20,NA,16S,4,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 4 a, b, d",26 May 2020,William Lam,WikiWorks743,Differences in the intestinal microbiota (diversity and composition) are associated with Vancomycin antibiotic in allogeneic hematopoietic stem cell transplant (allo-HSCT) patients,increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,NA
Study 283,"cross-sectional observational, not case-control",31749298,10.1111/1471-0528.15981,NA,"Borgogna JC, Shardell MD, Santori EK, Nelson TM, Rath JM, Glover ED, Ravel J, Gravitt PE, Yeoman CJ , Brotman RM",The vaginal metabolome and microbiota of cervical HPV-positive and HPV-negative women: a cross-sectional analysis,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 1,United States of America,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed using Roche Linear Array HPV Genotyping Test,13,26,30 days,16S,123,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,supplemental figure 3,26 May 2020,Cynthia Anderson,WikiWorks743,The association between vaginal taxa and detection status as identified by LEfSE,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus asaccharolyticus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus vaginalis",2|201174|1760|85004|31953|2701|2702;2|201174|84998|1643822|1643826|84111;2|1239|91061|1385|1378;2|201174|84998|84999|1643824|1380|1872650;2|1239|909932|1843489|31977;2|1239|91061|186826|186827|1375|87541;2|1239|1737404|1737405|1570339|162289|1258;2|1239|91061|186826|33958|2742598|1633,Complete,Fatima Zohra
Study 283,"cross-sectional observational, not case-control",31749298,10.1111/1471-0528.15981,NA,"Borgogna JC, Shardell MD, Santori EK, Nelson TM, Rath JM, Glover ED, Ravel J, Gravitt PE, Yeoman CJ , Brotman RM",The vaginal metabolome and microbiota of cervical HPV-positive and HPV-negative women: a cross-sectional analysis,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 1,United States of America,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed using Roche Linear Array HPV Genotyping Test,13,26,30 days,16S,123,Roche454,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,supplemental figure 3,26 May 2020,Cynthia Anderson,WikiWorks743,The association between vaginal taxa and detection status as identified by LEfSE,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus",2|201174|1760|85004|31953;2|201174|1760|2037|2049|2767327|82135;2|1239|91061|186826|33958|1578|109790;2|1239|91061|186826|33958|1578|47770,Complete,Fatima Zohra
Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,Experiment 1,China,Homo sapiens,gingiva,UBERON:0001828,chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,34,Illumina,Metastats,0.05,FALSE,NA,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,26 May 2020,Fatima Zohra,WikiWorks743,Predominant taxa composition of supragingival plaque at genus level,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella",2|1239|91061|186826|1300|1301;2|201174|1760|85007|1653|1716;2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207;2|976|117743|200644|2762318|59735,Complete,NA
Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,Experiment 1,China,Homo sapiens,gingiva,UBERON:0001828,chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,34,Illumina,Metastats,0.05,FALSE,NA,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3,26 May 2020,Fatima Zohra,WikiWorks743,Predominant taxa composition of supragingival plaque at genus level,decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836,Complete,NA
Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,Experiment 2,China,Homo sapiens,gingiva,UBERON:0001828,chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,345,Illumina,LEfSe,0.05,FALSE,2,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4,26 May 2020,Fatima Zohra,WikiWorks743,Species with different prevalencee or relative abundance,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sobrinus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter curvus",2|1239|91061|186826|1300|1301|28037;2|201174|1760|2037|2049|1654|1655;2|1239|91061|186826|1300|1301|1309;2|1239|91061|186826|33958|2767887|1624;2|976|117743|200644|49546|1016|44737;2|1239|91061|186826|1300|1301|1310;2|1239|91061|186826|33958|2742598|1613;2|1224|29547|213849|72294|194|200,Complete,NA
Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,Experiment 3,China,Homo sapiens,gingiva,UBERON:0001828,chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,3456,Illumina,LEfSe,0.05,FALSE,2,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 4,26 May 2020,Fatima Zohra,WikiWorks743,Species with different prevalencee or relative abundance,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Johnsonella|s__Johnsonella ignava,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella genomosp. P6,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.",2|976|200643|171549|171552|838|59823;2|1239|186801|186802|186803|43994|43995;2|976|200643|171549|171552|838|425941;2|1224|1236|135625|712|724|726;2|1239|186801|186802|186803|265975|1969407;2|976|200643|171549|171552|838|239138;2|32066|203490|203491|1129771|2755140|157692;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|28131;2|1224|28216|206351|481|482|192066,Complete,NA
Study 284,case-control,30300382,10.1371/journal.pone.0204674,NA,"Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ , Gan YH",Carious status and supragingival plaque microbiota in hemodialysis patients,PloS one,2018,Experiment 4,China,Homo sapiens,gingiva,UBERON:0001828,chronic kidney disease,EFO:0003884,healthy controls,Chronic kidney disease,chronic kidney disease patients undergoing hemodialysis,30,30,30 days,16S,3456,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex,smoking behavior",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 5,26 May 2020,Fatima Zohra,WikiWorks743,Bacterial load of Streptococcus mutans in supragingival plaque measured by quantitative real-time PCR,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,2|1239|91061|186826|1300|1301|1309,Complete,NA
Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,healthy controls,pediatric multiple sclerosis,early pediatric multiple sclerosis,16,18,2 months,16S,4,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Figure 3a, 3b",27 May 2020,Rimsha Azhar,WikiWorks743,Difference between multiple sclerosis and controls in the gut microbial communities,increased,"k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|1224|28221|213115|194924|35832;2|201174|1760|85004|31953|1678;2|1239|186801|186802;2|1224|28221|213115|194924|872;2|201174|84998|84999|84107;2|976|200643|171549|171552|838|165179;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|990719;2|1239|186801|186802|541000;2|1239|909932|1843488|909930|33024,Complete,NA
Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,healthy controls,pediatric multiple sclerosis,early pediatric multiple sclerosis,16,18,2 months,16S,4,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Figure 3a, 3b",27 May 2020,Rimsha Azhar,WikiWorks743,Difference between multiple sclerosis and controls in the gut microbial communities,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius",2|1239|186801|186802|186803|28050;2|1239|186801|186802|541000;2|976|200643|171549|171552|577309;2|1239|186801|186802;2|976|200643|171549|171552|838|165179;2|976|200643|171549|815|816;2|1239|186801|186802|216572|119852;2|1239|186801|186802|186804|1257|1261,Complete,NA
Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,IMD naive cases,IMD exposure multiple sclerosis cases,NA,9,9,2 months,16S,4,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2b,27 May 2020,Rimsha Azhar,WikiWorks743,Difference between multiple sclerosis and controls influenced by the immunomodulatory drug IMD exposure status of cases,increased,k__Bacteria|p__Actinobacteria,2|201174,Complete,NA
Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,IMD naive cases,IMD exposure multiple sclerosis cases,NA,9,9,2 months,16S,4,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 2b,27 May 2020,Rimsha Azhar,WikiWorks743,Difference between multiple sclerosis and controls influenced by the immunomodulatory drug IMD exposure status of cases,decreased,"k__Bacteria|p__Tenericutes,k__Bacteria|p__Cyanobacteria",2|544448;2|1117,Complete,NA
Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,healthy controls,IMD naive cases multiple sclerosis,NA,16,9,2 months,16S,4,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Supplementary Table 7a, Supp Table 7b",27 May 2020,Rimsha Azhar,"WikiWorks743,Lwaldron",Taxa enriched and depleted in the IMD naive cases vs. controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella stercorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus",2|1239|909932|1843488|909930|904;2|74201|203494|48461|1647988|239934|239935;2|201174|84998|84999|1643824|1380;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|28116;2|201174|1760|85004|31953|1678;2|1224|28221|213115|194924|35832;2|1239|186801|186802|186803|572511|33035;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|990719;2|1224|28216|80840|80864;2|1239|186801|186802|186803|33042;2|201174|84998|84999|84107;2|1224|28221|213115|194924|872;2|1239|186801|186802|186803|189330;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851|853;2|1224|1236|135625|712|724|729;2|1239|186801|186802|186803;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|119852;2|1239|186801|186802|541000;2|976|200643|171549|2005525|375288|823;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656|310297;2|976|200643|171549|171552|838|165179;2|976|200643|171549|171552|838|363265;2|1239|186801|186802|186806|113286;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544;2|1239|909932|1843489|31977|29465|39778;2|1239|186801|186802|186803|2316020|33038,Complete,NA
Study 285,case-control,27176462,10.1111/ene.13026,NA,"Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, Graves J, Lynch S , Waubant E",Gut microbiota in early pediatric multiple sclerosis: a case-control study,European journal of neurology,2016,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,multiple sclerosis,MONDO:0005301,healthy controls,IMD naive cases multiple sclerosis,NA,16,9,2 months,16S,4,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Supplementary Table 7a, Supp Table 7b",27 May 2020,Rimsha Azhar,WikiWorks743,Taxa enriched and depleted in the IMD naive cases vs. controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea",2|1239|186801|186802|541000;2|976|200643|171549|171552|838|165179;2|1239|91061|186826|33958|2767887|1623;2|976|200643|171549|171552|577309;2|1239|186801|186802|186803;2|976|200643|171549|171550;2|976|200643|171549|815|816;2|1239|186801|186802|216572|1263;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|815|816|820;2|976|200643|171549|1853231|574697;2|1239|909932|909929|1843491|52225|52226;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186804|1257|1261;2|1239|186801|186802|186803|207244;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|815|816|28111;2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|815|816|817;2|1239|526524|526525|2810280|135858;2|1239|909932|1843489|31977|39948;2|976|200643|171549|815|909656|387090;2|976|200643|171549|815|816|28116;2|1239|186801|186802|186803|189330,Complete,NA
Study 286,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi TT, Xin Z, Hua L, Zhao RX, Yang YL, Wang H, Zhang S, Liu W , Xie RR",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Healthy controls,graves orbitopathy,"The diagnosis of GO was established according to the EUGOGO Guidelines. The active GO was defined by a clinical activity score (CAS)≥3/7, and the severe GO was defined by NOSPECS score≥IV. CT or MRI was used to exclude any orbital space-occupying disease such as tumor or extraocular myositis.",32,33,4 weeks,16S,4,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,"Figure 4a, 4b, 4c",28 May 2020,Rimsha Azhar,"WikiWorks743,Rimsha,Fatima,LGeistlinger","Comparison of the bacterial abundance at the phylum, genus and species levels in patients with graves' orbitopathy and healthy controls",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes",2|976|200643|171549|171552|838|165179;2|976,Complete,Fatima
Study 286,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi TT, Xin Z, Hua L, Zhao RX, Yang YL, Wang H, Zhang S, Liu W , Xie RR",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,Healthy controls,graves orbitopathy,"The diagnosis of GO was established according to the EUGOGO Guidelines. The active GO was defined by a clinical activity score (CAS)≥3/7, and the severe GO was defined by NOSPECS score≥IV. CT or MRI was used to exclude any orbital space-occupying disease such as tumor or extraocular myositis.",32,33,4 weeks,16S,4,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,"Figure 4a, 4b, 4c",28 May 2020,Rimsha Azhar,"WikiWorks743,Rimsha,Fatima","Comparison of the bacterial abundance at the phylum, genus and species levels in patients with graves' orbitopathy and healthy controls",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Marseillibacter|s__Marseillibacter massiliensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|171550|239759|328814;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|572511;2|976|200643|171549|1853231|574697;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186806|1730|39496;2|1239;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|216572|1930587|1852369;2|976|200643|171549|815|909656|204516;2|1239|186801|186802|216572|1263,Complete,Fatima
Study 286,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi TT, Xin Z, Hua L, Zhao RX, Yang YL, Wang H, Zhang S, Liu W , Xie RR",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,healthy controls,graves orbitopathy,severe and active graves' orbitopathy,32,33,4 weeks,16S,4,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 1,Figure 5b,28 May 2020,Rimsha Azhar,"WikiWorks743,Fatima",Difference between the intestinal microbiome of patients with graves' orbitopathy and healthy controls by LEfSE,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549;2|976;2|976|200643;2|976|200643|171549|171552|838|165179;2|976|200643|171549|171552,Complete,Fatima
Study 286,"cross-sectional observational, not case-control",30674011,10.1007/s40618-019-1010-9,NA,"Shi TT, Xin Z, Hua L, Zhao RX, Yang YL, Wang H, Zhang S, Liu W , Xie RR",Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study,Journal of endocrinological investigation,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,Graves ophthalmopathy,EFO:1001466,healthy controls,graves orbitopathy,severe and active graves' orbitopathy,32,33,4 weeks,16S,4,Ion Torrent,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,decreased,unchanged,decreased,NA,unchanged,Signature 2,Figure 5b,28 May 2020,Rimsha Azhar,"WikiWorks743,Fatima",Difference between the intestinal microbiome of patients with graves' orbitopathy and healthy controls by LEfSE,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|186801;2|1239|186801|186802;2|1239;2|1239|186801|186802|186803,Complete,Fatima
Study 287,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M, Zolnik CP, Castle PE, Porras C, Herrero R, Gradissimo A, Gonzalez P, Safaeian M, Schiffman M , Burk RD",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,Experiment 1,Costa Rica,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 1 HPV (progression),HPV progression to CIN2+ lesion diagnosis,70,33,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4,27 May 2020,Cynthia Anderson,WikiWorks743,Bacteria associated with progression to CIN2+ identified using LEfSe,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas bennonis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylobacillus|s__Methylobacillus flagellatus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Methylophilaceae|g__Methylobacillus|s__Methylobacillus glycogenes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium atypicum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bergensis,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter canadensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema pallidum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus indolicus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria gonorrhoeae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",2|201174|1760|85004|31953|2701|2702;2|201174|1760|85004|31953|1678|216816|1679;2|1239|909932|1843489|31977|29465|187328;2|1239|1737404|1737405|1570339|165779|33034;2|201174|1760|2037|2049|2529408|52773;2|1239|186801|186802|186803|572511|1322;2|976|200643|171549|171551|836|501496;2|1239|91061|186826|186827|1375|87541;2|1224|28216|32003|32011|404|405;2|1224|28216|32003|32011|404|406;2|201174|1760|85007|1653|1716|191610;2|1239|1737404|1737405|1570339|162289|54005;2|1224|29547|213849|72294|194|827;2|1224|28211|204457|41297|13687|68569;2|976|200643|171549|171552|838|242750;2|1224|29547|213849|72294|194|449520;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|28137;2|203691|203692|136|2845253|157|160;2|1239|1737404|1737405|1570339|162289|33030;2|201174|1760|85004|31953|1678|1681;2|1224|28216|206351|481|482|485;2|201174|1760|2037|2049|2529408|1660,Complete,Fatima Zohra
Study 287,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M, Zolnik CP, Castle PE, Porras C, Herrero R, Gradissimo A, Gonzalez P, Safaeian M, Schiffman M , Burk RD",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,Experiment 1,Costa Rica,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 1 HPV (progression),HPV progression to CIN2+ lesion diagnosis,70,33,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 4,27 May 2020,Cynthia Anderson,WikiWorks743,Bacteria associated with progression to CIN2+ identified using LEfSe,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella paludivivens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|976|200643|171549|171552|838|185294;2|1239|91061|186826|33958|1578|147802,Complete,Fatima Zohra
Study 287,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M, Zolnik CP, Castle PE, Porras C, Herrero R, Gradissimo A, Gonzalez P, Safaeian M, Schiffman M , Burk RD",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,Experiment 2,Costa Rica,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 2 HPV (progression),HPV progression to CIN2+ lesion diagnosis,69,33,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4,27 May 2020,Cynthia Anderson,WikiWorks743,Bacteria associated with progression to CIN2+ identified using LEfSe,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas circumdentaria,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus prevotii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella bergeri,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium gleum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus",2|976|200643|171549|171552|838|419005;2|976|200643|171549|171551|836|29524;2|1239|1737404|1737405|1570339|543311|33033;2|1239|909932|1843489|31977|39948|487173;2|1239|1737404|1737405|1570339|165779|33034;2|1239|1737404|1737405|1570339|162289|54005;2|1239|186801|186802|186804|1870884|1496;2|1239|91061|1385|1378|84136;2|976|117743|200644|2762318|59732|250;2|1239|186801|186802|186803|33042|33043,Complete,Fatima Zohra
Study 287,time series / longitudinal observational,32214382,10.1371/journal.ppat.1008376,NA,"Usyk M, Zolnik CP, Castle PE, Porras C, Herrero R, Gradissimo A, Gonzalez P, Safaeian M, Schiffman M , Burk RD",Cervicovaginal microbiome and natural history of HPV in a longitudinal study,PLoS pathogens,2020,Experiment 2,Costa Rica,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV (clearance),Visit 2 HPV (progression),HPV progression to CIN2+ lesion diagnosis,69,33,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4,27 May 2020,Cynthia Anderson,WikiWorks743,Bacteria associated with progression to CIN2+ identified using LEfSe,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium minutum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii",2|201174|84998|84999|1643824|1380|1381;2|201174|1760|2037|2049|1654|544581,Complete,Fatima Zohra
Study 288,case-control,29502926,10.1016/j.numecd.2018.01.004,NA,"Verduci E, Moretti F, Bassanini G, Banderali G, Rovelli V, Casiraghi MC, Morace G, Borgo F , Borghi E",Phenylketonuric diet negatively impacts on butyrate production,"Nutrition, metabolism, and cardiovascular diseases : NMCD",2018,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,Phenylketonuria,ORPHANET:716,mild hyperphenylalaninemic with unrestricted diet,phenylketonuric with Phe-restricted diet,phenylketonuric patients with restricted (phenylalanine-free) diets,21,21,3 months,16S,23,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,29 May 2020,Aboud Ezzeddine,WikiWorks743,"Microbial quantification, in phenylketonuric (PKU) and mild hyperphenylalaninemia (MHP) children, of Faecalibacterium prausnitzii, and Roseburia spp",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186803|841;2|1239|91061|186826|33958|1578,Complete,NA
Study 289,case-control,31808612,10.1111/jcmm.14880,NA,"Sun Q, Xu X, Zhang J, Sun M, Tian Q, Li Q, Cao W, Zhang X, Wang H, Liu J, Zhang J, Meng X, Wu L, Song M, Liu H, Wang W , Wang Y",Association of suboptimal health status with intestinal microbiota in Chinese youths,Journal of cellular and molecular medicine,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,health trait,EFO:0007652,healthy controls,suboptimal health status,SHSQ-25 (SHS score >= 35),50,50,2 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 1,Figure 5,29 May 2020,Rimsha Azhar,WikiWorks743,LDA score of LEfSe analysis between suboptimal health status (SHS) and control group,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Cyanobacteria,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|1239|186801|186802|186807;2|1117;2|976|117743|200644|2762318|59732;2|976|200643|171549|171550;2|1239|186801|186802|216572|119852;2|74201;2|1239|186801|186802|216572|1263;2|1239|186801|186802|541000;2|1239|186801|186802|186803|841,Complete,NA
Study 289,case-control,31808612,10.1111/jcmm.14880,NA,"Sun Q, Xu X, Zhang J, Sun M, Tian Q, Li Q, Cao W, Zhang X, Wang H, Liu J, Zhang J, Meng X, Wu L, Song M, Liu H, Wang W , Wang Y",Association of suboptimal health status with intestinal microbiota in Chinese youths,Journal of cellular and molecular medicine,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,health trait,EFO:0007652,healthy controls,suboptimal health status,SHSQ-25 (SHS score >= 35),50,50,2 months,16S,4,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,increased,unchanged,increased,NA,unchanged,Signature 2,Figure 5,29 May 2020,Rimsha Azhar,WikiWorks743,LDA score of LEfSe analysis between suboptimal health status (SHS) and control group,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224|1236|91347|1903414|581;2|1224|28216|80840|119060|48736;2|1224|28216;2|1224|28216|80840|506;2|1224|28216|80840|995019|40544,Complete,NA
Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,Experiment 1,Netherlands,Homo sapiens,mouth,UBERON:0000165,oral mucositis,EFO:1001904,no ulcerative oral mucositis,ulcerative oral mucositis,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,29 May 2020,William Lam,WikiWorks743,Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|81852|1350;2|1239|91061|186826|1300|1301;2|1239|91061|1385|90964|1279;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|838,Complete,NA
Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,Experiment 1,Netherlands,Homo sapiens,mouth,UBERON:0000165,oral mucositis,EFO:1001904,no ulcerative oral mucositis,ulcerative oral mucositis,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,29 May 2020,William Lam,WikiWorks743,Minimum entropy decomposition nodes (MEDs) that significantly discriminate multiple myeloma patients that did not develop uclerative oral mucositis and patients that did develop uclerative oral mucositis before auto stem cell transplant identified by LEfSe,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|1654,Complete,NA
Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,Experiment 2,Netherlands,Homo sapiens,mouth,UBERON:0000165,oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 1, Figure 2a and text",29 May 2020,William Lam,WikiWorks743,Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.",2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|201174|1760|2037|2049|1654|29317;2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906|187326;2|1239|909932|1843489|31977|29465|1926307,Complete,NA
Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,Experiment 2,Netherlands,Homo sapiens,mouth,UBERON:0000165,oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 1, Figure 2a and text",29 May 2020,William Lam,WikiWorks743,Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in non-uclerative oral mucositis group,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2742598|1613;2|201174|1760|85004|31953|196081|230143,Complete,NA
Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,Experiment 3,Netherlands,Homo sapiens,mouth,UBERON:0000165,oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2a and text,29 May 2020,William Lam,WikiWorks743,Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella sanguinis",2|1239|91061|186826|1300|1301|113107;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1654|55565;2|1239|91061|1385|1378|1379;2|1239|91061|1385|1378|29391;2|1239|91061|1385|1378|84135,Complete,NA
Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,Experiment 3,Netherlands,Homo sapiens,mouth,UBERON:0000165,oral mucositis,EFO:1001904,one and two weeks after stem cell transplant,pre- and three month after auto stem cell transplant,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2a and text,29 May 2020,William Lam,WikiWorks743,Based on principle component analysis asses taxa were responsible for the observed microbial shifts over time in uclerative oral mucositis group,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus caprae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus warneri,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis",2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964|1279|29380;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1292;2|201174|1760|85004|31953|196081|230143;2|1239|91061|186826|81852|1350|1351,Complete,NA
Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,Experiment 4,Netherlands,Homo sapiens,mouth,UBERON:0000165,oral mucositis,EFO:1001904,low or no fungi load,0.1% or higher fungi load,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5 and text,29 May 2020,William Lam,WikiWorks743,Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|201174|1760|85004|31953|196081;2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578,Complete,NA
Study 290,time series / longitudinal observational,31729407,10.1038/s41598-019-53073-w,NA,"Laheij AMGA, Raber-Durlacher JE, Koppelmans RGA, Huysmans MDNJM, Potting C, van Leeuwen SJM, Hazenberg MD, Brennan MT, von Bültzingslöwen I, Johansson JE, de Soet JJ, Haverman TM, Buijs MJ, Brandt BW, Rozema FR, Blijlevens NMA , Zaura E",Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients,Scientific reports,2019,Experiment 4,Netherlands,Homo sapiens,mouth,UBERON:0000165,oral mucositis,EFO:1001904,low or no fungi load,0.1% or higher fungi load,patient developed uclerative oral mucositis,31,20,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5 and text,29 May 2020,William Lam,WikiWorks743,Principle component analysis of salivary microbial profiles based on fungal load relative to bacterial 16s rDNA,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|909932|1843489|31977|29465;2|201174|1760|2037|2049|1654;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1239|91061|186826|1300|1301,Complete,NA
Study 291,case-control,30263008,10.7150/ijbs.24151,NA,"Ishaq HM, Mohammad IS, Shahzad M, Ma C, Raza MA, Wu X, Guo H, Shi P , Xu J",Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients,International journal of biological sciences,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Graves disease,EFO:0004237,healthy controls,graves disease,graves' disease patients,11,27,2 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,"Fig 5, Fig6, Table 6,7 and text",30 May 2020,Rimsha Azhar,WikiWorks743,Gut microbial composition differences between Graves' disease and control at different levels,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii",2|976|200643|171549|171552;2|1224|1236|135625|712;2|976|200643|171549|171552|838;2|1224|1236|135625|712|724;2|1224|29547|213849|72294|194|204;2|1239|909932|1843489|31977|29465|1926307;2|1224|1236|91347|1903414|581|582,Complete,NA
Study 291,case-control,30263008,10.7150/ijbs.24151,NA,"Ishaq HM, Mohammad IS, Shahzad M, Ma C, Raza MA, Wu X, Guo H, Shi P , Xu J",Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients,International journal of biological sciences,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Graves disease,EFO:0004237,healthy controls,graves disease,graves' disease patients,11,27,2 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Fig 5, Fig6, Table 6,7 and text",30 May 2020,Rimsha Azhar,WikiWorks743,Gut microbial composition differences between Graves' disease and control at different levels,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.",2|1224|1236|91347|543;2|1239|909932|1843489|31977;2|976|200643|171549|171550;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|216851;2|1239|91061|186826|33958|1578|1596;2|976|200643|171549|171550|239759|1872444,Complete,NA
Study 292,prospective cohort,32150591,10.1371/journal.ppat.1008348,NA,"Oku S, Takeshita T, Futatsuki T, Kageyama S, Asakawa M, Mori Y, Miyamoto T, Hata J, Ninomiya T, Kashiwazaki H , Yamashita Y",Disrupted tongue microbiota and detection of nonindigenous bacteria on the day of allogeneic hematopoietic stem cell transplantation,PLoS pathogens,2020,Experiment 1,Japan,Homo sapiens,tongue,UBERON:0001723,graft versus host disease,MONDO:0013730,community-dwelling,allogeneic-hematopoietic stem cell transplant,patient ages 36-69 years old undergoing allogeneic- hematopoietic stem cell transplantation,164,45,NA,16S,12,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Fig. 2, Table 2, Table 3 and Supplemental Table S1",31 May 2020,William Lam,WikiWorks743,Relative abundances of predominant bacterial genera in the tongue microbiota of community-dwelling adults and allogeneic-hematopoietic stem cell transplantation patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus paracasei,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Xanthomonas|s__Xanthomonas arboricola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus rhamnosus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus casei,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter ursingii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella|s__Brucella anthropi,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia acidovorans,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria macacae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas stutzeri",2|1239|91061|186826|33958|2759736|1597;2|1239|91061|1385|90964|1279|1283;2|1239|91061|1385|90964|1279|1290;2|1224|28216|80840|119060|48736|329;2|1224|1236|135614|32033|338|56448;2|1239|186801|186802|31979|1485;2|1239|91061|186826|81852|1350|53345;2|1239|91061|186826|33958|2759736|47715;2|1239|91061|186826|33958|2759736|1582;2|201174|1760|85007|1653|1716|38304;2|1224|1236|2887326|468|469;2|1239|91061|186826|81852|1350|1351;2|976|117743|200644|49546|1016;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|1313;2|1224|1236|135614|32033|40323|40324;2|1224|1236|2887326|468|469|108980;2|1224|28216|80840|80864|219181|1898956;2|1224|1236|91347|543|547|158836;2|1239|1737404|1737405|1570339|150022|1260;2|201174|1760|2037|2049|2767327|82135;2|1224|28211|356|118882|234|529;2|1224|28216|80840|80864|80865|80866;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|33958|1243|1246;2|1224|28216|206351|481|482|496;2|1239|186801|186802|31979|1485|1492;2|1239|909932|909929|1843491|970|2053611;2|1224|1236|72274|135621|286|316,Complete,NA
Study 292,prospective cohort,32150591,10.1371/journal.ppat.1008348,NA,"Oku S, Takeshita T, Futatsuki T, Kageyama S, Asakawa M, Mori Y, Miyamoto T, Hata J, Ninomiya T, Kashiwazaki H , Yamashita Y",Disrupted tongue microbiota and detection of nonindigenous bacteria on the day of allogeneic hematopoietic stem cell transplantation,PLoS pathogens,2020,Experiment 1,Japan,Homo sapiens,tongue,UBERON:0001723,graft versus host disease,MONDO:0013730,community-dwelling,allogeneic-hematopoietic stem cell transplant,patient ages 36-69 years old undergoing allogeneic- hematopoietic stem cell transplantation,164,45,NA,16S,12,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Fig. 2, Table 2, Table 3 and Supplemental Table S1",31 May 2020,William Lam,WikiWorks743,Relative abundances of predominant bacterial genera in the tongue microbiota of community-dwelling adults and allogeneic-hematopoietic stem cell transplantation patients,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum",2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838;2|1224|28216|206351|481|482;2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|32066|203490|203491|203492|848;2|1239|91061|1385|1378;2|976|200643|171549|171552|1283313;2|32066|203490|203491|1129771|32067;2|201174|84998|84999|1643824|1380;2|1239|526524|526525|128827|123375;2|1239|186801|186802|186803|265975;2|1224|29547|213849|72294|194;2|1239|186801|186802|186803|1164882,Complete,NA
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 1,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,Baseline HPV-,Baseline HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,unchanged,Signature 1,Figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,increased,"k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Tenericutes,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma",2|544448|31969;2|544448;2|544448|31969|2085;2|544448|31969|2085|2092;2|544448|31969|2085|2092|2129,Complete,Fatima Zohra
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 1,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,Baseline HPV-,Baseline HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,unchanged,Signature 2,figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,decreased,"k__Bacteria|p__Deinococcus-Thermus|c__Deinococci,k__Bacteria|p__Deinococcus-Thermus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Listeriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1297|188787;2|1297;2|1239|186801|186802|216572|216851;2|1239|1737404|1582879;2|1239|91061|1385|186820;2|1239|91061|1385|186820|2755;2|1224|1236|135613|72276;2|1224|1236|118969|118968|873565;2|1224|1236|118969|118968;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848,Complete,Fatima Zohra
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 2,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,no new acquisition of HPV within a year,new acquisition of HPV within a year,New HPV-type acquisition confirmed by HPV assay and genotyping,109,24,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,2|201174|1760|2037|2049|1654,Complete,Fatima Zohra
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 3,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,with at least one HPV type cleared in a year,without any HPV type cleared,No HPV-type cleared confirmed by HPV assay and genotyping,75,15,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status,decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales",2|1224|28211|204455|31989;2|1224|28211|204455,Complete,Fatima Zohra
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 4,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma|s__Ureaplasma parvum,2|544448|31969|2085|2092|2129|134821,Complete,Fatima Zohra
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 4,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by HPV assay and genotyping,43,90,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,decreased,"k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella|s__Ezakiella massiliensis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1239|1737404|1582879|1852374;2|1224|1236|72274|135621|286|287,Complete,Fatima Zohra
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 5,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,no new acquisition of HPV within a year,new acquisition of HPV within a year,New HPV-type acquisition confirmed by HPV assay and genotyping,109,24,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oulorum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus",2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|171552|838|28133;2|976|200643|171549|171552|838|28136;2|1239|909932|1843489|31977|39948|218538,Complete,Fatima Zohra
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 6,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,with any HPV type cleared in a year,without any HPV type cleared,No HPV-type cleared confirmed by HPV assay and genotyping,75,15,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella asaccharolytica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Myxococcales|f__Labilitrichaceae|g__Labilithrix|s__Labilithrix luteola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnotalea|s__Lachnotalea glycerini",2|1239|91061|1385|1378|502393;2|976|200643|171549|171552|838|419005;2|1224|28221|29|1524216|1524217|1391654;2|1239|186801|186802|186803|1763508|1763509,Complete,Fatima Zohra
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 7,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,no HPV type persisted,at least one HPV type persisted,Any HPV-type persisted confirmed by HPV assay and genotyping,64,29,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Microvirga|s__Microvirga lupini,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus radiopugnans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium|s__Anaerobacterium chartisolvens",2|976|200643|171549|171552|838|386414;2|1224|28211|356|119045|186650|420324;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|186803|33042|410072;2|1297|188787|118964|183710|1298|1182571;2|1239|186801|186802|216572|1486725|1297424,Complete,Fatima Zohra
Study 293,time series / longitudinal observational,30463989,10.1158/1940-6207.CAPR-18-0233,NA,"Ritu W, Enqi W, Zheng S, Wang J, Ling Y , Wang Y","Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women","Cancer prevention research (Philadelphia, Pa.)",2019,Experiment 7,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,no HPV type persisted,at least one HPV type persisted,Any HPV-type persisted confirmed by HPV assay and genotyping,64,29,2 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,figure 3,1 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to HPV status at the OTU level,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,2|1239|91061|186826|33958|1578|1584,Complete,Fatima Zohra
Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,baseline,post-induction therapy,6 weeks of remission induction therapy,112,97,NA,16S,123,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,"Table 1, Figure 1 and  2, Supplemental Table S3",2 June 2020,William Lam,WikiWorks743,Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post induction,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239;2|1239|186801|186802|31979;2|1239|91061|186826|1300;2|1239|91061|186826|81852;2|1239|91061|186826|33958,Complete,NA
Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,baseline,post-induction therapy,6 weeks of remission induction therapy,112,97,NA,16S,123,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,"Table 1, Figure 1 and  2, Supplemental Table S3",2 June 2020,William Lam,WikiWorks743,Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post induction,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Verrucomicrobia",2|976;2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|541000;2|201174;2|74201,Complete,NA
Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,baseline,post-consolidation therapy,8 weeks of consolidation,112,107,NA,16S,123,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Table 1, Figure 1 and  2, Supplemental Table S3",2 June 2020,William Lam,WikiWorks743,Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to postconsildation,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239;2|1239|186801|186802|186803|572511|1955243;2|1239|186801|186802|31979;2|1239|91061|186826|33958,Complete,NA
Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,baseline,post-consolidation therapy,8 weeks of consolidation,112,107,NA,16S,123,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Table 1, Figure 1 and  2, Supplemental Table S3",2 June 2020,William Lam,WikiWorks743,Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to postconsildation,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Actinobacteria",2|976;2|201174,Complete,NA
Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,baseline,post re-induction therapy,120 weeks of continuation phase with the last 17-20 weeks of reinduction II therapy,112,90,NA,16S,123,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 1,"Table 1, Figure 1 and  2, Supplemental Table S3",2 June 2020,William Lam,WikiWorks743,Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post re-induction,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|1239;2|1239|186801|186802|31979;2|1239|91061|186826|81852;2|1239|91061|186826|33958,Complete,NA
Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,baseline,post re-induction therapy,120 weeks of continuation phase with the last 17-20 weeks of reinduction II therapy,112,90,NA,16S,123,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,decreased,unchanged,decreased,NA,NA,Signature 2,"Table 1, Figure 1 and  2, Supplemental Table S3",2 June 2020,William Lam,WikiWorks743,Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post re-induction,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Verrucomicrobia",2|1239|186801|186802|541000;2|1239|186801|186802|216572|216851|1971605;2|201174;2|74201,Complete,NA
Study 294,time series / longitudinal observational,29518185,10.1093/cid/ciy153,NA,"Hakim H, Dallas R, Wolf J, Tang L, Schultz-Cherry S, Darling V, Johnson C, Karlsson EA, Chang TC, Jeha S, Pui CH, Sun Y, Pounds S, Hayden RT, Tuomanen E , Rosch JW",Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,non-febrile neutropenia,febrile neutropenia,fever as an oral temperature more than 38.0°C persisting for more than 1 hour; neutropenia as an absolute neutrophil count less than or equal to 500 cells per microliter after baseline first sampled,42,122,NA,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplemental Table S6, Figure 5a",2 June 2020,William Lam,WikiWorks743,Comparison of baseline diversity and composition between acute lymphoblastic leukemia children with and without febrile neutropenia occurring throughout therapy,increased,k__Bacteria|p__Proteobacteria,2|1224,Complete,NA
Study 295,"cross-sectional observational, not case-control",31555603,10.3389/fcimb.2019.00294,NA,"Zhou Y, Wang L, Pei F, Ji M, Zhang F, Sun Y, Zhao Q, Hong Y, Wang X, Tian J , Wang Y",Patients With LR-HPV Infection Have a Distinct Vaginal Microbiota in Comparison With Healthy Controls,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,negative control,low risk HPV,LR-HPV+ according to results of screening,20,42,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Figure 4B,2 June 2020,Cynthia Anderson,"WikiWorks743,Lwaldron",Comparisons of vaginal bacteria between the NC and HPV-LR groups,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Tenericutes",2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|976|200643|171549|171550|239759;2|201174|1760|85004|31953|1678;2|1224|28221|213115|194924|35832;2|1239|186801|186802|186803|572511;2|1224|28216|80840|119060;2|976|200643|171549|1853231|574697;2|1239|186801;2|1239|186801|186802|31979|1485;2|1224|28216|80840|80864;2|976|200643|171549|2005519|1348911;2|1239|186801|186802|186803|33042;2|1224|28216|80840|80864|80865;2|1239|909932|1843489|31977|39948;2|1224|28211|356|212791;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802;2|1239|186801|186802|186803|1407607;2|32066;2|32066|203490|203491;2|32066|203490;2|1239|186801|186802|204475;2|1224|2008785|119069|206349;2|1224|2008785|119069;2|1224|2008785|119069|206349|70774;2|1239|186801|186802|186803;2|32066|203490|203491|1129771;2|1239|909932|1843489|31977|906;2|544448|31969;2|1239|186801|186802|541000;2|1224|1236|135625|712|745;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|186802|186804;2|1239|186801|186802|186804|1257;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171550;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1200657;2|32066|203490|203491|1129771|168808;2|1224|28216|80840|995019|40544;2|1224|28216|80840|995019;2|544448,Complete,Fatima
Study 295,"cross-sectional observational, not case-control",31555603,10.3389/fcimb.2019.00294,NA,"Zhou Y, Wang L, Pei F, Ji M, Zhang F, Sun Y, Zhao Q, Hong Y, Wang X, Tian J , Wang Y",Patients With LR-HPV Infection Have a Distinct Vaginal Microbiota in Comparison With Healthy Controls,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,negative control,low risk HPV,LR-HPV+ according to results of screening,20,42,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,NA,increased,NA,NA,Signature 2,Figure 4B,2 June 2020,Cynthia Anderson,WikiWorks743,Comparisons of vaginal bacteria between the NC and HPV-LR groups,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Nitrososphaera,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Archaea|p__Thaumarchaeota,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales,k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae",2|1224|1236|72274|135621|351;2|1224|1236|72274|135621|286;2|1224|1236|72274;2|1224|1236;2|976|117743|200644|49546|237;2|1224|1236|135614|32033|68;2|1224|1236|135624|83763|83770;2157|651137|1643678|1033996|1033997|497726;2|1224|1236|135624|83763;2157|651137|1643678|1033996;2|1224|29547|213849|72293|209;2|1224|29547|213849|72293;2157|651137;2|1224|1236|135624;2157|651137|1643678|1033996|1033997,Complete,Fatima Zohra
Study 296,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, Wang J, Li J, Lin J, Su M, Li G, Wu M, Qiu L, Xiang J, Xie L, Jia W , Zhou W",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,health control,multiple myeloma,newly diagnosed multiple myeloma patients,16,20,NA,16S,12,RT-qPCR,DESeq2,0.01,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental table S2,4 June 2020,William Lam,WikiWorks743,The differential species and subspecies identified by DESeq2 (abs(log2(fold change)) > 1 and adjusted P < 0.05) enriched in multiple myeloma patients and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella ruminicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella fusca,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter aphrophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera elsdenii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter valericigenes",2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|244366;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1302;2|1224|1236|91347|543|547|550;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1304;2|201174|1760|85004|31953|1678|1689;2|1224|1236|91347|543|544|546;2|201174|84998|84999|84107|102106|74426;2|1239|91061|186826|1300|1301|28037;2|1224|1236|91347|543|570|548;2|976|200643|171549|171552|838|839;2|976|200643|171549|171552|838|589436;2|1239|91061|186826|1300|1301|1328;2|976|200643|171549|171552|838|28132;2|1239|186801|186802|1392389|1297617;2|1239|91061|186826|1300|1301|1313;2|1224|1236|91347|543|160674|54291;2|201174|1760|85004|31953|1678|1680;2|1224|1236|135625|712|416916|732;2|1224|1236|91347|543|547|61645;2|1239|909932|1843489|31977|906|907;2|1239|186801|186802|216572|459786|351091,Complete,NA
Study 296,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, Wang J, Li J, Lin J, Su M, Li G, Wu M, Qiu L, Xiang J, Xie L, Jia W , Zhou W",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,health control,multiple myeloma,newly diagnosed multiple myeloma patients,16,20,NA,16S,12,RT-qPCR,DESeq2,0.01,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental table S2,4 June 2020,William Lam,WikiWorks743,The differential species and subspecies identified by DESeq2 (abs(log2(Fold Change)) > 1 and adjusted P < 0.05) enriched in multiple myeloma patients and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pasteurianus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium baratii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saccharobutylicum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio proteoclasticus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio hungatei,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium saccharoperbutylacetonicum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Herbinix|s__Herbinix luporum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium beijerinckii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Paeniclostridium|s__Paeniclostridium sordellii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium botulinum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum|s__Bifidobacterium catenulatum subsp. kashiwanohense,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium varium",2|1239|91061|186826|1300|1301|197614;2|1239|186801|186802|186803|1506553|66219;2|1239|186801|186802|31979|1485|1561;2|1239|186801|186802|31979|1485|169679;2|1239|186801|186802|186803|830|43305;2|1239|186801|186802|186804|1870884|1496;2|1239|186801|186802|186803|830|185008;2|976|200643|171549|815|816|246787;2|1239|186801|186802|31979|1485|36745;2|976|200643|171549|2005525|375288|1869337;2|976|200643|171549|815|816|28116;2|1239|186801|186802|186803|1663717|1679721;2|976|200643|171549|815|816|818;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802|186803|28050|39485;2|976|200643|171549|815|816|47678;2|201174|1760|85004|31953|1678|1686;2|1239|186801|186802|31979|1485|1520;2|1239|186801|186802|186804|1849828|1505;2|1239|186801|186802|31979|1485|1491;2|1239|186801|186802|186803|207244|649756;2|1239|909932|909929|1843491|158846|158847;2|1239|186801|186802|31979|1485|1492;2|201174|1760|85004|31953|1678|1686|630129;2|201174|1760|85004|31953|1678|28026;2|32066|203490|203491|203492|848|856,Complete,NA
Study 296,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, Wang J, Li J, Lin J, Su M, Li G, Wu M, Qiu L, Xiang J, Xie L, Jia W , Zhou W",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,health control,multiple myeloma,newly diagnosed multiple myeloma patients,18,19,NA,WMS,12,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 1c,1d, 2b",4 June 2020,William Lam,WikiWorks743,Nitrogen- recycling bacteria species with differential abundance in multiple myeloma patients and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella|s__Raoultella ornithinolytica,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella variicola,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae",2|1224|1236|91347|543|160674|54291;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|547|550;2|1224|1236|91347|543|570|548;2|1224|1236|91347|543|570|244366;2|1224|1236|91347|543|570|573;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1302;2|1239|91061|186826|1300|1301|1313,Complete,NA
Study 296,case-control,32466801,10.1186/s40168-020-00854-5,NA,"Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, Wang J, Li J, Lin J, Su M, Li G, Wu M, Qiu L, Xiang J, Xie L, Jia W , Zhou W",Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria,Microbiome,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,multiple myeloma,EFO:0001378,health control,multiple myeloma,newly diagnosed multiple myeloma patients,18,19,NA,WMS,12,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 1c,1d, 2b",4 June 2020,William Lam,WikiWorks743,Nitrogen- recycling bacteria species with differential abundance in multiple myeloma patients and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica",2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|186803|2719231|84030,Complete,NA
Study 297,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y, Hong Z, Wang W, Gu L, Gao H, Qiu L , Di W",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,Experiment 1,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,human papilloma virus infection,EFO:0001668,non pregnant no HPV,non pregnant high risk HPV,non pregnant high risk HPV confirmed using HPV genotyping kit,30,19,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 5,3 June 2020,Cynthia Anderson,WikiWorks743,The unique taxa and microbiomarkers for different groups,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",2|201174|1760|85004|31953|1678;2|976;2|1239|91061|1385;2|1239|91061|1385|186817;2|1239|91061|1385|186817|1386,Complete,Fatima Zohra
Study 297,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y, Hong Z, Wang W, Gu L, Gao H, Qiu L , Di W",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,Experiment 1,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,human papilloma virus infection,EFO:0001668,non pregnant no HPV,non pregnant high risk HPV,non pregnant high risk HPV confirmed using HPV genotyping kit,30,19,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 5,3 June 2020,Cynthia Anderson,WikiWorks743,The unique taxa and microbiomarkers for different groups,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826,Complete,Fatima Zohra
Study 297,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y, Hong Z, Wang W, Gu L, Gao H, Qiu L , Di W",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,Experiment 2,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,human papilloma virus infection,EFO:0001668,pregnant no HPV,pregnant high risk HPV,pregnant high risk HPV confirmed using HPV genotyping kit,48,38,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 5,3 June 2020,Cynthia Anderson,WikiWorks743,The unique taxa and microbiomarkers for different groups,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax",2|1224;2|1224|28216;2|1224|28216|80840|80864;2|1224|28216|80840;2|1224|28216|80840|80864|12916,Complete,Fatima Zohra
Study 297,prospective cohort,31370796,10.1186/s12879-019-4279-6,NA,"Chen Y, Hong Z, Wang W, Gu L, Gao H, Qiu L , Di W",Association between the vaginal microbiome and high-risk human papillomavirus infection in pregnant Chinese women,BMC infectious diseases,2019,Experiment 2,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,human papilloma virus infection,EFO:0001668,pregnant no HPV,pregnant high risk HPV,pregnant high risk HPV confirmed using HPV genotyping kit,48,38,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 5,3 June 2020,Cynthia Anderson,WikiWorks743,The unique taxa and microbiomarkers for different groups,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061;2|1239|186801|186802|186803;2|1239|186801;2|1239|186801|186802;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,Fatima Zohra
Study 298,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña JR, Smith DP, Sahasrabhojane P, Wadsworth WD, Fellman BM, Ajami NJ, Shpall EJ, Daver N, Guindani M, Petrosino JF, Kontoyiannis DP , Shelburne SA",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,Experiment 1,United States of America,Homo sapiens,"feces,mouth","UBERON:0001988,UBERON:0000165",acute myeloid leukemia,EFO:0000222,oral,stool,stool samples collected from 59 patients with acute myeloid leukemia after induction chemotherapy,483,365,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 1a, Figure 4, Supplemental Figure S1",5 June 2020,William Lam,WikiWorks743,"The significant differences in relative abundances of genera all patient stability categories (stable, average or variable) based on either the coefficient of variation (CV) of the Shannon diversity index between oral and stool samples after induction chemotherapy",increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|74201|203494|48461|1647988|239934;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1239|186801|186802|186803|46205;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300|1301;2|1239|91061|1385|90964|1279;2|1239|186801|186802|216572|292632,Complete,NA
Study 298,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña JR, Smith DP, Sahasrabhojane P, Wadsworth WD, Fellman BM, Ajami NJ, Shpall EJ, Daver N, Guindani M, Petrosino JF, Kontoyiannis DP , Shelburne SA",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,Experiment 1,United States of America,Homo sapiens,"feces,mouth","UBERON:0001988,UBERON:0000165",acute myeloid leukemia,EFO:0000222,oral,stool,stool samples collected from 59 patients with acute myeloid leukemia after induction chemotherapy,483,365,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 1a, Figure 4, Supplemental Figure S1",5 June 2020,William Lam,WikiWorks743,"The significant differences in relative abundances of genera all patient stability categories (stable, average or variable) based on either the coefficient of variation (CV) of the Shannon diversity index between oral and stool samples after induction chemotherapy",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|838;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300|1301,Complete,NA
Study 298,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña JR, Smith DP, Sahasrabhojane P, Wadsworth WD, Fellman BM, Ajami NJ, Shpall EJ, Daver N, Guindani M, Petrosino JF, Kontoyiannis DP , Shelburne SA",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,Experiment 2,United States of America,Homo sapiens,"feces,mouth","UBERON:0001988,UBERON:0000165",acute myeloid leukemia,EFO:0000222,no infection,infection,acute myeloid leukemia patients that were microbiologically documented with infection during induction chemotherapy before neutrophil recovery,30,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 5a, e",5 June 2020,William Lam,WikiWorks743,Oral temporal instability of microbiome α-diversity is associated with infectious outcomes during chemotherapy,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135614|32033|40323;2|1239|91061|186826|1300|1301,Complete,NA
Study 298,time series / longitudinal observational,28245856,10.1186/s13073-017-0409-1,NA,"Galloway-Peña JR, Smith DP, Sahasrabhojane P, Wadsworth WD, Fellman BM, Ajami NJ, Shpall EJ, Daver N, Guindani M, Petrosino JF, Kontoyiannis DP , Shelburne SA",Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients,Genome medicine,2017,Experiment 3,United States of America,Homo sapiens,"feces,mouth","UBERON:0001988,UBERON:0000165",acute myeloid leukemia,EFO:0000222,no infection,infection,acute myeloid leukemia patients that were microbiologically documented with infection during induction chemotherapy before neutrophil recovery,30,15,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 5b, e",5 June 2020,William Lam,WikiWorks743,Stool temporal instability of microbiome α-diversity is associated with infectious outcomes during chemotherapy,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 299,time series / longitudinal observational,32115690,10.1002/ijc.32942,NA,"De Pietri S, Ingham AC, Frandsen TL, Rathe M, Krych L, Castro-Mejía JL, Nielsen DS, Nersting J, Wehner PS, Schmiegelow K, Hasle H, Pamp SJ , Müller K",Gastrointestinal toxicity during induction treatment for childhood acute lymphoblastic leukemia: The impact of the gut microbiota,International journal of cancer,2020,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,no induction chemotherapy,induction chemotherapy,children (ages 1-18 years old) newly diagnosed with Acute Lymphoblastic Leukemia and undergoing induction chemotherapy according to the Nordic Society of Paediatric Haematology and Oncology (NOPHO),19,51,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 2, 4, Table 2",7 June 2020,William Lam,WikiWorks743,Relative abundance of Enterococcus spp. and Lachnospiraceae spp. compared to Day 1 to Day 15 of 29 days of induction chemotherapy,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,2|1239|91061|186826|81852|1350|35783,Complete,NA
Study 299,time series / longitudinal observational,32115690,10.1002/ijc.32942,NA,"De Pietri S, Ingham AC, Frandsen TL, Rathe M, Krych L, Castro-Mejía JL, Nielsen DS, Nersting J, Wehner PS, Schmiegelow K, Hasle H, Pamp SJ , Müller K",Gastrointestinal toxicity during induction treatment for childhood acute lymphoblastic leukemia: The impact of the gut microbiota,International journal of cancer,2020,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,acute lymphoblastic leukemia,EFO:0000220,no induction chemotherapy,induction chemotherapy,children (ages 1-18 years old) newly diagnosed with Acute Lymphoblastic Leukemia and undergoing induction chemotherapy according to the Nordic Society of Paediatric Haematology and Oncology (NOPHO),19,51,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 2, 4, Table 2",7 June 2020,William Lam,WikiWorks743,Relative abundance of Enterococcus spp. and Lachnospiraceae spp. compared to Day 1 to Day 15 of 29 days of induction chemotherapy,decreased,NA,NA,Complete,NA
Study 300,time series / longitudinal observational,28714953,10.1038/nn.4606,NA,"Shen S, Lim G, You Z, Ding W, Huang P, Ran C, Doheny J, Caravan P, Tate S, Hu K, Kim H, McCabe M, Huang B, Xie Z, Kwon D, Chen L , Mao J",Gut microbiota is critical for the induction of chemotherapy-induced pain,Nature neuroscience,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,non- graft- versus- host disease,acute graft- versus- host disease,individual's receiving Hematopoietic cell transplantation (HCT) and having a grade 1-4 for acute graft-versus-host-disease,14,52,NA,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,"Figure 2, text, table 2",9 June 2020,William Lam,WikiWorks743,Specific Bacteria at neutrophil recovery (more than 500 neutrophils per millimeter cube) correlated with subsequent development of Severe Acute Graft-versus-Host Disease in patient's receiving Hematopoietic cell transplantation (HCT),increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa",2|1239|186801|186802|186803|841|301301;2|1239|186801|186802|186803|1432051|1924109;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|81852|1350|1354;2|1239|91061|186826|33958|2767887|1624;2|1239|91061|186826|33958|2742598|1613;2|976|200643|171549|815|909656|357276;2|1239|526524|526525|128827|123375|102148;2|201174|1760|85006|1268|32207|43675,Complete,NA
Study 300,time series / longitudinal observational,28714953,10.1038/nn.4606,NA,"Shen S, Lim G, You Z, Ding W, Huang P, Ran C, Doheny J, Caravan P, Tate S, Hu K, Kim H, McCabe M, Huang B, Xie Z, Kwon D, Chen L , Mao J",Gut microbiota is critical for the induction of chemotherapy-induced pain,Nature neuroscience,2017,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,non- graft- versus- host disease,acute graft- versus- host disease,individual's receiving Hematopoietic cell transplantation (HCT) and having a grade 1-4 for acute graft-versus-host-disease,14,52,NA,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 2,"Figure 2, text, table 2",9 June 2020,William Lam,WikiWorks743,Specific Bacteria at neutrophil recovery (more than 500 neutrophils per millimeter cube) correlated with subsequent development of Severe Acute Graft-versus-Host Disease in patient's receiving Hematopoietic cell transplantation (HCT),decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__Erysipelatoclostridium ramosum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Candidatus Soleaferrea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae",2|1239|526524|526525|128827|1505663|1547;2|976|200643|171549|815|816|818;2|1239|186801|186802|186803|572511|89014;2|1239|186801|186802|1470353;2|1239|186801|186802|31979|580596|2049021;2|1239|186801|186802|186803|572511|1955243;2|1239|186801|186802|186803|189330|2040332;2|1239|186801|186802|216572|1263|41978;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|47678,Complete,NA
Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,Experiment 1,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV infection through PCR confirmation,9,9,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 3,9 June 2020,Cynthia Anderson,WikiWorks743,A comparison of the vaginal microbiota among nine HPV infection-discordant twin pairs,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|906;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066;2|32066|203490|203491|1129771|168808,Complete,Fatima Zohra
Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,Experiment 1,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV infection through PCR confirmation,9,9,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 3,9 June 2020,Cynthia Anderson,WikiWorks743,A comparison of the vaginal microbiota among nine HPV infection-discordant twin pairs,decreased,NA,NA,Complete,Fatima Zohra
Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,Experiment 2,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ through PCR confirmation,26,19,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1b,9 June 2020,Cynthia Anderson,WikiWorks743,Comparison of the vaginal microbiotas of the HIV+ and HIV- women without CIN,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales",2|32066|203490|203491|1129771|168808;2|32066|203490|203491|203492;2|32066|203490|203491,Complete,Fatima Zohra
Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,Experiment 3,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HR-HPV+,"HR-HPV+ through PCR confirmation, HPV genotype 16, 18, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 66",26,13,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,figure 1c,9 June 2020,Cynthia Anderson,WikiWorks743,Comparison of the vaginal microbiotas of HIV- and women infected with high risk high risk HPV types,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales",2|32066|203490|203491|1129771|168808;2|32066|203490|203491|203492;2|32066|203490|203491,Complete,Fatima Zohra
Study 301,"cross-sectional observational, not case-control",23717441,10.1371/journal.pone.0063514,NA,"Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J , Ko G",Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort,PloS one,2013,Experiment 3,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HR-HPV+,"HR-HPV+ through PCR confirmation, HPV genotype 16, 18, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 66",26,13,6 months,16S,23,Roche454,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,figure 1c,9 June 2020,Cynthia Anderson,WikiWorks743,Comparison of the vaginal microbiotas of HIV- and women infected with high risk high risk HPV types,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,2|1239|91061|186826,Complete,Fatima Zohra
Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,Experiment 1,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,healthy control,exacerbated asthma,physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation,21,20,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,8 July 2020,Lucy Mellor,WikiWorks743,Distinct bacterial composition in subjects with exacerbated asthma and healthy controls (phylum level),increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria",2|976;2|1224,Complete,NA
Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,Experiment 2,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,healthy control,non-exacerbated asthma,"physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care.",21,31,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 2,8 July 2020,Lucy Mellor,WikiWorks743,Distinct bacterial composition in subjects with non-exacerbated asthma and healthy controls (phyum level),increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria",2|976;2|1224,Complete,NA
Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,Experiment 3,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,non-exacerbated asthma,exacerbated asthma,physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation,31,20,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 3,10 June 2020,Victoria Goulbourne,WikiWorks743,Linear discriminant analysis (LDA) demonstrated distinct bacterial genera enriched in exacerbated and non-exacerbated asthma,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|976|200643|171549|171552|838;2|1224|1236|2887326|468|222991;2|201174|1760|85004|31953|2701,Complete,Lucy Mellor
Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,Experiment 3,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,non-exacerbated asthma,exacerbated asthma,physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation,31,20,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 3,10 June 2020,Victoria Goulbourne,WikiWorks743,Linear discriminant analysis (LDA) demonstrated distinct bacterial genera enriched in exacerbated and non-exacerbated asthma,decreased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,2|1239|909932|1843489|31977|39948,Complete,Lucy Mellor
Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,Experiment 4,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,healthy control,asthma,"physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care or with an encounter diagnosis of asthma exacerbation",21,51,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 4, text",8 July 2020,Lucy Mellor,WikiWorks743,Species differentially abundant between asthmatics and health controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccalis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges|s__Alkanindiges hongkongensis",2|976|200643|171549|171552|838|28127;2|1239|909932|1843489|31977|39948|218538;2|201174|1760|85004|31953|2701|2702;2|1224|1236|2887326|468|222991|208968,Complete,NA
Study 302,case-control,29518419,10.1016/j.jaci.2018.02.020,NA,"Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A , Bunyavanich S",The nasal microbiome in asthma,The Journal of allergy and clinical immunology,2018,Experiment 5,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,healthy control,asthma,"physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care or with an encounter diagnosis of asthma exacerbation",21,51,NA,16S,34,RT-qPCR,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,10 June 2020,Victoria Goulbourne,WikiWorks743,Difference in fold change between asthmatics and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccalis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",2|976|200643|171549|171552|838|28127;2|201174|1760|85004|31953|2701|2702,Complete,Lucy Mellor
Study 303,prospective cohort,26147207,10.1111/apt.13302,NA,"Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, Moreau P, Potel G, de La Cochetière MF, Batard E , Knights D",Chemotherapy-driven dysbiosis in the intestinal microbiome,Alimentary pharmacology & therapeutics,2015,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"non-Hodgkin's lymphoma patients post myeloablative conditiong regimen (chemotherapy) fecal sampling for 5 consecutive days of high-dose Carmustine, Etoposide, Aracytine and Melphalan and with no antibiotics treatment after starting regimen",15,28,discontinue antibiotics 1 day before chemotherapy treatment and 7 days within chemotherapy treatment,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Figure 2, 3b, Supplemental Table S1a-c, text",11 June 2020,William Lam,WikiWorks743,"Relative taxa abundance for non-Hodgkins Lymphoma patients from the fecal samples collected before and after chemotherapy, at the phylum, family and genera level",increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1224;2|1224|1236|91347|543;2|1239|91061|186826|186827;2|976|200643|171549|171551;2|1239|91061|186826|81852;2|1239|91061|186826|186828;2|1224|1236|91347|543|544;2|976|200643|171549|2005525|375288;2|1239|91061|186826|81852|1350,Complete,NA
Study 303,prospective cohort,26147207,10.1111/apt.13302,NA,"Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, Moreau P, Potel G, de La Cochetière MF, Batard E , Knights D",Chemotherapy-driven dysbiosis in the intestinal microbiome,Alimentary pharmacology & therapeutics,2015,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"non-Hodgkin's lymphoma patients post myeloablative conditiong regimen (chemotherapy) fecal sampling for 5 consecutive days of high-dose Carmustine, Etoposide, Aracytine and Melphalan and with no antibiotics treatment after starting regimen",15,28,discontinue antibiotics 1 day before chemotherapy treatment and 7 days within chemotherapy treatment,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Figure 2, 3b, Supplemental Table S1a-c, text",11 June 2020,William Lam,WikiWorks743,"Relative taxa abundance for non-Hodgkins Lymphoma patients from the fecal samples collected before and after chemotherapy, at the phylum, family and genera level",decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|1239;2|201174;2|1239|186801|186802|186803;2|1239|186801|186802|541000;2|201174|1760|85004|31953;2|201174|84998|84999|84107;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|33042;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|186803|841;2|1224|1236|91347|543;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543|570;2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|119852;2|1239|186801|186802|186803|28050;2|1239|909932|1843489|31977|906;2|201174|1760|85004|31953|1678;2|201174|84998|1643822|1643826|447020;2|1239|1737404|1737405|1570339|165779;2|201174|84998|84999|84107|102106,Complete,NA
Study 304,randomized controlled trial,27411009,10.1016/j.cmet.2016.06.016,NA,"Reijnders D, Goossens GH, Hermes GD, Neis EP, van der Beek CM, Most J, Holst JJ, Lenaerts K, Kootte RS, Nieuwdorp M, Groen AK, Olde Damink SW, Boekschoten MV, Smidt H, Zoetendal EG, Dejong CH , Blaak EE",Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial,Cell metabolism,2016,Experiment 1,Netherlands,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,or placebo (microcrystalline cellulose),oral intake of vancomycin (directed against Gram-positive bacteria),"low-active (<3 hr organized sports activities per week), weight-stable (<2 kg body weight change 3 months prior to inclusion) overweight/obese (BMI 25–35 kg/m2) Caucasian men, between 35 and 70 years with impaired glucose metabolism (either fasting glucose >5.6 mmol/l, and/or 2 hr glucose between 7.8–11 mmol/l) and insulin resistant (homeostasis model assessment for insulin resistance; HOMA-IR > 2.2).",37,38,3 months,16S,NA,Human Intestinal Tract Chip,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,decreased,NA,Signature 1,Table S1,8 June 2020,Mst Afroza Parvin,"WikiWorks743,Lwaldron",Significantly different microbial taxa after 7 days intervention with vancomycin and placebo in feces using linear mixed models,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax|s__Anaerovorax odorimutans,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter|s__Papillibacter cinnamivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella nexilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] cellulosi",2|1239|186801|186802|186803|207244|105841;2|1239|186801|186802|543314|109326|109327;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|572511|40520;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186803|33042|33043;2|1239|186801|186802|186803|189330|39486;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186803|140625|140626;2|1239|186801|186802|186803|28050|28052;2|1239|186801|186802|186803|2719231|29370;2|1239|91061|186826|33958|2767842|1590;2|1239|186801|186802|216572|100175|100176;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|186803|1506577|29361;2|1239|186801|186802|216572|29343,Complete,Rimsha Azhar
Study 305,case-control,32237205,10.1002/cam4.3027,NA,"Tsementzi D, Pena-Gonzalez A, Bai J, Hu YJ, Patel P, Shelton J, Dolan M, Arluck J, Khanna N, Conrad L, Scott I, Eng TY, Konstantinidis KT , Bruner DW",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,Experiment 1,NA,Homo sapiens,vagina,UBERON:0000996,"Genital neoplasm, female",EFO:1001331,healthy,cancer,postmenopausal women(naturally or due to hysterectomy) with endometrial or cervical cancer treated with radiotherapy with or without surgey and/or chemotherapy,69,65,course of the study,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,unchanged,increased,increased,NA,NA,increased,Signature 1,"Figure 3, Supplemental Figure 2",10 June 2020,Fatima Zohra,WikiWorks743,Differentially abundant bacterial operational taxonomic units between endometrial and cervical cancer and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria",2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|1239|1737404|1737405|1570339|162289;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|165779;2|1239|909932|1843489|31977|39948;2|32066|203490|203491|1129771|168808;2|544448|31969|2085|2092|2093;2|1239|1737404|1582879;2|1239|186801|186802|186803|437755;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186804|1257;2|32066|203490|203491|1129771|32067|104608;2|201174|1760|2037|2049|2050;2|976;2|32066,Complete,NA
Study 305,case-control,32237205,10.1002/cam4.3027,NA,"Tsementzi D, Pena-Gonzalez A, Bai J, Hu YJ, Patel P, Shelton J, Dolan M, Arluck J, Khanna N, Conrad L, Scott I, Eng TY, Konstantinidis KT , Bruner DW",Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women,Cancer medicine,2020,Experiment 1,NA,Homo sapiens,vagina,UBERON:0000996,"Genital neoplasm, female",EFO:1001331,healthy,cancer,postmenopausal women(naturally or due to hysterectomy) with endometrial or cervical cancer treated with radiotherapy with or without surgey and/or chemotherapy,69,65,course of the study,16S,4,Illumina,LEfSe,0.05,FALSE,3,NA,NA,unchanged,increased,increased,NA,NA,increased,Signature 2,"Figure 3, Supplemental Figure 2",10 June 2020,Fatima Zohra,WikiWorks743,Differentially abundant bacterial operational taxonomic units between endometrial and cervical cancer and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria",2|1239|186801|186802|186803|177971;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|1239;2|201174;2|1224,Complete,NA
Study 306,prospective cohort,31951695,10.21101/cejph.a5393,NA,"Parco S, Benericetti G, Vascotto F , Palmisciano G",Microbiome and diversity indices during blood stem cells transplantation - new perspectives?,Central European journal of public health,2019,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,pre- allogeneic hematopoietic stem cell transplant,post- allogeneic hematopoietic stem cell transplant,children between 3 and 10 years of age that has undergone allogeneic hematopoeitic stem cell transplantation and hospitalized at Institute for Maternal and Child Health of Trieste,5,5,NA,16S,123,Ion Torrent,T-Test,NA,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 4, 5, 6",12 June 2020,William Lam,WikiWorks743,Faecal microbiota levels of pre- and post allogeneic hematopoetic stem cell transplant in child with graft-versus- host- disease,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida",2|1224|1236|91347|543|160674;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|838;2|1239|91061|186826|33958|1578;2|1224|1236|72274|135621|286|303,Complete,NA
Study 306,prospective cohort,31951695,10.21101/cejph.a5393,NA,"Parco S, Benericetti G, Vascotto F , Palmisciano G",Microbiome and diversity indices during blood stem cells transplantation - new perspectives?,Central European journal of public health,2019,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,pre- allogeneic hematopoietic stem cell transplant,post- allogeneic hematopoietic stem cell transplant,children between 3 and 10 years of age that has undergone allogeneic hematopoeitic stem cell transplantation and hospitalized at Institute for Maternal and Child Health of Trieste,5,5,NA,16S,123,Ion Torrent,T-Test,NA,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 4, 5, 6",12 June 2020,William Lam,WikiWorks743,Faecal microbiota levels of pre- and post allogeneic hematopoetic stem cell transplant in child with graft-versus- host- disease,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas putida",2|1224|1236|91347|543|413496;2|1224|1236|91347|543|160674;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|838;2|1239|91061|186826|33958|1578;2|1224|1236|72274|135621|286|303,Complete,NA
Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Negative control group (CLT),moxifloxacin treated group (MXF),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,"Supplementary table 3, Supplementary figure 1",11 June 2020,Mst Afroza Parvin,WikiWorks743,A detailed analysis of the MGSs that differed significantly between treatment groups,increased,"k__Archaea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia",2157;2|1239|186801|186802|186803|572511,Complete,NA
Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Negative control group (CLT),moxifloxacin treated group (MXF),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,"Supplementary table 3, Supplementary figure 1",11 June 2020,Mst Afroza Parvin,"WikiWorks743,Lwaldron",A detailed analysis of the MGSs that differed significantly between treatment groups,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium|s__Cloacibacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|171550|239759|328814;2|976|200643|171549;2|976|200643|171549|2005519|397864|487174;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|28026;2|1224|28221|213115|194924|35832|35833;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|572511|1955243;2|976|200643|171549|1853231|574697;2|976|200643|171549|1853231|574697|544645;2|1239|526524|526525|2810280|135858;2|976|117743|200644|2762318|501783|1913682;2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979|1485|1506;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239;2|1224|1236|135625|712|724|729;2|1239|186801|186802|186804|1505657|261299;2|1239|186801|186802|186803|28050|39485;2|1239|186801|186802|186803;2|976|200643|171549|1853231|283168|28118;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|459786|1945593;2|1239|186801|186802|541000;2|976|200643|171549|2005525|375288|823;2|1224|28216|80840|995019|577310|487175;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|216572|1263|40519;2|1239|91061|186826|1300|1301|1318,Complete,NA
Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,Experiment 2,France,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,moxifloxacin treated group (MXF),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,14,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,"Supplementary table 3, Supplementary figure 1",14 June 2020,Mst Afroza Parvin,WikiWorks743,A detailed analysis of the MGSs that differed significantly between treatment groups,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium|s__Cloacibacterium sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp.,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis",2|976|200643|171549|2005525|375288|823;2|1224|28221|213115|194924|35832|35833;2|1239|186801|186802|186803|841|360807;2|976|200643|171549|1853231|283168|28118;2|1239|186801|186802|186803;2|1239|186801|186802|186803|572511|1955243;2|1239|186801|186802|31979|1485|1506;2|1239;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|1263|40519;2|976|200643|171549|171550|239759|328814;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|216851;2|1224|28216|80840|995019|577310|487175;2|976|117743|200644|2762318|501783|1913682;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|171550|239759|328813;2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|459786|1945593;2|1239|526524|526525|2810280|100883;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|1853231|574697|544645;2|1239|186801|186802|541000;2|1239|186801|186802;2|1239|186801|186802|186806|1730;2|976|200643|171549|171550|239759|28117;2|976|200643|171549|1853231|574697;2|976|200643|171549|2005519|397864|487174;2|1239|186801|186802|186803|28050|39485;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|186803|189330|39486;2|1224|1236|135625|712|724|729;2|976|200643|171549|171550|239759|1288121,Complete,NA
Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,Experiment 2,France,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,moxifloxacin treated group (MXF),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,14,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,"Supplementary table 3, Supplementary figure 1",14 June 2020,Mst Afroza Parvin,WikiWorks743,A detailed analysis of the MGSs that differed significantly between treatment groups,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,2|1239|186801|186802|186803|572511,Complete,NA
Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,Experiment 3,France,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Negative control group (CLT),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Supplementary table 3, Supplementary figure 1",14 June 2020,Mst Afroza Parvin,WikiWorks743,A detailed analysis of the MGSs that differed significantly between treatment groups,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239;2|1239|186801|186802|186803,Complete,NA
Study 307,randomized controlled trial,29186529,10.1093/infdis/jix604,NA,"de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F , Andremont A",Protection of the Human Gut Microbiome From Antibiotics,The Journal of infectious diseases,2018,Experiment 3,France,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Negative control group (CLT),DAV132+moxifloxacin treated group (MXF+DAV132),healthy male and female volunteers aged >18 years,8,14,3 months,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Supplementary table 3, Supplementary figure 1",14 June 2020,Mst Afroza Parvin,WikiWorks743,A detailed analysis of the MGSs that differed significantly between treatment groups,decreased,"k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",2|1224|28221|213115|194924|35832|35833;2|201174|1760|85004|31953|1678|1680;2|1239|186801|186802|186804|1505657|261299;2|201174|1760|85004|31953|1678|28026;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|216572|946234|292800,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 1,United States of America,Mus musculus,small intestine,UBERON:0002108,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure S3,13 June 2020,Zyaijah Bailey,"WikiWorks743,Lwaldron",Histograms of relative abundance of selected statistically differentially abundant genera in the small intestine.,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|1239|91061|186826|33958;2|976|200643|171549,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 1,United States of America,Mus musculus,small intestine,UBERON:0002108,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure S3,13 June 2020,Zyaijah Bailey,"WikiWorks743,Lwaldron",Histograms of relative abundance of selected statistically differentially abundant genera in the small intestine.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae",2|1239|91061|186826|33958|1578;2|1239|91061|1385|90964|1279;2|1239|91061|186826|186827,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 2,United States of America,Mus musculus,feces,UBERON:0001988,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure S6,13 June 2020,Zyaijah Bailey,WikiWorks743,Individual abundance histograms of bacterial lineages changing particularly in the fecal samples,increased,NA,NA,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 2,United States of America,Mus musculus,feces,UBERON:0001988,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure S6,13 June 2020,Zyaijah Bailey,WikiWorks743,Individual abundance histograms of bacterial lineages changing particularly in the fecal samples,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|976|200643|171549|815|816;2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578;2|1239|526524|526525|2810281|191303,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 3,United States of America,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 1,Figure S4,13 June 2020,Zyaijah Bailey,WikiWorks743,Histograms of relative abundance of selected statistically differentially abundant genera in the cecum.,increased,NA,NA,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 3,United States of America,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 2,Figure S4,13 June 2020,Zyaijah Bailey,WikiWorks743,Histograms of relative abundance of selected statistically differentially abundant genera in the cecum.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|976|200643|171549|815|816;2|1239|91061|1385|90964|1279;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|119852,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 4,United States of America,Mus musculus,stomach,UBERON:0000945,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 1,Figure S2,13 June 2020,Zyaijah Bailey,"WikiWorks743,Lwaldron",Histograms of relative abundance of selected statistically differentially abundant genera in the stomach,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|1239|91061|186826|33958;2|976|200643|171549,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 4,United States of America,Mus musculus,stomach,UBERON:0000945,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,unchanged,unchanged,NA,NA,increased,Signature 2,Figure S2,13 June 2020,Zyaijah Bailey,WikiWorks743,Histograms of relative abundance of selected statistically differentially abundant genera in the stomach,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 5,United States of America,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 1,Figure S5,13 June 2020,Zyaijah Bailey,WikiWorks743,Histograms of relative abundance of selected statistically differentially abundant genera in the colon,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 5,United States of America,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,unchanged,NA,NA,increased,Signature 2,Figure S5,13 June 2020,Zyaijah Bailey,WikiWorks743,Histograms of relative abundance of selected statistically differentially abundant genera in the colon,decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Anaeroplasma,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|526524|526525|2810281|191303;2|544448|31969|186332|186333|2086;2|1239|186801|186802|31979|1485,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 6,United States of America,Mus musculus,"feces,stomach,caecum,small intestine,colon","UBERON:0001988,UBERON:0000945,UBERON:0001153,UBERON:0002108,UBERON:0001155",air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 5,13 June 2020,Zyaijah Bailey,WikiWorks743,LEfSe analysis of all samples revealed genera altered with PM exposure throughout the GI tract,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|1578,Complete,NA
Study 308,laboratory experiment,29783199,10.1016/j.envpol.2018.04.130,NA,"Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS , Mutlu GM",Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome,"Environmental pollution (Barking, Essex : 1987)",2018,Experiment 6,United States of America,Mus musculus,"feces,stomach,caecum,small intestine,colon","UBERON:0001988,UBERON:0000945,UBERON:0001153,UBERON:0002108,UBERON:0001155",air pollution,ENVO:02500037,Filtered air group,PM 2.5 air exposed group,Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES),10,10,NA,16S,NA,Roche454,LEfSe,0.05,FALSE,5,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 5,13 June 2020,Zyaijah Bailey,WikiWorks743,LEfSe analysis of all samples revealed genera altered with PM exposure throughout the GI tract,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1239|91061|186826|33958;2|976|200643|171549|171550,Complete,NA
Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,Experiment 1,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 2, supplemental table 1",15 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to CIN status,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oleovorans,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Heliobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976|200643|171549|171551;2|1239|91061|186826|33958|2742598|1598;2|976|200643|171549|2005525|375288;2|1224|1236|118969|118968;2|1224|1236|118969|118968|59195;2|1224|1236|72274|135621|286|330;2|1224|1236|118969|444;2|976|200643|171549|1853231|574697;2|1239|186801|186802|31984;2|976|200643|171549|815|816|28111,Complete,Fatima Zohra
Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,Experiment 1,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 2, supplemental table 1",15 June 2020,Cynthia Anderson,WikiWorks743,Linear discriminant effect size (LEfSe) analysis comparing differentially abundant taxa according to CIN status,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales",2|1239|186801|186802|541000;2|1239|186801|186802,Complete,Fatima Zohra
Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,Experiment 2,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,<=38.8% 8-OHdG-positive cervical cells,>38.8% 8-OHdG-positive cervical cells,patients with >38.8% of 8-OHdG-positive cervical cells,NA,NA,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplemental Figure 2,24 June 2020,Cynthia Anderson,WikiWorks743,LEfSe comparing differentially abundant taxa according to 8-OH status,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Limnohabitans,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium",2|1224|28216;2|1224|28216|80840;2|1224|28216|80840|80864;2|1224|1236|72274|135621|351;2|1224|1236|72274|135621|286;2|1224|28211|356;2|1224|28216|80840|75682;2|1224|28211|356|82115;2|1224|28211|356|82115|357;2|1224|28216|80840|80864|665874;2|1224|28211|204458|76892|20,Complete,Fatima Zohra
Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,Experiment 2,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,<=38.8% 8-OHdG-positive cervical cells,>38.8% 8-OHdG-positive cervical cells,patients with >38.8% of 8-OHdG-positive cervical cells,NA,NA,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplemental Figure 2,24 June 2020,Cynthia Anderson,WikiWorks743,LEfSe comparing differentially abundant taxa according to 8-OH status,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,Fatima Zohra
Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,Experiment 3,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Supplemental Table 2,24 June 2020,Cynthia Anderson,WikiWorks743,Log2-fold difference in sequence reads for OTUs according to CIN status,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri",2|74201|203494|48461|1647988|239934|239935;2|1239|91061|186826|33958|2742598|1598,Complete,Fatima Zohra
Study 309,"cross-sectional observational, not case-control",26935422,10.1158/1940-6207.CAPR-15-0350,NA,"Piyathilake CJ, Ollberding NJ, Kumar R, Macaluso M, Alvarez RD , Morrow CD",Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses,"Cancer prevention research (Philadelphia, Pa.)",2016,Experiment 3,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,CIN1,CIN2+,patients with CIN2+ confirmed by colposcopy,90,340,NA,16S,4,Illumina,Negative Binomial Regression,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Supplemental Table 2,24 June 2020,Cynthia Anderson,WikiWorks743,Log2-fold difference in sequence reads for OTUs according to CIN status,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|976|200643|171549|171552|838|165179;2|1239|186801|186802|186803|572511|33035;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|171552|838|28132;2|1239|186801|186802|31979|1485|1502;2|1239|91061|186826|1300|1301|1311;2|74201|203494|48461|1647988|239934|239935,Complete,Fatima Zohra
Study 310,prospective cohort,24402367,10.1007/s00248-013-0355-4,NA,"Montassier E, Batard E, Massart S, Gastinne T, Carton T, Caillon J, Le Fresne S, Caroff N, Hardouin JB, Moreau P, Potel G, Le Vacon F , de La Cochetière MF",16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation,Microbial ecology,2014,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"patients ages 40 to 60 years old diagnosis with non-Hodgkin's lymphoma undergoing post-chemotherapy high-dose carmustine, etoposide, aracytin and melphalan",8,8,all antibiotics after starting chemotherapy,16S,56,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 2, 4, 5, text",15 June 2020,William Lam,WikiWorks743,"Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data",increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1224;2|976;2|976|200643|171549|815|816;2|1224|1236|91347|543|561,Complete,NA
Study 310,prospective cohort,24402367,10.1007/s00248-013-0355-4,NA,"Montassier E, Batard E, Massart S, Gastinne T, Carton T, Caillon J, Le Fresne S, Caroff N, Hardouin JB, Moreau P, Potel G, Le Vacon F , de La Cochetière MF",16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation,Microbial ecology,2014,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,non-Hodgkins lymphoma,EFO:0005952,pre-chemotherapy,post-chemotherapy,"patients ages 40 to 60 years old diagnosis with non-Hodgkin's lymphoma undergoing post-chemotherapy high-dose carmustine, etoposide, aracytin and melphalan",8,8,all antibiotics after starting chemotherapy,16S,56,Roche454,T-Test,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 2, 4, 5, text",15 June 2020,William Lam,WikiWorks743,"Cumulative percentage of family and genera sequences detected in the prechemotherapy and postchemotherapy fecl, compared using multiple Wilcoxon rank tests for paired data",decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239;2|201174;2|1239|91061|186826|186827|46123;2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|186806|264995;2|201174|1760|2037|2049|28263;2|201174|1760|85007|1653|1716;2|1239|1737404|1737405|1570339|150022;2|1239|909932|1843489|31977|906;2157|28890|183925|2158|2159|2316;2|201174|1760|2037|2049|2050;2|1239|91061|1385|186822|44249;2|201174|1760|85004|31953|196082;2|1239|186801|186802|186804|1257;2|508458|649775|649776|649777|638847;2|201174|1760|85006|1268|32207;2|1239|91061|1385|90964|1279;2|201174|1760|2037|2049|184869;2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|841;2|201174|1760|85004|31953|1678,Complete,NA
Study 311,time series / longitudinal observational,25893458,10.1038/bmt.2015.16,NA,"Biagi E, Zama D, Nastasi C, Consolandi C, Fiori J, Rampelli S, Turroni S, Centanni M, Severgnini M, Peano C, de Bellis G, Basaglia G, Gotti R, Masetti R, Pession A, Brigidi P , Candela M",Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT,Bone marrow transplantation,2015,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,pre- engraftment,post- engraftment,"malignant or non-malignant disease patients from four transplantation centers (Bologna, Pavia, Rome and Verona) that underwent allogeneic hematopoietic stem cell transplant with or without myeloablative conditioning regimen, who did not develop acute graft-versus-host disease post- enrichment",17,17,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3b, c, d, and supplemental table S1, text",16 June 2020,William Lam,WikiWorks743,"Average relative abundances in pre-HSCT and engrafment samples, of the main discriminant genera between the two time points in subjects who did not develop acute graft-versus- host disease (non-aGvHD)",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|119852,Complete,NA
Study 311,time series / longitudinal observational,25893458,10.1038/bmt.2015.16,NA,"Biagi E, Zama D, Nastasi C, Consolandi C, Fiori J, Rampelli S, Turroni S, Centanni M, Severgnini M, Peano C, de Bellis G, Basaglia G, Gotti R, Masetti R, Pession A, Brigidi P , Candela M",Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT,Bone marrow transplantation,2015,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,pre- engraftment,post- engraftment,"malignant or non-malignant disease patients from four transplantation centers (Bologna, Pavia, Rome and Verona) that underwent allogeneic hematopoietic stem cell transplant with or without myeloablative conditioning regimen, who developed skin acute graft-versus-host disease post- enrichment",13,13,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3b, c, d, and supplemental table S1, text",16 June 2020,William Lam,WikiWorks743,"Average relative abundances in pre-HSCT and engrafment samples, of the main discriminant genera between the two time points in subjects who developed acute graft-versus- host disease (I-II grade) at a skin level (Skin aGvHD)",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|119852,Complete,NA
Study 312,prospective cohort,26971496,10.1007/s00253-016-7410-2,NA,"Aloisio I, Quagliariello A, De Fanti S, Luiselli D, De Filippo C, Albanese D, Corvaglia LT, Faldella G , Di Gioia D",Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions,Applied microbiology and biotechnology,2016,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants born by mothers negative to GBS,Infants born by mothers positive to GBS and received IAP,Infants of Mothers positive to Streptococcus (GBS) and received intrapartum antibiotic prophylaxis (IAP),10,10,perinatal antibiotics,16S,23456789,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Table S3, Text",16 June 2020,Mst Afroza Parvin,WikiWorks743,Evaluation of microbial genus composition between Control and IAP groups,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|201174|1760|85004|31953;2|976|200643|171549|815,Complete,NA
Study 312,prospective cohort,26971496,10.1007/s00253-016-7410-2,NA,"Aloisio I, Quagliariello A, De Fanti S, Luiselli D, De Filippo C, Albanese D, Corvaglia LT, Faldella G , Di Gioia D",Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions,Applied microbiology and biotechnology,2016,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants born by mothers negative to GBS,Infants born by mothers positive to GBS and received IAP,Infants of Mothers positive to Streptococcus (GBS) and received intrapartum antibiotic prophylaxis (IAP),10,10,perinatal antibiotics,16S,23456789,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Table S3, Text",16 June 2020,Mst Afroza Parvin,WikiWorks743,Evaluation of microbial genus composition between Control and IAP groups,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
Study 313,prospective cohort,27121964,10.1186/s13073-016-0301-4,NA,"Montassier E, Al-Ghalith GA, Ward T, Corvec S, Gastinne T, Potel G, Moreau P, de la Cochetiere MF, Batard E , Knights D",Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection,Genome medicine,2016,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,non-Hodgkins lymphoma,EFO:0005952,non-bloodstream infection,bloodstream infection,"participants had blood stream infection, diagnosis with non-Hodgkins lymphoma (NHL), undergone hematopoeitic stem cell transplant and chemotherapy that did not had a history of inflammatory bowel disease, no exposure to probiotics, prebiotics or broad-soectrium antibiotics, no administered nasal-tube feeding or parenteral nutrition in a month prior to initiation of the study",17,11,NA,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 2, 3, aditional file 5a and b, 7",17 June 2020,William Lam,WikiWorks743,Relative abundance of the differentiated taxa in samples collected prior to treatment in patients who developed subsequent Blood Stream Infections and patients who did not develop Blood Stream Infections,increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,NA
Study 313,prospective cohort,27121964,10.1186/s13073-016-0301-4,NA,"Montassier E, Al-Ghalith GA, Ward T, Corvec S, Gastinne T, Potel G, Moreau P, de la Cochetiere MF, Batard E , Knights D",Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection,Genome medicine,2016,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,non-Hodgkins lymphoma,EFO:0005952,non-bloodstream infection,bloodstream infection,"participants had blood stream infection, diagnosis with non-Hodgkins lymphoma (NHL), undergone hematopoeitic stem cell transplant and chemotherapy that did not had a history of inflammatory bowel disease, no exposure to probiotics, prebiotics or broad-soectrium antibiotics, no administered nasal-tube feeding or parenteral nutrition in a month prior to initiation of the study",17,11,NA,16S,56,Roche454,Mann-Whitney (Wilcoxon),0.15,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 2, 3, aditional file 5a and b, 7",17 June 2020,William Lam,WikiWorks743,Relative abundance of the differentiated taxa in samples collected prior to treatment in patients who developed subsequent Blood Stream Infections and patients who did not develop Blood Stream Infections,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Chloroflexi|c__Dehalococcoidia|o__Dehalococcoidales|f__Dehalococcoidaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas",2|976|200643|171549|2005519;2|1239|186801|186802|990719;2|1224|28221|213115|194924;2|200795|301297|1202465|1202464;2|1224|28216|80840|506;2|1224|28216|80840|75682;2|976|200643|171549|1853231;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186807|51514;2|1224|28216|80840|995019|40544;2|1224|28216|80840|75682|846;2|1239|186801|186802|990719|990721;2|1239|186801|186802|216572|119852;2|976|200643|171549|1853231|574697,Complete,NA
Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,Experiment 1,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 12 months",42,45,NA,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,17 June 2020,Cynthia Anderson,WikiWorks743,LEfSe analysis identified baseline vaginal microbiota biomarkers associated with clinical outcomes at 12 months follow-up,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Actinobacteria|c__Actinomycetia",2|976|200643|171549|171552|838|386414;2|1239|909932;2|1239|909932|909929;2|201174|84998|84999;2|1239|186801|186802;2|201174|84998|84999|1643824|1380;2|201174|1760|2037|2049|2767327|82135;2|201174|84998|84999|84107;2|32066;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|906;2|32066|203490;2|32066|203490|203491;2|1239|1737404|1737405|1570339|543311;2|1239|186801;2|1239|186801|186802|186803;2|976|200643|171549|171552|838;2|976;2|976|200643;2|976|200643|171549|171552;2|976|200643|171549;2|201174|1760,Complete,Fatima Zohra
Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,Experiment 1,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 12 months",42,45,NA,16S,12,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,17 June 2020,Cynthia Anderson,WikiWorks743,LEfSe analysis identified baseline vaginal microbiota biomarkers associated with clinical outcomes at 12 months follow-up,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes",2|1239|91061|186826;2|1239|91061;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239,Complete,Fatima Zohra
Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,Experiment 2,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 12 months",42,45,NA,16S,12,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,increased,Signature 1,Figure 4,24 June 2020,Cynthia Anderson,WikiWorks743,Outcomes at 12-month follow-up according to baseline VMB composition at baseline,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",2|976|200643|171549|171552|838|386414;2|201174|1760|85004|31953|2701|2702,Complete,Fatima Zohra
Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,Experiment 3,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 24 months",63,24,NA,16S,12,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,increased,Signature 1,Supplementary Figure 2,7 July 2020,Cynthia Anderson,WikiWorks743,Outcomes at 24 month follow-up according to baseline VMB composition at baseline,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis",2|201174|1760|85004|31953|2701|2702;2|976|200643|171549|171552|838|386414,Complete,Fatima Zohra
Study 314,time series / longitudinal observational,32332850,10.1038/s41467-020-15856-y,NA,"Mitra A, MacIntyre DA, Ntritsos G, Smith A, Tsilidis KK, Marchesi JR, Bennett PR, Moscicki AB , Kyrgiou M",The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions,Nature communications,2020,Experiment 4,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,CIN regression,CIN non-regression,"histology proven CIN2, no regression after 24 months among women with no regression after 12 months",21,14,NA,16S,12,Illumina,Welch's T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,unchanged,unchanged,Signature 1,Supplementary Figure 3,7 July 2020,Cynthia Anderson,WikiWorks743,Supplementary Figure 3. Outcomes at 24 months according to VMB composition at 12 months in a subgroup of 35 women with ongoing disease,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii,2|1239|91061|186826|186827|1375|87541,Complete,Fatima Zohra
Study 315,time series / longitudinal observational,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Infants to mothers didn't receive IAP,Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,22,18,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S1,  Text",18 June 2020,Mst Afroza Parvin,WikiWorks743,"Levels (relative frequencies; %) of the bacterial families showing differences, in at least one time point analyzed, between infants from mothers receiving IAP and those whose mothers did not receive it.",increased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1224|29547|213849|72294;2|1239|186801|186802|31979;2|1224|29547|213849|72293;2|976|200643|171549|171552;2|976|200643|171549|171550,Complete,NA
Study 315,time series / longitudinal observational,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Infants to mothers didn't receive IAP,Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,22,18,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S1,  Text",18 June 2020,Mst Afroza Parvin,WikiWorks743,"Levels (relative frequencies; %) of the bacterial families showing differences, in at least one time point analyzed, between infants from mothers receiving IAP and those whose mothers did not receive it.",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria",2|201174|1760|85004|31953;2|201174,Complete,NA
Study 315,time series / longitudinal observational,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,breast-fed Infants to mothers didn't receive IAP,Breast-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,18,11,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S2,  Text",18 June 2020,Mst Afroza Parvin,WikiWorks743,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Verrucomicrobia",2|1239;2|74201,Complete,NA
Study 315,time series / longitudinal observational,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,breast-fed Infants to mothers didn't receive IAP,Breast-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,18,11,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S2,  Text",18 June 2020,Mst Afroza Parvin,WikiWorks743,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Bacteroidetes",2|201174;2|976,Complete,NA
Study 315,time series / longitudinal observational,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,Experiment 3,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Formula-fed Infants to mothers didn't receive IAP,Formula-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,4,7,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S2,  Text",18 June 2020,Mst Afroza Parvin,WikiWorks743,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,NA
Study 315,time series / longitudinal observational,28789705,10.1186/s40168-017-0313-3,NA,"Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, Fernández N, Alaez L, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Ventura M , Gueimonde M",Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates,Microbiome,2017,Experiment 3,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Formula-fed Infants to mothers didn't receive IAP,Formula-fed Infants to mothers received IAP,Full-term (gestational ages >37 weeks) vaginally delivered infants born after an uncomplicated pregnancy,4,7,During pregnancy or postnatal period (Mothers); during the study period (infants),16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S2,  Text",18 June 2020,Mst Afroza Parvin,WikiWorks743,Relative proportion (%; mean ± sd) of the five main bacterial phyla in the samples from breast and formula-fed infants either exposed of not to IAP,decreased,k__Bacteria|p__Actinobacteria,2|201174,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,premature birth,EFO:0003917,2-day old Full-term infants(born after uncomplicated pregnancy),2-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|201174|1760|85004|31953;2|1224|28216|80840|80864;2|201174|1760|85009|31957;2|1239|91061|186826|1300;2|201174;2|1239|91061;2|1239|91061|186826|33958,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,premature birth,EFO:0003917,2-day old Full-term infants(born after uncomplicated pregnancy),2-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|976|200643|171549|815;2|1239|186801|186802|31979;2|201174|1760|85006|1268;2|1224|1236|135625|712;2|976|200643|171549|171551,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,premature birth,EFO:0003917,10-day old Full-term infants(born after uncomplicated pregnancy),10-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria",2|1224|1236|91347|543;2|201174|1760|85006|1268;2|1224|1236,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,premature birth,EFO:0003917,10-day old Full-term infants(born after uncomplicated pregnancy),10-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|815;2|201174|1760|85004|31953;2|1239|186801|186802|31979;2|201174|84998|84999|84107;2|1239|91061|186826|81850;2|1224|1236|135625|712;2|976|200643|171549|171551;2|201174|1760;2|1239|909932|1843489|31977,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 3,Spain,Homo sapiens,feces,UBERON:0001988,premature birth,EFO:0003917,30-day old Full-term infants(born after uncomplicated pregnancy),30-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria",2|1224|1236|91347|543;2|201174|1760|85006|1268;2|1224|1236,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 3,Spain,Homo sapiens,feces,UBERON:0001988,premature birth,EFO:0003917,30-day old Full-term infants(born after uncomplicated pregnancy),30-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|815;2|201174|1760|85004|31953;2|1239|186801|186802|31979;2|201174|84998|84999|84107;2|1239|91061|186826|81850;2|1224|1236|135625|712;2|976|200643|171549|171551;2|201174|1760;2|1239|909932|1843489|31977,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 4,Spain,Homo sapiens,feces,UBERON:0001988,premature birth,EFO:0003917,90-day old Full-term infants(born after uncomplicated pregnancy),90-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria",2|1224|1236|91347|543;2|201174|1760|85006|1268;2|1224|1236,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 4,Spain,Homo sapiens,feces,UBERON:0001988,premature birth,EFO:0003917,90-day old Full-term infants(born after uncomplicated pregnancy),90-day old Pre-term,born at gestational ages between 24 and 32 weeks,13,27,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|815;2|201174|1760|85004|31953;2|1239|186801|186802|31979;2|201174|84998|84999|84107;2|1239|91061|186826|81850;2|1224|1236|135625|712;2|976|200643|171549|171551;2|201174|1760;2|1239|909932|1843489|31977,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 5,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,2-day old full-term neonates not exposed to antibiotics (IAP/postnatal),2-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,2|1239|91061|186826|81850,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 6,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,10-day old full-term neonates not exposed to antibiotics (IAP/postnatal),10-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae",2|201174|1760|85006|1268;2|201174|1760|85009|31957,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 7,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,30-day old full-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli",2|1224|28216|80840|80864;2|1239|91061|1385|90964;2|1239|91061,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 8,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,90-day old full-term neonates not exposed to antibiotics (IAP/postnatal),90-day old pre-tem neonates exposed to antibiotics (IAP),antenatal/postnatal antibiotic exposure,14,10,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|541000,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 9,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,30-day old full-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP),IAP exposure,5,14,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota,increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 9,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,30-day old full-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP),IAP exposure,5,14,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales",2|201174|1760|85004|31953;2|1239|91061|186826|1300;2|201174|1760;2|1239|91061|186826,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 10,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal),30-day old pre-tem neonates exposed to antibiotics (IAP/postnatal),pre-term infants and mothers exposed to antibiotics,5,9,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|91061|1385|90964;2|1224|1236|91347|543,Complete,NA
Study 316,time series / longitudinal observational,25444008,10.1016/j.jpeds.2014.09.041,NA,"Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A , Gueimonde M",Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics,The Journal of pediatrics,2015,Experiment 11,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,90-day old pre-term neonates not exposed to antibiotics (IAP/postnatal),90-day old pre-tem neonates exposed to antibiotics (IAP/postnatal),pre-term infants and mothers exposed to antibiotics,5,9,NA,16S,34,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,text,19 June 2020,Mst Afroza Parvin,WikiWorks743,Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,2|201174|1760|85004|31953,Complete,NA
Study 317,prospective cohort,32012716,10.3390/microorganisms8020179,NA,"Wong WSW, Sabu P, Deopujari V, Levy S, Shah AA, Clemency N, Provenzano M, Saadoon R, Munagala A, Baker R, Baveja R, Mueller NT, Dominguez-Bello MG, Huddleston K, Niederhuber JE , Hourigan SK",Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome,Microorganisms,2020,Experiment 1,United States of America,Homo sapiens,meconium,UBERON:0007109,antimicrobial agent,CHEBI:33281,without prenatal antibiotics usages,infants delivered to mothers with,infants delivered to mothers given prenatal antibiotics (antibiotics given to mother from conception to 2 days prior to delivery),88,17,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Text,21 June 2020,Mst Afroza Parvin,WikiWorks743,3.3. Alpha Diversity;   3.4. Relative abundance of Taxa,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1239|186801|186802|31979|1485;2|1224|1236|91347|543,Complete,NA
Study 317,prospective cohort,32012716,10.3390/microorganisms8020179,NA,"Wong WSW, Sabu P, Deopujari V, Levy S, Shah AA, Clemency N, Provenzano M, Saadoon R, Munagala A, Baker R, Baveja R, Mueller NT, Dominguez-Bello MG, Huddleston K, Niederhuber JE , Hourigan SK",Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome,Microorganisms,2020,Experiment 2,United States of America,Homo sapiens,meconium,UBERON:0007109,antimicrobial agent,CHEBI:33281,without peripartum antibiotics usages,infants delivered to mothers with,infants delivered to mothers given preipartum antibiotics (antibiotics given to mother 2 days prior to delivery to during delivery),43,62,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 1,Text,21 June 2020,Mst Afroza Parvin,WikiWorks743,3.3. Alpha Diversity; 3.4. Relative abundance of Taxa,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|28211|356|82115|357;2|1239|91061|186826|1300|1301,Complete,NA
Study 317,prospective cohort,32012716,10.3390/microorganisms8020179,NA,"Wong WSW, Sabu P, Deopujari V, Levy S, Shah AA, Clemency N, Provenzano M, Saadoon R, Munagala A, Baker R, Baveja R, Mueller NT, Dominguez-Bello MG, Huddleston K, Niederhuber JE , Hourigan SK",Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome,Microorganisms,2020,Experiment 2,United States of America,Homo sapiens,meconium,UBERON:0007109,antimicrobial agent,CHEBI:33281,without peripartum antibiotics usages,infants delivered to mothers with,infants delivered to mothers given preipartum antibiotics (antibiotics given to mother 2 days prior to delivery to during delivery),43,62,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,increased,NA,unchanged,Signature 2,Text,21 June 2020,Mst Afroza Parvin,WikiWorks743,3.3. Alpha Diversity; 3.4. Relative abundance of Taxa,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,NA
Study 318,prospective cohort,28733895,10.1007/s00277-017-3069-8,NA,"Doki N, Suyama M, Sasajima S, Ota J, Igarashi A, Mimura I, Morita H, Fujioka Y, Sugiyama D, Nishikawa H, Shimazu Y, Suda W, Takeshita K, Atarashi K, Hattori M, Sato E, Watakabe-Inamoto K, Yoshioka K, Najima Y, Kobayashi T, Kakihana K, Takahashi N, Sakamaki H, Honda K , Ohashi K",Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation,Annals of hematology,2017,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,non-acute graft-versus-host disease,acute graft-versus-host disease,"participants that developed acute graft-versus-host disease after allogeneic hematopoeitic transplant and graded accordinly to pattern of organ involvement and clinical performance status using a system introduced by Glucksberg et al. (Severity Index), which includes late-onset of acute graft-versus-host disease (more than 100 days after transplantation)",NA,107,NA,16S,12,Roche454,T-Test,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,21 June 2020,William Lam,WikiWorks743,pre-transplant relative abundance of phylum-level gut microbial diversity on the non-acute graft-versus-host disease compared to acute graft-versus-host disease in outcomes of allogeneic hematopoietic stem cell transplantation,increased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 318,prospective cohort,28733895,10.1007/s00277-017-3069-8,NA,"Doki N, Suyama M, Sasajima S, Ota J, Igarashi A, Mimura I, Morita H, Fujioka Y, Sugiyama D, Nishikawa H, Shimazu Y, Suda W, Takeshita K, Atarashi K, Hattori M, Sato E, Watakabe-Inamoto K, Yoshioka K, Najima Y, Kobayashi T, Kakihana K, Takahashi N, Sakamaki H, Honda K , Ohashi K",Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation,Annals of hematology,2017,Experiment 2,Japan,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,non-acute graft-versus-host disease,acute graft-versus-host disease,"participants that developed acute graft-versus-host disease after allogeneic hematopoeitic transplant and graded accordinly to pattern of organ involvement and clinical performance status using a system introduced by Glucksberg et al. (Severity Index), which includes late-onset of acute graft-versus-host disease (more than 100 days after transplantation)",NA,107,NA,16S,12,Roche454,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,21 June 2020,William Lam,WikiWorks743,pre-transplant genus-level gut microbial diversity on the non-acute graft-versus-host disease compared to acute graft-versus-host disease in outcomes of allogeneic hematopoietic stem cell transplantation,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186806|1730,Complete,NA
Study 319,laboratory experiment,29665823,10.1186/s12989-018-0252-6,NA,"Wang W, Zhou J, Chen M, Huang X, Xie X, Li W, Cao Q, Kan H, Xu Y , Ying Z",Exposure to concentrated ambient PM<sub>2.5</sub> alters the composition of gut microbiota in a murine model,Particle and fibre toxicology,2018,Experiment 1,China,Mus musculus,feces,UBERON:0001988,air pollution,ENVO:02500037,mice exposed to PM 2.5 (CAP),mice exposed to filtered air (FA),male C57Bl/6 J mice exposed to PM2.5 (CAP),10,10,NA,16S,4,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,unchanged,Signature 1,Figure 4 & text,21 June 2020,Zyaijah Bailey,WikiWorks743,The differential taxa between FA- and CAP-exposed mice. a) the cladogram of faecal bacterial community,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales",2|976|200643|171549|171550;2|1239|186801|186802|186803|248744;2|544448|31969|2085|2092|2093;2|544448|31969|2085|2092;2|544448|31969|2085,Complete,NA
Study 319,laboratory experiment,29665823,10.1186/s12989-018-0252-6,NA,"Wang W, Zhou J, Chen M, Huang X, Xie X, Li W, Cao Q, Kan H, Xu Y , Ying Z",Exposure to concentrated ambient PM<sub>2.5</sub> alters the composition of gut microbiota in a murine model,Particle and fibre toxicology,2018,Experiment 1,China,Mus musculus,feces,UBERON:0001988,air pollution,ENVO:02500037,mice exposed to PM 2.5 (CAP),mice exposed to filtered air (FA),male C57Bl/6 J mice exposed to PM2.5 (CAP),10,10,NA,16S,4,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,increased,increased,increased,NA,unchanged,Signature 2,Figure 4 & text,21 June 2020,Zyaijah Bailey,WikiWorks743,The differential taxa between FA- and CAP-exposed mice. a) the cladogram of faecal bacterial community,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria",2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186804;2|1224|29547|213849|72293|209;2|1224|29547|213849|72293;2|1224|29547|213849;2|1224|29547,Complete,NA
Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  intrapartum antibiotic,infants(6-weeks) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Table S1, Figure S2 & Text, Figure 1",22 June 2020,Mst Afroza Parvin,WikiWorks743,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|1239|186801|186802|216572|119852;2|1239|186801|186802|186806|113286;2|201174|1760|2037|2049|184869;2|1239|909932|1843489|31977|29465|39778,Complete,NA
Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  intrapartum antibiotic,infants(6-weeks) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Table S1, Figure S2 & Text, Figure 1",22 June 2020,Mst Afroza Parvin,WikiWorks743,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263,Complete,NA
Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  intrapartum antibiotic,infants(1-year) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Table S1, Figure S2 & Text, Figure 1",22 June 2020,Mst Afroza Parvin,WikiWorks743,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|1239|186801|186802|216572|119852;2|1239|186801|186802|186806|113286;2|201174|1760|2037|2049|184869;2|1239|909932|1843489|31977|29465|39778,Complete,NA
Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  intrapartum antibiotic,infants(1-year) to mothers exposed to intrapartum antibiotic,vaginally delivered at full-term (>37 weeks of gestation),179,87,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Table S1, Figure S2 & Text, Figure 1",22 June 2020,Mst Afroza Parvin,WikiWorks743,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|815|816;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|841,Complete,NA
Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  antibiotic,"infants(6-weeks) to mothers exposed to  antibiotics (amoxicillin, penicillin or ampicillin)",vaginally delivered at full-term (>37 weeks of gestation),179,55,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Table S1, Figure S2 & Text, Figure 1, Figure 3",22 June 2020,Mst Afroza Parvin,WikiWorks743,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|976|200643|171549|815|816;2|976|200643|171549|815|816|28116;2|201174|1760|85004|31953|1678,Complete,NA
Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  antibiotic,"infants(1-year) to mothers exposed to  antibiotics (amoxicillin, penicillin or ampicillin)",vaginally delivered at full-term (>37 weeks of gestation),179,55,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Table S1, Figure S2 & Text, Figure 1, Figure 3",22 June 2020,Mst Afroza Parvin,WikiWorks743,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus",2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|2316020|33038,Complete,NA
Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants (1-year) to mothers unexposed to  antibiotic,"infants(1-year) to mothers exposed to  antibiotics (amoxicillin, penicillin or ampicillin)",vaginally delivered at full-term (>37 weeks of gestation),179,55,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Table S1, Figure S2 & Text, Figure 1, Figure 3",22 June 2020,Mst Afroza Parvin,WikiWorks743,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|815|816;2|976|200643|171549|815|816|817;2|1239|186801|186802|31979|1485;2|1239|909932|909929|1843491|158846;2|1239|91061|186826|1300|1301,Complete,NA
Study 320,prospective cohort,31006170,10.1111/1471-0528.15799,NA,"Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR , Madan JC",Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 5,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants (6-weeks) to mothers unexposed to  antibiotic,infants(6-weeks) to mothers exposed to multi-class antibiotics,vaginally delivered at full-term (>37 weeks of gestation),179,12,NA,16S,45,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,increased,NA,unchanged,NA,NA,Signature 1,"Table S1, Figure S2 & Text, Figure 1, Figure 3",22 June 2020,Mst Afroza Parvin,WikiWorks743,MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).,increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,2|1239|909932|1843489|31977|29465|39778,Complete,NA
Study 321,time series / longitudinal observational,24819377,10.1038/pr.2014.69,NA,"Dardas M, Gill SR, Grier A, Pryhuber GS, Gill AL, Lee YH , Guillet R",The impact of postnatal antibiotics on the preterm intestinal microbiome,Pediatric research,2014,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,10 d old 2 day treatment infants,10 d old 7-10 day treatment infants,born at gestational ages less than 32 weeks,15,12,NA,16S,123,Roche454,NA,NA,FALSE,NA,NA,delivery procedure,NA,decreased,NA,NA,NA,unchanged,Signature 1,"Table 2, table 3",23 June 2020,Mst Afroza Parvin,WikiWorks743,Characteristics and outcomes of breast milk–fed infants at age 10 d & 30 d,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|91061|186826|1300|1357;2|976|200643|171549|815|816,Complete,NA
Study 322,time series / longitudinal observational,30959164,10.1016/j.bbmt.2019.04.007,NA,"El Jurdi N, Filali-Mouhim A, Salem I, Retuerto M, Dambrosio NM, Baer L, Lazarus HM, Caimi P, Cooper B, Tomlinson B, Metheny L, Malek E, Otegbeye F, Sekaly RP, Ghannoum M , de Lima M",Gastrointestinal Microbiome and Mycobiome Changes during Autologous Transplantation for Multiple Myeloma: Results of a Prospective Pilot Study,Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation,2019,Experiment 1,Sweden,Homo sapiens,"buccal mucosa,lower lip","UBERON:0006956,UBERON:0001835",oral mucositis,EFO:1001904,reference,newly diagnosis maligancies,patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden),38,37,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1a, Supplemental Table S2",23 June 2020,William Lam,WikiWorks743,Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy),increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Derxia",2|1239|91061|186826|186827|46123;2|1239|91061|186826|1300|1357;2|1224|28216|80840|506|203697,Complete,NA
Study 322,time series / longitudinal observational,30959164,10.1016/j.bbmt.2019.04.007,NA,"El Jurdi N, Filali-Mouhim A, Salem I, Retuerto M, Dambrosio NM, Baer L, Lazarus HM, Caimi P, Cooper B, Tomlinson B, Metheny L, Malek E, Otegbeye F, Sekaly RP, Ghannoum M , de Lima M",Gastrointestinal Microbiome and Mycobiome Changes during Autologous Transplantation for Multiple Myeloma: Results of a Prospective Pilot Study,Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation,2019,Experiment 1,Sweden,Homo sapiens,"buccal mucosa,lower lip","UBERON:0006956,UBERON:0001835",oral mucositis,EFO:1001904,reference,newly diagnosis maligancies,patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden),38,37,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Figure 1a, Supplemental Table S2",23 June 2020,William Lam,WikiWorks743,Comparison of the oral bacterial community between reference individuals and patients at the time of malignancy diagnosis (before chemotherapy),decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus",2|201174|1760|85004|31953;2|201174|1760|85007|1653|1716;2|201174|84998|84999|84107;2|976|200643|171549|2005523|346096;2|976|117747;2|1239|91061|1385|1378;2|1239|186801|186802|186803;2|32066|203490|203491|203492|848;2|1224|1236|135622|267890|22;2|1224|1236|135619|28256|2745;2|1224|1236|135625|712|713,Complete,NA
Study 322,time series / longitudinal observational,30959164,10.1016/j.bbmt.2019.04.007,NA,"El Jurdi N, Filali-Mouhim A, Salem I, Retuerto M, Dambrosio NM, Baer L, Lazarus HM, Caimi P, Cooper B, Tomlinson B, Metheny L, Malek E, Otegbeye F, Sekaly RP, Ghannoum M , de Lima M",Gastrointestinal Microbiome and Mycobiome Changes during Autologous Transplantation for Multiple Myeloma: Results of a Prospective Pilot Study,Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation,2019,Experiment 2,Sweden,Homo sapiens,"buccal mucosa,lower lip","UBERON:0006956,UBERON:0001835",oral mucositis,EFO:1001904,no oral mucositis,oral mucositis,patients that are newly diagnosed with malignancies (before chemotherapy treatment) that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization),12,25,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 2a, Supplemental Table 2",23 June 2020,William Lam,WikiWorks743,Comparison of the oral bacterial community at the time of malignancy diagnosis (before chemotherapy) in patients who later developed oral mucositis and those who did not develop oral mucositis,increased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta",2|976|117743|200644|49546|1016;2|1239|91061|186826|1300|1357;2|32066;2|203691|203692|136|137|146,Complete,NA
Study 322,time series / longitudinal observational,30959164,10.1016/j.bbmt.2019.04.007,NA,"El Jurdi N, Filali-Mouhim A, Salem I, Retuerto M, Dambrosio NM, Baer L, Lazarus HM, Caimi P, Cooper B, Tomlinson B, Metheny L, Malek E, Otegbeye F, Sekaly RP, Ghannoum M , de Lima M",Gastrointestinal Microbiome and Mycobiome Changes during Autologous Transplantation for Multiple Myeloma: Results of a Prospective Pilot Study,Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation,2019,Experiment 3,Sweden,Homo sapiens,"buccal mucosa,lower lip","UBERON:0006956,UBERON:0001835",oral mucositis,EFO:1001904,at malignancy diagnosis,during chemotherapy,patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization) during chemotherapy treatment,12,12,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,23 June 2020,William Lam,WikiWorks743,Comparison of the oral bacterial community at the  time point of malignancy diagnosis and during chemotherapy in those who have oral mucositis,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 322,time series / longitudinal observational,30959164,10.1016/j.bbmt.2019.04.007,NA,"El Jurdi N, Filali-Mouhim A, Salem I, Retuerto M, Dambrosio NM, Baer L, Lazarus HM, Caimi P, Cooper B, Tomlinson B, Metheny L, Malek E, Otegbeye F, Sekaly RP, Ghannoum M , de Lima M",Gastrointestinal Microbiome and Mycobiome Changes during Autologous Transplantation for Multiple Myeloma: Results of a Prospective Pilot Study,Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation,2019,Experiment 3,Sweden,Homo sapiens,"buccal mucosa,lower lip","UBERON:0006956,UBERON:0001835",oral mucositis,EFO:1001904,at malignancy diagnosis,during chemotherapy,patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that has later developed oral mucositis (graded by the World Health Organization) during chemotherapy treatment,12,12,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,23 June 2020,William Lam,WikiWorks743,Comparison of the oral bacterial community at the  time point of malignancy diagnosis and during chemotherapy in those who have oral mucositis,decreased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Derxia",2|1224;2|1224|28216|80840|506|203697,Complete,NA
Study 322,time series / longitudinal observational,30959164,10.1016/j.bbmt.2019.04.007,NA,"El Jurdi N, Filali-Mouhim A, Salem I, Retuerto M, Dambrosio NM, Baer L, Lazarus HM, Caimi P, Cooper B, Tomlinson B, Metheny L, Malek E, Otegbeye F, Sekaly RP, Ghannoum M , de Lima M",Gastrointestinal Microbiome and Mycobiome Changes during Autologous Transplantation for Multiple Myeloma: Results of a Prospective Pilot Study,Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation,2019,Experiment 4,Sweden,Homo sapiens,"buccal mucosa,lower lip","UBERON:0006956,UBERON:0001835",oral mucositis,EFO:1001904,at malignancy diagnosis,during chemotherapy,patients that are newly diagnosed with malignancies that are between ages 4 and 18 years old that are treated with cytostatic drug and has a national population registration number (Sweden) that did not develop oral mucositis (graded by the World Health Organization) during chemotherapy treatment,10,10,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,23 June 2020,William Lam,WikiWorks743,Comparison of the oral bacterial community at the  time point of malignancy diagnosis and during chemotherapy in those who do not have oral mucositis,increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Xanthomonas,2|1224|1236|135614|32033|338,Complete,NA
Study 322,time series / longitudinal observational,30959164,10.1016/j.bbmt.2019.04.007,NA,"El Jurdi N, Filali-Mouhim A, Salem I, Retuerto M, Dambrosio NM, Baer L, Lazarus HM, Caimi P, Cooper B, Tomlinson B, Metheny L, Malek E, Otegbeye F, Sekaly RP, Ghannoum M , de Lima M",Gastrointestinal Microbiome and Mycobiome Changes during Autologous Transplantation for Multiple Myeloma: Results of a Prospective Pilot Study,Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation,2019,Experiment 5,Sweden,Homo sapiens,"buccal mucosa,lower lip","UBERON:0006956,UBERON:0001835",oral mucositis,EFO:1001904,all samples,mucositis lesions,"during chemotherapy, samples were taken from 12 (out of 25) patients in mucositis group and 10 (out of 12) patients in no mucositis group, with 5 patients taken samples from twice",97,27,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Supplemental Table S4, Figure S1, S2",23 June 2020,William Lam,WikiWorks743,Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Archaea|p__candidate phylum NAG2,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|201174|1760|2037|2049|1654;2|201174|1760|85004|31953|196081;2|1239|91061|1385|186817|1386;2|976|200643|171549|171550;2|1239|91061|1385|90964|1279;2|1239|91061|186826|186827|46123;2|1239|91061|186826|1300|1357;2157|1448937;2|1239|526524|526525|128827,Complete,NA
Study 322,time series / longitudinal observational,30959164,10.1016/j.bbmt.2019.04.007,NA,"El Jurdi N, Filali-Mouhim A, Salem I, Retuerto M, Dambrosio NM, Baer L, Lazarus HM, Caimi P, Cooper B, Tomlinson B, Metheny L, Malek E, Otegbeye F, Sekaly RP, Ghannoum M , de Lima M",Gastrointestinal Microbiome and Mycobiome Changes during Autologous Transplantation for Multiple Myeloma: Results of a Prospective Pilot Study,Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation,2019,Experiment 5,Sweden,Homo sapiens,"buccal mucosa,lower lip","UBERON:0006956,UBERON:0001835",oral mucositis,EFO:1001904,all samples,mucositis lesions,"during chemotherapy, samples were taken from 12 (out of 25) patients in mucositis group and 10 (out of 12) patients in no mucositis group, with 5 patients taken samples from twice",97,27,NA,16S,NA,Roche454,T-Test,0.05,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Supplemental Table S4, Figure S1, S2",23 June 2020,William Lam,WikiWorks743,Relative abundance (%) of taxa with different levels between all mucosal samples from lip and bucca and samples from mucositis lesions,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|724;2|1224|1236|135614|32033|40323;2|544448|31969|2085|2092|2093,Complete,NA
Study 323,prospective cohort,30365522,10.1371/journal.pone.0206366,NA,"Romano-Keeler J, Shilts MH, Tovchigrechko A, Wang C, Brucker RM, Moore DJ, Fonnesbeck C, Meng S, Correa H, Lovvorn HN, Tang YW, Hooper L, Bordenstein SR, Das SR , Weitkamp JH",Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure,PloS one,2018,Experiment 1,United States of America,Homo sapiens,"mucosa of small intestine,feces","UBERON:0001204,UBERON:0001988",necrotizing enterocolitis,EFO:0003928,non-NEC,NEC,infants who underwent intestinal resection at <180 days of age,14,10,NA,16S,123,Roche454,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 5,24 June 2020,Fatima Zohra,WikiWorks743,Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC),increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|186801|186802|31979|1485;2|1239|91061|1385|90964|1279,Complete,NA
Study 323,prospective cohort,30365522,10.1371/journal.pone.0206366,NA,"Romano-Keeler J, Shilts MH, Tovchigrechko A, Wang C, Brucker RM, Moore DJ, Fonnesbeck C, Meng S, Correa H, Lovvorn HN, Tang YW, Hooper L, Bordenstein SR, Das SR , Weitkamp JH",Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure,PloS one,2018,Experiment 2,United States of America,Homo sapiens,"mucosa of small intestine,feces","UBERON:0001204,UBERON:0001988",necrotizing enterocolitis,EFO:0003928,non-NEC,NEC,infants who underwent intestinal resection at <180 days of age,14,10,NA,16S,1234,Roche454,DESeq2,0.1,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Figure 5,24 June 2020,Fatima Zohra,WikiWorks743,Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC),decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Arcobacter,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Alicyclobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium",2|1224|29547|213849|2808963|28196;2|1239|1737404|1737405|1570339|150022;2|1239|91061|1385|186823|29330;2|201174|1760|2037|2049|1654;2|1224|1236|72274|135621|286;2|976|117743|200644|2762318|59732;2|1224|28216|80840|80864|283;2|1239|91061|186826|1300|1301;2|201174|1760|85007|1653|1716,Complete,NA
Study 323,prospective cohort,30365522,10.1371/journal.pone.0206366,NA,"Romano-Keeler J, Shilts MH, Tovchigrechko A, Wang C, Brucker RM, Moore DJ, Fonnesbeck C, Meng S, Correa H, Lovvorn HN, Tang YW, Hooper L, Bordenstein SR, Das SR , Weitkamp JH",Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure,PloS one,2018,Experiment 3,United States of America,Homo sapiens,"mucosa of small intestine,feces","UBERON:0001204,UBERON:0001988",necrotizing enterocolitis,EFO:0003928,non-NEC,NEC,infants who underwent intestinal resection at <180 days of age,14,10,NA,16S,1234,Roche454,DESeq2,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 6,24 June 2020,Fatima Zohra,WikiWorks743,Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC) after adjusting,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 324,"cross-sectional observational, not case-control",30565661,10.1002/ijc.32007,NA,"Feng J, Zhao F, Sun J, Lin B, Zhao L, Liu Y, Jin Y, Li S, Li A , Wei Y",Alterations in the gut microbiota and metabolite profiles of thyroid carcinoma patients,International journal of cancer,2019,Experiment 1,China,Homo sapiens,"blood,feces","UBERON:0000178,UBERON:0001988",thyroid carcinoma,EFO:0002892,healthy control,thyroid carcinoma,at least one solid lesion identified by thyroid ultrasonagraphy,35,30,NA,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 2a,24 June 2020,Rimsha Azhar,WikiWorks743,Gut microbiome phylotype alterations at the phylum and genus levels in thyroid carcinoma,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Archaea|p__Candidatus Bathyarchaeota,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes",2|1239|186801|186802|186804|1505657;2|1224|1236|91347|543|570;2|1239|186801|186802|186803|207244;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|186803|33042;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|292632;2157|928852;2|1239|186801|186802|186803|2569097|39488;2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|1578;2|976|200643|171549|171550;2|1239|186801|186802|186804;2|1239|526524|526525|128827;2|1224|1236|91347|543;2|1239|91061|186826|33958;2|1239|186801|186802|990719;2|1239|91061|186826|1300;2|1224;2|1239,Complete,NA
Study 324,"cross-sectional observational, not case-control",30565661,10.1002/ijc.32007,NA,"Feng J, Zhao F, Sun J, Lin B, Zhao L, Liu Y, Jin Y, Li S, Li A , Wei Y",Alterations in the gut microbiota and metabolite profiles of thyroid carcinoma patients,International journal of cancer,2019,Experiment 1,China,Homo sapiens,"blood,feces","UBERON:0000178,UBERON:0001988",thyroid carcinoma,EFO:0002892,healthy control,thyroid carcinoma,at least one solid lesion identified by thyroid ultrasonagraphy,35,30,NA,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 2a,24 June 2020,Rimsha Azhar,"WikiWorks743,Lwaldron",Gut microbiome phylotype alterations at the phylum and genus levels in thyroid carcinoma,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus",2|1239|909932|1843488|909930;2|976|200643|171549|171552|1283313;2|976|200643|171549|815;2|976|200643|171549|815|816;2|976;2|1239|186801|186802|186803|1506553;2|1239|909932|909929|1843491|158846;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171552|838;2|976|200643|171549|171552;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|2316020|33038,Complete,NA
Study 325,case-control,31141234,10.1111/1346-8138.14933,NA,"Shapiro J, Cohen NA, Shalev V, Uzan A, Koren O , Maharshak N",Psoriatic patients have a distinct structural and functional fecal microbiota compared with controls,The Journal of dermatology,2019,Experiment 1,Israel,Homo sapiens,feces,UBERON:0001988,psoriasis,EFO:0000676,healthy controls,psoriasis,patients with active psoriatic disease diagnosed by a senior dermatologist,22,24,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,comorbidity,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4,25 June 2020,Rimsha Azhar,WikiWorks743,Comparison of genera signatures between psoriatic patients and the control participants,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|216851;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|33042;2|1239|186801|186802|543314|86331;2|1239|186801|186802|186803|189330;2|1239|186801|186802|990719|990721;2|201174|1760|2037|2049|1654;2|201174|84998|84999|84107|102106,Complete,NA
Study 325,case-control,31141234,10.1111/1346-8138.14933,NA,"Shapiro J, Cohen NA, Shalev V, Uzan A, Koren O , Maharshak N",Psoriatic patients have a distinct structural and functional fecal microbiota compared with controls,The Journal of dermatology,2019,Experiment 1,Israel,Homo sapiens,feces,UBERON:0001988,psoriasis,EFO:0000676,healthy controls,psoriasis,patients with active psoriatic disease diagnosed by a senior dermatologist,22,24,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,comorbidity,sex",NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4,25 June 2020,Rimsha Azhar,WikiWorks743,Comparison of genera signatures between psoriatic patients and the control participants,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|976|200643|171549|1853231|574697;2|1224|28221|213115|194924|35832;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544;2|1239|186801|186802|186803|28050;2|976|200643|171549|171552|577309,Complete,NA
Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,"non-small cell lung carcinoma,renal cell carcinoma","EFO:0003060,EFO:0000681",Non-Responders,Responders,"non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease",36,42,NA,WMS,NA,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2b, Supplemental Figure S4",26 June 2020,William Lam,WikiWorks743,Comparsion of partial response/ stable disease and progressive disease in fecal samples of all patients with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus porcorum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|186806|1730|142586;2|1239|186801|186802|186803;2|1239|526524|526525|128827;2|1239|186801|186802|1392389;2|976|200643|171549|171550|239759|214856;2|976|200643|171549|815|816|29523;2|508458|649775|649776|649777|508459|1197717;2|1239|91061|186826|81852|1350|1352;2|976|200643|171549|171552|838,Complete,NA
Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,"non-small cell lung carcinoma,renal cell carcinoma","EFO:0003060,EFO:0000681",Non-Responders,Responders,"non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease",36,42,NA,WMS,NA,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2b, Supplemental Figure S4",26 June 2020,William Lam,WikiWorks743,Comparsion of partial response/ stable disease and progressive disease in fecal samples of all patients with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",2|976|200643|171549|171552|838;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802;2|1239|186801|186802|186803|2719313|208479;2|1239|186801|186802|186803|572511;2|976|200643|171549|815|816|626929;2|1224;2|976|200643|171549|815|816|291645;2|976|200643|171549|2005525|375288|823,Complete,NA
Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,Experiment 2,France,Homo sapiens,feces,UBERON:0001988,"non-small cell lung carcinoma,renal cell carcinoma","EFO:0003060,EFO:0000681",Progressive- Free- Survival more less than 30 days,Progressive -Free- Survival more than 30 days,"non-small cell lung carcinoma or renal carcinoma patients (excluding ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease that are Progressive- Free- Survival greater than 3 months",NA,NA,"ampicillin, colistin, and streptomycin",WMS,NA,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2c, Supplemental Figure S5b",26 June 2020,William Lam,WikiWorks743,Comparsion of patients with partial progressive survival free more than 3 months and less than 3 in fecal samples of patients (excluding those treated with antibiotics) with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|1239|186801|186802|186806|1730|142586;2|976|200643|171549|171550|239759;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|1392389;2|976|200643|171549|815|816|291645;2|976|200643|171549|815|816|371601;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803;2|1239;2|1239|186801|186802;2|1239|186801|186802|216572|1263;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802|216572|946234|292800;2|976|200643|171549|815|816|47678;2|1239|186801|186802|216572|1263|41978,Complete,NA
Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,Experiment 2,France,Homo sapiens,feces,UBERON:0001988,"non-small cell lung carcinoma,renal cell carcinoma","EFO:0003060,EFO:0000681",Progressive- Free- Survival more less than 30 days,Progressive -Free- Survival more than 30 days,"non-small cell lung carcinoma or renal carcinoma patients (excluding ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease that are Progressive- Free- Survival greater than 3 months",NA,NA,"ampicillin, colistin, and streptomycin",WMS,NA,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2c, Supplemental Figure S5b",26 June 2020,William Lam,WikiWorks743,Comparsion of patients with partial progressive survival free more than 3 months and less than 3 in fecal samples of patients (excluding those treated with antibiotics) with non-small cell lung cell lung carcinoma (NSCLC) or renal cell carcinoma (RCC) reponse at 3 months of PD-1 monoclonal antibodies (mAB) treatment,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|2005525|375288|823;2|1239|186801|186802;2|1239|186801|186802|216572|244127|169435;2|1239|186801|186802|186803;2|1239|526524|526525|128827,Complete,NA
Study 326,time series / longitudinal observational,29097494,10.1126/science.aan3706,NA,"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria JC, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G , Zitvogel L",Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors,"Science (New York, N.Y.)",2018,Experiment 3,France,Homo sapiens,feces,UBERON:0001988,"non-small cell lung carcinoma,renal cell carcinoma","EFO:0003060,EFO:0000681",Non-Responders,Responders,"non-small cell lung carcinoma or renal carcinoma patients (all samples regardless of ampicillin, colistin, and streptomycin (ATB) anitbiotic treatment) that have been treated with PD-1 blockage with partial response or stable disease",16,16,NA,WMS,NA,Mass spectrometry,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2g,26 June 2020,William Lam,WikiWorks743,"Culturomics-based analyses of fecal samples in 16 Responders and 16 Non-Responders Non-Small Cell Lung Carcinoma patients (defined as the best clinical outcome) before PD-1 blockage immunotherapy, each commensal colony having been identified by mass spectrometry",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum",2|1239|91061|1385|90964|1279|1283;2|201174|1760|85007|1653|1716|169292,Complete,NA
Study 327,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink RD, van Zoeren-Grobben D, Renes IB, van Lingen RA, Norbruis OF, Martin R, Groot Jebbink LJ, Knol J , Belzer C",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,Experiment 1,Netherlands,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control(no treatment),infants received short-term(<3days) antibiotic treatment,infants born between 32-42 weeks of gestation and admitted to the hospital level III neonatal intesive care or level II neonatal ward,28,22,NA,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Text,28 June 2020,Mst Afroza Parvin,WikiWorks743,"Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 327,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink RD, van Zoeren-Grobben D, Renes IB, van Lingen RA, Norbruis OF, Martin R, Groot Jebbink LJ, Knol J , Belzer C",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,Experiment 1,Netherlands,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control(no treatment),infants received short-term(<3days) antibiotic treatment,infants born between 32-42 weeks of gestation and admitted to the hospital level III neonatal intesive care or level II neonatal ward,28,22,NA,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Text,28 June 2020,Mst Afroza Parvin,WikiWorks743,"Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|91347|543|561;2|1239|91061|186826|1300|1301,Complete,NA
Study 327,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink RD, van Zoeren-Grobben D, Renes IB, van Lingen RA, Norbruis OF, Martin R, Groot Jebbink LJ, Knol J , Belzer C",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,Experiment 2,Netherlands,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control(no treatment),infants received long-term(>5days) antibiotic treatment,infants born between 32-42 weeks of gestation and admitted to the hospital level III neonatal intesive care or level II neonatal ward,28,13,NA,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Text,28 June 2020,Mst Afroza Parvin,WikiWorks743,"Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|91061|186826|33958|1578;2|1239|91061|186826|81852|1350,Complete,NA
Study 327,time series / longitudinal observational,32380969,10.1186/s12887-020-02067-z,NA,"Zwittink RD, van Zoeren-Grobben D, Renes IB, van Lingen RA, Norbruis OF, Martin R, Groot Jebbink LJ, Knol J , Belzer C",Dynamics of the bacterial gut microbiota in preterm and term infants after intravenous amoxicillin/ceftazidime treatment,BMC pediatrics,2020,Experiment 2,Netherlands,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control(no treatment),infants received long-term(>5days) antibiotic treatment,infants born between 32-42 weeks of gestation and admitted to the hospital level III neonatal intesive care or level II neonatal ward,28,13,NA,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Text,28 June 2020,Mst Afroza Parvin,WikiWorks743,"Differences in gut microbiota composition between infants receiving no, short or long antibiotic treatment",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|91347|543|561;2|1239|91061|186826|1300|1301,Complete,NA
Study 328,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, Neimann A, Brusca S, Patel T, Manasson J, Pamer EG, Littman DR , Abramson SB","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,psoriatic arthritis,EFO:0003778,healthy controls,psoriatic arthiritis,patients fulfilling the criteria of the Classification of Psoriatic arthritis (CASPAR),17,16,3 months,16S,12,Roche454,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1a, Figure 2a",28 June 2020,Rimsha Azhar,WikiWorks743,Differences in bacterial taxa between patients with psoriatic arthritis  (PsA) compared to healthy controls (HLT),decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus",2|1239|186801;2|74201|203494;2|74201;2|74201|203494|48461|1647988|239934;2|74201|203494|48461;2|1239|186801|186802|186803|46205;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|33042,Complete,NA
Study 328,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, Neimann A, Brusca S, Patel T, Manasson J, Pamer EG, Littman DR , Abramson SB","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,psoriatic arthritis,EFO:0003778,healthy controls,skin psoriasis,patients fulfilling the criteria of the Classification of Psoriatic arthritis (CASPAR),17,15,3 months,16S,12,Roche454,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,"Figure 1b, Figure 2b",28 June 2020,Rimsha Azhar,WikiWorks743,Differences in bacterial taxa between patients with skin psoriasis (PS) compared to healthy controls (HLT),decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes",2|976|200643|171549|171551;2|976|200643|171549|2005525|375288;2|1239|186801;2|1239|526524|526525|128827;2|1239|526524;2|201174|1760;2|201174;2|1239|526524|526525|2810280|100883;2|1239|526524|526525;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803;2|1239|186801|186802|541000;2|976,Complete,NA
Study 328,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, Neimann A, Brusca S, Patel T, Manasson J, Pamer EG, Littman DR , Abramson SB","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,psoriatic arthritis,EFO:0003778,skin psoriasis,psoriatic arthiritis,patients fulfilling the criteria of the Classification of Psoriatic arthritis (CASPAR),15,16,3 months,16S,12,Roche454,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1c, Figure 2c",28 June 2020,Rimsha Azhar,WikiWorks743,Difference in bactrial taxa between psoriatic arthiritis compared to psoriasis samples,increased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidetes",2|1239|526524|526525|2810280|100883;2|976,Complete,NA
Study 328,"cross-sectional observational, not case-control",25319745,10.1002/art.38892,NA,"Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, Neimann A, Brusca S, Patel T, Manasson J, Pamer EG, Littman DR , Abramson SB","Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease","Arthritis & rheumatology (Hoboken, N.J.)",2015,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,psoriatic arthritis,EFO:0003778,skin psoriasis,psoriatic arthiritis,patients fulfilling the criteria of the Classification of Psoriatic arthritis (CASPAR),15,16,3 months,16S,12,Roche454,LEfSe,0.2,TRUE,2,"age,ethnic group,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1c, Figure 2c",28 June 2020,Rimsha Azhar,WikiWorks743,Difference in bactrial taxa between psoriatic arthiritis compared to psoriasis samples,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobia",2|1239;2|1239|186801;2|1239|186801|186802;2|74201|203494|48461|203557;2|74201,Complete,NA
Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control group,Postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,30 June 2020,Mst Afroza Parvin,WikiWorks743,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control group,Postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,30 June 2020,Mst Afroza Parvin,WikiWorks743,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control group,IAP group (4-day old infant),"Term, vaginally delivered infants",47,44,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,30 June 2020,Mst Afroza Parvin,WikiWorks743,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,Experiment 3,Finland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control group,IAP group (6-month old infant),"Term, vaginally delivered infants",47,44,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,30 June 2020,Mst Afroza Parvin,WikiWorks743,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,NA
Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,Experiment 4,Finland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,30 June 2020,Mst Afroza Parvin,WikiWorks743,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,Experiment 4,Finland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (2-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 5,30 June 2020,Mst Afroza Parvin,WikiWorks743,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,Experiment 5,Finland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (4-day old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,30 June 2020,Mst Afroza Parvin,WikiWorks743,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 329,prospective cohort,31337807,10.1038/s41598-019-46964-5,NA,"Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM , Tejesvi MV",Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants,Scientific reports,2019,Experiment 6,Finland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,control group,IAP+postnatal antibiotic group (6-month old infant),"Term, vaginally delivered infants",47,29,NA,16S,45,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 5,30 June 2020,Mst Afroza Parvin,WikiWorks743,The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,NA
Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,Experiment 1,Finland,Homo sapiens,placenta,UBERON:0001987,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ placenta sample determined by PCR and genotyped with Multimetrix,26,13,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 1 + text,30 June 2020,Cynthia Anderson,WikiWorks743,The bacterial microbiota in placenta samples negative and positive for HPV DNA,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|544448|31969|2085|2092|2129;2|1239|91061|186826|33958|1578|147802,Complete,Fatima Zohra
Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,Experiment 2,Finland,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ cervical sample determined by PCR and genotyped with Multimetrix,30,9,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2 + text,7 July 2020,Cynthia Anderson,WikiWorks743,The bacterial microbiota in cervical samples negative and positive for HPV DNA,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners",2|1239|91061|186826|33958|1578;2|544448|31969|2085|2092|2129;2|1239|91061|186826|33958|1578|147802,Complete,Fatima Zohra
Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,Experiment 2,Finland,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ cervical sample determined by PCR and genotyped with Multimetrix,30,9,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2 + text,7 July 2020,Cynthia Anderson,WikiWorks743,The bacterial microbiota in cervical samples negative and positive for HPV DNA,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1239|186801|186802|186804;2|1239|91061|186826|81852;2|1224|1236|135625|712|724;2|1239|186801|186802|186804|1257,Complete,Fatima Zohra
Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,Experiment 3,Finland,Homo sapiens,mouth,UBERON:0000165,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ oral sample determined by PCR and genotyped with Multimetrix,26,13,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 3 + text,7 July 2020,Cynthia Anderson,WikiWorks743,The bacterial microbiota in oral samples negative and positive for HPV DNA,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia",2|201174|1760|85004|31953;2|1239|1737404|1737405|1570339|150022,Complete,Fatima Zohra
Study 330,"cross-sectional observational, not case-control",29955075,10.1038/s41598-018-27980-3,NA,"Tuominen H, Rautava S, Syrjänen S, Collado MC , Rautava J","HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa",Scientific reports,2018,Experiment 3,Finland,Homo sapiens,mouth,UBERON:0000165,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ oral sample determined by PCR and genotyped with Multimetrix,26,13,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 3 + text,7 July 2020,Cynthia Anderson,WikiWorks743,The bacterial microbiota in oral samples negative and positive for HPV DNA,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,Fatima Zohra
Study 331,case-control,29320965,10.1089/thy.2017.0395,NA,"Zhao F, Feng J, Li J, Zhao L, Liu Y, Chen H, Jin Y, Zhu B , Wei Y",Alterations of the Gut Microbiota in Hashimoto's Thyroiditis Patients,Thyroid : official journal of the American Thyroid Association,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"presence of euthyroidism, free thyroxine, and thyrotropin without hormonal therapy",27,50,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2a, 2b, table 3",30 June 2020,Rimsha Azhar,WikiWorks743,Comparisons of the relative abundance using LEfSe analysis,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium",2|1239;2|1239|186801|186802|186803;2|1239|186801|186802|186804;2|1239|91061|186826|1300;2|1239|186801|186802|31979;2|1224|1236|135625|712;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|841;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186804|1501226;2|1239|526524|526525|128827;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|292632;2|1224|1236|135625|712|724;2|1239|186801|186802|216572|1263|438033;2|1239|186801|186802|31979|580596;2|1239|186801|186802|186806|1730|42322,Complete,NA
Study 331,case-control,29320965,10.1089/thy.2017.0395,NA,"Zhao F, Feng J, Li J, Zhao L, Liu Y, Chen H, Jin Y, Zhu B , Wei Y",Alterations of the Gut Microbiota in Hashimoto's Thyroiditis Patients,Thyroid : official journal of the American Thyroid Association,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"presence of euthyroidism, free thyroxine, and thyrotropin without hormonal therapy",27,50,3 months,16S,34,Illumina,LEfSe,0.05,TRUE,3,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 2a, 2b, table 3",30 June 2020,Rimsha Azhar,WikiWorks743,Comparisons of the relative abundance using LEfSe analysis,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Gaiellales|f__Gaiellaceae|g__Gaiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Gaiellales|f__Gaiellaceae,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Synergistetes",2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|838;2|976|200643|171549|171552|1283313;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|186803|1506553;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|201174|84995|1154584|1154585|1154586;2|976|200643|171549|815;2|976|200643|171549|171552;2|976|200643|171549|171551;2|1239|909932|1843488|909930;2|201174|84995|1154584|1154585;2|976;2|508458,Complete,NA
Study 332,case-control,28903182,10.1016/j.biopha.2017.08.101,NA,"Ishaq HM, Mohammad IS, Guo H, Shahzad M, Hou YJ, Ma C, Naseem Z, Wu X, Shi P , Xu J",Molecular estimation of alteration in intestinal microbial composition in Hashimoto's thyroiditis patients,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"The Thyroid stimulating hormone(TSH) was higher than 5 μIU/ml, T4 was lower than 4.2 μg/dl, T3 was lower than 0.78 ng/ml, anti-thyroid peroxidase antibodies level was higher than 15 IU/ml, and anti-thyroglobulin antibodies was more than 30%",12,29,60 days,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 1,Table 7,30 June 2020,Rimsha Azhar,WikiWorks743,Hashimoto's thyroid gut microbial phylotypes from pyrosequencing,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus flavefaciens,2|1239|186801|186802|216572|1263|1265,Complete,NA
Study 332,case-control,28903182,10.1016/j.biopha.2017.08.101,NA,"Ishaq HM, Mohammad IS, Guo H, Shahzad M, Hou YJ, Ma C, Naseem Z, Wu X, Shi P , Xu J",Molecular estimation of alteration in intestinal microbial composition in Hashimoto's thyroiditis patients,Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Hashimoto's thyroiditis,EFO:0003779,healthy controls,hashimoto's thyroiditis patients,"The Thyroid stimulating hormone(TSH) was higher than 5 μIU/ml, T4 was lower than 4.2 μg/dl, T3 was lower than 0.78 ng/ml, anti-thyroid peroxidase antibodies level was higher than 15 IU/ml, and anti-thyroglobulin antibodies was more than 30%",12,29,60 days,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,unchanged,Signature 2,Table 7,30 June 2020,Rimsha Azhar,WikiWorks743,Hashimoto's thyroid gut microbial phylotypes from pyrosequencing,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,2|1239|91061|186826|33958|1578|1596,Complete,NA
Study 333,"cross-sectional observational, not case-control",30042470,10.1038/s41372-018-0172-1,NA,"Imoto N, Morita H, Amanuma F, Maruyama H, Watanabe S , Hashiguchi N",Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study,Journal of perinatology : official journal of the California Perinatal Association,2018,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,without (non-Abx) use of maternal antimicrobial agents at delivery,infants with (Abx),Healthy infants,14,19,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,NA,NA,NA,Signature 1,Table 2,1 July 2020,Mst Afroza Parvin,WikiWorks743,Relative abundance of the six most common bacterial genera in all infants (n = 33) and in those with and without use of maternal antibiotics and with Cesarean or vaginal delivery,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
Study 334,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou ZH, Liu D, Li HD, Zhu DP, He Y, Hou T , Yu JL",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,prenatal antibiotic free group (PAF group),infants(14-d old) exposed to prenatal antibiotic therapy (PAT group),Pre-term infants,12,12,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Figure 1b, c; Figure 4a,b",1 July 2020,Mst Afroza Parvin,WikiWorks743,LEfSe results on gut microbiomes of preterm infants,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Saccharicrinis,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales",2|976|200643|1970189|558415|1618113;2|1224|29547;2|976|117743|200644,Complete,NA
Study 334,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou ZH, Liu D, Li HD, Zhu DP, He Y, Hou T , Yu JL",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,prenatal antibiotic free group (PAF group),infants(14-d old) exposed to prenatal antibiotic therapy (PAT group),Pre-term infants,12,12,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Figure 1b, c; Figure 4a,b",1 July 2020,Mst Afroza Parvin,WikiWorks743,LEfSe results on gut microbiomes of preterm infants,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1239|186801|186802;2|1239|186801;2|201174|1760|85004|31953|1678,Complete,NA
Study 334,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou ZH, Liu D, Li HD, Zhu DP, He Y, Hou T , Yu JL",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants exposed to antibiotic <=7day (L group),infants exposed to antibiotic >7day (H group),Pre-term infants,11,11,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 8,1 July 2020,Mst Afroza Parvin,WikiWorks743,LEfSe analysis showed significant differences in microbial community structure between the H and L groups.,increased,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,2|1224|28216,Complete,NA
Study 334,time series / longitudinal observational,29554907,10.1186/s12941-018-0264-y,NA,"Zou ZH, Liu D, Li HD, Zhu DP, He Y, Hou T , Yu JL",Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units,Annals of clinical microbiology and antimicrobials,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,infants exposed to antibiotic <=7day (L group),infants exposed to antibiotic >7day (H group),Pre-term infants,11,11,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 8,1 July 2020,Mst Afroza Parvin,WikiWorks743,LEfSe analysis showed significant differences in microbial community structure between the H and L groups.,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae",2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953,Complete,NA
Study 335,laboratory experiment,23638009,10.1371/journal.pone.0062220,NA,"Kish L, Hotte N, Kaplan GG, Vincent R, Tso R, Gänzle M, Rioux KP, Thiesen A, Barkema HW, Wine E , Madsen KL",Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome,PloS one,2013,Experiment 1,Canada,Mus musculus,feces,UBERON:0001988,air pollution,ENVO:02500037,healthy mice,wild type mice fed mouse chow with PM10,Wild-type 129/SvEv mice in chronic treatement group were  fed mouse chow ± PM10 (0.09 gm/kg) for 35 days,7,8,NA,16S,NA,Non-quantitative PCR,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,2 July 2020,Zyaijah Bailey,WikiWorks743,Microbiota composition in stool samples from WT and IL-10−/− mice after 35 days of treatment with PM10.,increased,k__Bacteria|p__Verrucomicrobia,2|74201,Complete,NA
Study 335,laboratory experiment,23638009,10.1371/journal.pone.0062220,NA,"Kish L, Hotte N, Kaplan GG, Vincent R, Tso R, Gänzle M, Rioux KP, Thiesen A, Barkema HW, Wine E , Madsen KL",Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome,PloS one,2013,Experiment 2,Canada,Mus musculus,feces,UBERON:0001988,air pollution,ENVO:02500037,healthy mice,IL-10−/−  mice fed mouse chow with PM10,IL-10−/−  mice in chronic treatement group were  fed mouse chow ± PM10 (0.09 gm/kg) for 35 days,9,7,NA,16S,NA,Non-quantitative PCR,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,2 July 2020,Zyaijah Bailey,WikiWorks743,Microbiota composition in stool samples from WT and IL-10−/− mice after 35 days of treatment with PM10.,increased,"k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Tenericutes",2|74201;2|544448,Complete,NA
Study 335,laboratory experiment,23638009,10.1371/journal.pone.0062220,NA,"Kish L, Hotte N, Kaplan GG, Vincent R, Tso R, Gänzle M, Rioux KP, Thiesen A, Barkema HW, Wine E , Madsen KL",Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome,PloS one,2013,Experiment 2,Canada,Mus musculus,feces,UBERON:0001988,air pollution,ENVO:02500037,healthy mice,IL-10−/−  mice fed mouse chow with PM10,IL-10−/−  mice in chronic treatement group were  fed mouse chow ± PM10 (0.09 gm/kg) for 35 days,9,7,NA,16S,NA,Non-quantitative PCR,PLS-DA (Partial least square discriminant analysis),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,2 July 2020,Zyaijah Bailey,WikiWorks743,Microbiota composition in stool samples from WT and IL-10−/− mice after 35 days of treatment with PM10.,decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,NA
Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 3),combination of penicillin and moxalactam group (postnatal day 3),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,2 July 2020,Mst Afroza Parvin,"WikiWorks743,Chloe",Composition Analysis of Microbiota,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Actinobacteria",2|976|200643|171549|815|816;2|976;2|1239|91061|186826|33958|1578;2|1224|28211|204457|41297|13687;2|201174,Complete,Chloe
Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 3),combination of penicillin and moxalactam group (postnatal day 3),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Text,2 July 2020,Mst Afroza Parvin,WikiWorks743,Composition Analysis of Microbiota,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Chloe
Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 3),piperacillin-tazobactam group (postnatal day 3),"pre-term neonates receiving piperacillin-tazobactam (75 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,2 July 2020,Mst Afroza Parvin,"WikiWorks743,Chloe",Composition Analysis of Microbiota,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Bacteroidetes",2|201174;2|976,Complete,Chloe
Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 7),combination of penicillin and moxalactam group (postnatal day 7),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,2 July 2020,Mst Afroza Parvin,"WikiWorks743,Chloe",Composition Analysis of Microbiota,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|976;2|1224|1236|91347|543|1940338,Complete,Chloe
Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 7),piperacillin-tazobactam group (postnatal day 7),"pre-term neonates receiving piperacillin-tazobactam (75 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,2 July 2020,Mst Afroza Parvin,WikiWorks743,Composition Analysis of Microbiota,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|976|200643|171549|815|816;2|1239|91061|186826|81852|1350,Complete,Chloe
Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic free group (postnatal day 7),piperacillin-tazobactam group (postnatal day 7),"pre-term neonates receiving piperacillin-tazobactam (75 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Text,2 July 2020,Mst Afroza Parvin,WikiWorks743,Composition Analysis of Microbiota,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,2|1224|1236|91347|543|570,Complete,Chloe
Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,piperacillin-tazobactam group (postnatal day 3),combination of penicillin and moxalactam group (postnatal day 3),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Text,30 March 2022,Chloe,Chloe,NA,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,Chloe
Study 336,prospective cohort,28808302,10.1038/s41598-017-08530-9,NA,"Zhu D, Xiao S, Yu J, Ai Q, He Y, Cheng C, Zhang Y , Pan Y",Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants,Scientific reports,2017,Experiment 6,China,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,piperacillin-tazobactam group (postnatal day 7),combination of penicillin and moxalactam group (postnatal day 7),"pre-term neonates given a treatment regimen of penicillin (10U kg-1, twice a day) combined with moxalactam (40 mg kg-1, twice a day)",12,12,NA,16S,34,Illumina,"ANOVA,T-Test",0.05,FALSE,NA,"birth weight,delivery procedure,gestational age,sex",NA,NA,NA,NA,unchanged,NA,NA,Signature 1,Text,30 March 2022,Chloe,Chloe,NA,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,Chloe
Study 337,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M, Differding MK, Benjamin-Neelon SE, Østbye T, Hoyo C , Mueller NT",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,not exposed to antibiotics during the second trimester,3-month-old infants either exposed,infants born after 28 weeks gestation with no congenital abnormalities,56,12,NA,16S,4,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Table S2",3 July 2020,Mst Afroza Parvin,WikiWorks743,Association of second-trimester antibiotic exposure and infant gut microbiome at 3 and 12 months,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,2|1239|186801|186802|186803|1407607,Complete,NA
Study 337,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M, Differding MK, Benjamin-Neelon SE, Østbye T, Hoyo C , Mueller NT",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,not exposed to antibiotics during the second trimester,3-month-old infants exposed,infants born after 28 weeks gestation with no congenital abnormalities,56,12,NA,16S,4,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Table S2",3 July 2020,Mst Afroza Parvin,WikiWorks743,Association of second-trimester antibiotic exposure and infant gut microbiome at 3 and 12 months,decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus antri",2|74201|203494|48461|1647988|239934|239935;2|1224|1236|91347|543;2|1239|91061|186826|1300|1301;2|976|200643|171549|815|816;2|1224|1236|135625|712;2|1239|909932|1843489|31977|29465;2|201174|1760|2037|2049|2529408|1660;2|1239|186801|186802|31979|1485|137838;2|1239|91061|1385|90964|1279;2|1239|91061|186826|33958|2742598|227943,Complete,NA
Study 337,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M, Differding MK, Benjamin-Neelon SE, Østbye T, Hoyo C , Mueller NT",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,not exposed to antibiotics during the second trimester,12-month-old infants either exposed,infants born after 28 weeks gestation with no congenital abnormalities,40,10,NA,16S,4,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1, Table S2",3 July 2020,Mst Afroza Parvin,WikiWorks743,Association of second-trimester antibiotic exposure and infant gut microbiome at 3 and 12 months,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|909932|1843489|31977|29465;2|1239|186801|186802|186804;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803,Complete,NA
Study 337,prospective cohort,31226994,10.1186/s12941-019-0318-9,NA,"Zhang M, Differding MK, Benjamin-Neelon SE, Østbye T, Hoyo C , Mueller NT",Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome,Annals of clinical microbiology and antimicrobials,2019,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,not exposed to antibiotics during the second trimester,12-month-old infants either exposed,infants born after 28 weeks gestation with no congenital abnormalities,40,10,NA,16S,4,Illumina,Beta Binomial Regression,0.05,TRUE,NA,NA,"body mass index,education level,household income,marital status,maternal age,race,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1, Table S2",3 July 2020,Mst Afroza Parvin,WikiWorks743,Association of second-trimester antibiotic exposure and infant gut microbiome at 3 and 12 months,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium",2|1224|1236|91347|543;2|74201|203494|48461|1647988|239934;2|976|200643|171549|815|816;2|976|200643|171549|171550|239759;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|423477;2|1239|186801|186802|186804;2|1239|186801|186802|186803|572511;2|1239|186801|186802|204475;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803|1506553,Complete,NA
Study 338,case-control,31976177,10.7717/peerj.8317,NA,"Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X , Wei P",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,volunteers between the ages of 6-11 years old,23,28,4 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,"Figure 2, Text",4 July 2020,Mst Afroza Parvin,WikiWorks743,"Alpha diversity metrics (Chao1 index, observed species, PD whole tree and Simpson index) of OTU-level fecal bacterial communities;  The relative abundance of fecal bacterial communities",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|186801|186802|216572|216851;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|186803|28050;2|1239|909932|909929|1843491|158846;2|1224|1236|135625|712|724,Complete,NA
Study 338,case-control,31976177,10.7717/peerj.8317,NA,"Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X , Wei P",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,volunteers between the ages of 6-11 years old,23,28,4 weeks,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,"Figure 2, Text",4 July 2020,Mst Afroza Parvin,WikiWorks743,"Alpha diversity metrics (Chao1 index, observed species, PD whole tree and Simpson index) of OTU-level fecal bacterial communities;  The relative abundance of fecal bacterial communities",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|1239|186801|186802|216572|119852;2|1239|909932|1843489|31977|39948,Complete,NA
Study 338,case-control,31976177,10.7717/peerj.8317,NA,"Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X , Wei P",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,volunteers between the ages of 6-11 years old,23,28,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,"Figure 2, Figure 5",4 July 2020,Mst Afroza Parvin,"WikiWorks743,Lwaldron","Alpha diversity metrics (Chao1 index, observed species, PD whole tree and Simpson index) of OTU-level fecal bacterial communities; Different structures of gut microbiota in the two groups.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Acetitomaculum|s__Acetitomaculum ruminis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium dolichum CAG:375,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Pasteuriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus",2|1239|186801|186802|186803|31980|2382;2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|1224|28216|80840|506;2|1239|91061;2|1224|28216;2|1224|28216|80840;2|1224|29547|213849|72294|194;2|1239|91061|186826|186828;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485|1502;2|1239|186801|186802|186806|1730|1263076;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|727;2|1224|1236|135625|712|724|729;2|1239|186801|186802|186803|28050;2|1239|91061|186826;2|32066|203490|203491|1129771;2|1239|909932|909929|1843491|158846;2|201174|1760|85006|1268;2|1224|1236|135625;2|1239|91061|1385|538998;2|1239|186801|186802|186804;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|909656|387090;2|976|200643|171549|171552|838|165179;2|1224;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|39778;2|1239|186801|186802|186803|1506577|36835;2|1239|186801|186802|186803|2316020|33038,Complete,NA
Study 338,case-control,31976177,10.7717/peerj.8317,NA,"Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X , Wei P",Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing,PeerJ,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,volunteers between the ages of 6-11 years old,23,28,4 weeks,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,"Figure 2, Figure 5",4 July 2020,Mst Afroza Parvin,"WikiWorks743,Lwaldron","Alpha diversity metrics (Chao1 index, observed species, PD whole tree and Simpson index) of OTU-level fecal bacterial communities; Different structures of gut microbiota in the two groups.",decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Defluviitaleaceae|g__Defluviitalea,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae|g__Rickettsiella|s__Rickettsiella massiliensis,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hathewaya,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pelomonas|s__Pelomonas saccharophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Tenericutes",2|201174;2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171550|239759;2|976|200643|171549|171550|239759|626932;2|1239|186801|186802|216572|244127;2|976|200643|171549|815|816|820;2|976|200643|171549|2005519;2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1680;2|1224|28221|213115|194924|35832;2|1239|186801|186802|990719|990721;2|1239|186801|186802|990719;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998;2|1239|186801|186802|1185407|1185408;2|1224|28221;2|1224|28221|213115|194924|872;2|1224|28221|213115|194924;2|1224|28221|213115;2|1224|1236|118969|118968|59195|676517;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524;2|1239|186801|186802|186806|1730;2|1239|186801|186802|31979|1769729;2|1239|526524|526525|128827|61170;2|544448|31969;2|1239|186801|186802|216572|119852;2|1224|28216|80840|75682|846;2|1224|28216|80840|75682|846|847;2|1224|28216|80840|75682;2|1224|28216|80840|80864|335058|304;2|1239|186801|186802|186807;2|976|200643|171549|171552|838;2|976|200643|171549|171550;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|44748;2|1239|91061|186826|1300|1301|1302;2|544448,Complete,NA
Study 339,laboratory experiment,28211537,10.1038/srep42906,NA,"Li R, Yang J, Saffari A, Jacobs J, Baek KI, Hough G, Larauche MH, Ma J, Jen N, Moussaoui N, Zhou B, Kang H, Reddy S, Henning SM, Campen MJ, Pisegna J, Li Z, Fogelman AM, Sioutas C, Navab M , Hsiai TK",Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites,Scientific reports,2017,Experiment 1,United States of America,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,vehicle control,mice exposed to UFP,C57BL/6 mice exposed to UFP (Ultrafine particles),11,12,NA,16S,4,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 & Supplemental Figure S1& Text,4 July 2020,Zyaijah Bailey,WikiWorks743,The relative abundance of bacteria was calculated based on operational taxonomic units (OTUs). (A) Overview of the relative abundance of gut bacteria depicted at the phylum level in mice exposed to vehicle control vs. UFP.,increased,k__Bacteria|p__Verrucomicrobia,2|74201,Complete,NA
Study 339,laboratory experiment,28211537,10.1038/srep42906,NA,"Li R, Yang J, Saffari A, Jacobs J, Baek KI, Hough G, Larauche MH, Ma J, Jen N, Moussaoui N, Zhou B, Kang H, Reddy S, Henning SM, Campen MJ, Pisegna J, Li Z, Fogelman AM, Sioutas C, Navab M , Hsiai TK",Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites,Scientific reports,2017,Experiment 1,United States of America,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,vehicle control,mice exposed to UFP,C57BL/6 mice exposed to UFP (Ultrafine particles),11,12,NA,16S,4,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2 & Supplemental Figure S1& Text,4 July 2020,Zyaijah Bailey,WikiWorks743,The relative abundance of bacteria was calculated based on operational taxonomic units (OTUs). (A) Overview of the relative abundance of gut bacteria depicted at the phylum level in mice exposed to vehicle control vs. UFP.,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Cyanobacteria,k__Bacteria|p__Actinobacteria",2|1239;2|1117;2|201174,Complete,NA
Study 340,prospective cohort,30568265,10.1038/s41366-018-0290-z,NA,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-overweight/non-obese children,obese/overweight,"Children who participated in the VDAART clinical trial-a a two arm, double-blind, placebo controlled, randomized, clinical trial of vitamin D supplementation in the pregnant mother to prevent asthma and allergy in childhood in three clinical centers across the United States",356,146,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 1,6 July 2020,Mst Afroza Parvin,WikiWorks743,Mean relative abundances of the top 20 bacterial genera of A) overweight/obese and B) non-overweight/non-obese children.,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,2|1239|186801|186802|186803|189330,Complete,NA
Study 340,prospective cohort,30568265,10.1038/s41366-018-0290-z,NA,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-overweight/non-obese children,obese/overweight,"Children who participated in the VDAART clinical trial-a a two arm, double-blind, placebo controlled, randomized, clinical trial of vitamin D supplementation in the pregnant mother to prevent asthma and allergy in childhood in three clinical centers across the United States",356,146,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 1,6 July 2020,Mst Afroza Parvin,WikiWorks743,Mean relative abundances of the top 20 bacterial genera of A) overweight/obese and B) non-overweight/non-obese children.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239|186801|186802|216572|1263;2|74201|203494|48461|1647988|239934;2|976|200643|171549|2005525|375288,Complete,NA
Study 340,prospective cohort,30568265,10.1038/s41366-018-0290-z,NA,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-overweight/non-obese children,obese/overweight,"Children who participated in the VDAART clinical trial-a a two arm, double-blind, placebo controlled, randomized, clinical trial of vitamin D supplementation in the pregnant mother to prevent asthma and allergy in childhood in three clinical centers across the United States",356,146,NA,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,NA,education level,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 3,6 July 2020,Mst Afroza Parvin,WikiWorks743,Unadjusted and adjusted associations between the top 20 most abundant genera in 502 stool samples and overweight/obesity at the age of 3 years,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,2|1239|186801|186802|186803|189330,Complete,NA
Study 340,prospective cohort,30568265,10.1038/s41366-018-0290-z,NA,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-overweight/non-obese children,obese/overweight,"Children who participated in the VDAART clinical trial-a a two arm, double-blind, placebo controlled, randomized, clinical trial of vitamin D supplementation in the pregnant mother to prevent asthma and allergy in childhood in three clinical centers across the United States",356,146,NA,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,NA,education level,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 3,6 July 2020,Mst Afroza Parvin,WikiWorks743,Unadjusted and adjusted associations between the top 20 most abundant genera in 502 stool samples and overweight/obesity at the age of 3 years,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|976|200643|171549|171551;2|1239|186801|186802|186804,Complete,NA
Study 340,prospective cohort,30568265,10.1038/s41366-018-0290-z,NA,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-overweight/non-obese children,obese/overweight,"Children who participated in the VDAART clinical trial-a a two arm, double-blind, placebo controlled, randomized, clinical trial of vitamin D supplementation in the pregnant mother to prevent asthma and allergy in childhood in three clinical centers across the United States",356,146,NA,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"antibiotic therapy,body mass index,breast feeding,delivery procedure,education level,formula feeding,marital status,race,watching tv",NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 4,6 July 2020,Mst Afroza Parvin,WikiWorks743,Adjusted associations between relative abundances of 7 genera and overweight/obesity at the age of 3 years.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|841;2|1239|91061|186826|1300|1301,Complete,NA
Study 340,prospective cohort,30568265,10.1038/s41366-018-0290-z,NA,"Karvonen AM, Sordillo JE, Gold DR, Bacharier LB, O'Connor GT, Zeiger RS, Beigelman A, Weiss ST , Litonjua AA",Gut microbiota and overweight in 3-year old children,International journal of obesity (2005),2019,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-overweight/non-obese children,obese/overweight,"Children who participated in the VDAART clinical trial-a a two arm, double-blind, placebo controlled, randomized, clinical trial of vitamin D supplementation in the pregnant mother to prevent asthma and allergy in childhood in three clinical centers across the United States",356,146,NA,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,NA,"antibiotic therapy,body mass index,breast feeding,delivery procedure,education level,formula feeding,marital status,race,watching tv",NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 4,6 July 2020,Mst Afroza Parvin,WikiWorks743,Adjusted associations between relative abundances of 7 genera and overweight/obesity at the age of 3 years.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|976|200643|171549|2005525|375288;2|1239|186801|186802|186804,Complete,NA
Study 341,prospective cohort,30157953,10.1186/s40168-018-0531-3,NA,"Shanahan ER, Shah A, Koloski N, Walker MM, Talley NJ, Morrison M , Holtmann GJ",Influence of cigarette smoking on the human duodenal mucosa-associated microbiota,Microbiome,2018,Experiment 1,Australia,Homo sapiens,small intestine,UBERON:0002108,nicotine dependence,EFO:0003768,never smoked,"patients with FD, ID,or CD who currently smoked","patient with FD,ID or CD with who previously or currently smokes",41,61,2 months,16S,678,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3& Text,7 July 2020,Zyaijah Bailey,WikiWorks743,Linear discriminant analysis effect size (LEfSe) method to identify bacterial OTUs that are associated with smoking status.,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 341,prospective cohort,30157953,10.1186/s40168-018-0531-3,NA,"Shanahan ER, Shah A, Koloski N, Walker MM, Talley NJ, Morrison M , Holtmann GJ",Influence of cigarette smoking on the human duodenal mucosa-associated microbiota,Microbiome,2018,Experiment 2,Australia,Homo sapiens,small intestine,UBERON:0002108,nicotine dependence,EFO:0003768,never smoked,"patients with FD, ID,or CD who currently smokes","patient with FD,ID or CD with who previously or currently smokes",41,61,2 months,16S,678,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 3 & Text,7 July 2020,Zyaijah Bailey,WikiWorks743,Linear discriminant analysis effect size (LEfSe) method to identify bacterial OTUs that are associated with smoking status.,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 1,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children who did not experience more than one exacerbation,Children who experienced exacerbtion,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table E5,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differential association with exacerbation, viral outcomes, and clinical events after adjustment for age",decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 2,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children with no rhinovirus infection,Children with any rhinovirus infection,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table E5,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differential association with exacerbation, viral outcomes, and clinical events after adjustment for age",increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 2,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children with no rhinovirus infection,Children with any rhinovirus infection,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table E5,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differential association with exacerbation, viral outcomes, and clinical events after adjustment for age",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 3,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children RV-,Children with rhinovirus-A (RV-A),"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table E5,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differential association with exacerbation, viral outcomes, and clinical events after adjustment for age",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 3,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children RV-,Children with rhinovirus-A (RV-A),"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table E5,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differential association with exacerbation, viral outcomes, and clinical events after adjustment for age",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 4,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,older children,Younger children,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,2|1224|1236|2887326|468|475,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 5,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children who did not experience more than one exacerbation,Children who experienced exacerbation,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,2|1224|1236|2887326|468|475,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 5,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children who did not experience more than one exacerbation,Children who experienced exacerbation,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|1239|91061|186826|186828|1651;2|201174|1760|85007|1653|1716;2|1224|1236|135625|712|724;2|1239|91061|1385|90964|1279,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 6,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,no viral illnesses,Viral illnesses,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,2|1224|1236|2887326|468|475,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 6,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,no viral illnesses,Viral illnesses,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 7,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children with no rhinovirus infection,Children with any rhinovirus infection,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 7,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children with no rhinovirus infection,Children with any rhinovirus infection,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 8,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children rhinovirus negative,Children with rhinovirus A infection,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 8,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children rhinovirus negative,Children with rhinovirus A infection,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 9,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children rhinovirus neagtive,Children with rhinovirus C infection,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 9,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,children rhinovirus neagtive,Children with rhinovirus C infection,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 10,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,no respiratory illness,Respiratory illness,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 342,randomized controlled trial,31201890,10.1016/j.jaci.2019.05.035,NA,"McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ , Lynch SV",Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma,The Journal of allergy and clinical immunology,2019,Experiment 10,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,asthma,MONDO:0004979,no respiratory illness,Respiratory illness,"physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both",NA,3122,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table I,7 July 2020,Victoria Goulbourne,WikiWorks743,"Distinct nasal airway differentially associated with exacerbation, viral outcomes, and clinical events",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus",2|201174|1760|85007|1653|1716;2|1239|91061|1385|90964|1279,Complete,NA
Study 343,time series / longitudinal observational,31873965,10.1002/cncr.32641,NA,"Rashidi A, Kaiser T, Graiziger C, Holtan SG, Rehman TU, Weisdorf DJ, Dunny GM, Khoruts A , Staley C",Gut dysbiosis during antileukemia chemotherapy versus allogeneic hematopoietic cell transplantation,Cancer,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,leukemia,EFO:0000565,Allogeneic Hematopoeitic Stem Cell Transplant,Antileukemic,Intensive chemotherapy (involving induction and re-induction.salvage) was defined as any regimen requiring a planned hospitalization of approximately 4 weeks. patients can not be enrolled twice in the same study with exception of 3 patients that went into allogeneic hematopoeitic stem cell transplant study,20,20,NA,16S,4,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Supplementary Table S3, Supplementary Figure S2",7 July 2020,William Lam,WikiWorks743,Phylogenetic biomarkers of domination of acute leukemia treated with antileukemia compared with allogeneic hematopoeitic stem cell transplant,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288,Complete,NA
Study 343,time series / longitudinal observational,31873965,10.1002/cncr.32641,NA,"Rashidi A, Kaiser T, Graiziger C, Holtan SG, Rehman TU, Weisdorf DJ, Dunny GM, Khoruts A , Staley C",Gut dysbiosis during antileukemia chemotherapy versus allogeneic hematopoietic cell transplantation,Cancer,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,leukemia,EFO:0000565,Allogeneic Hematopoeitic Stem Cell Transplant,Antileukemic,Intensive chemotherapy (involving induction and re-induction.salvage) was defined as any regimen requiring a planned hospitalization of approximately 4 weeks. patients can not be enrolled twice in the same study with exception of 3 patients that went into allogeneic hematopoeitic stem cell transplant study,20,20,NA,16S,4,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Supplementary Table S3, Supplementary Figure S2",7 July 2020,William Lam,WikiWorks743,Phylogenetic biomarkers of domination of acute leukemia treated with antileukemia compared with allogeneic hematopoeitic stem cell transplant,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|91061|186826|81852|1350;2|976|200643|171549|815|816,Complete,NA
Study 344,laboratory experiment,31935575,10.1016/j.chemosphere.2020.125879,NA,"Liu W, Zhou Y, Yong Li Y, Qin L, Yu R, Li Y, Chen Y , Xu",Effects of PM<sub>2.5</sub> exposure during gestation on maternal gut microbiota and pregnancy outcomes,Chemosphere,2020,Experiment 1,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice exposed suspension from extracts of “blank” filter,mice exposed to Pm 2.5 suspension,exposed to PM2.5 suspension,12,12,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,increased,decreased,increased,NA,increased,Signature 1,"Figure 4a, text",7 July 2020,Zyaijah Bailey,"WikiWorks743,Lwaldron","the most differentially abundant taxa between the two groups were identified through the LDA score which was generated from LEfSe analysis (phylum to genus: p, phylum; c, class; o, order; f, family; g, genus)",increased,"k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Proteobacteria,k__Archaea|p__candidate phylum NAG2,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales",2|1224|28221;2|1239|186801|186802|216572|946234;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|1239|186801|186802|216572|459786;2|1224;2157|1448937;2|32066|203490|203491|203492|848;2|1224|28221|213115|194924;2|1224|28221|213115,Complete,NA
Study 344,laboratory experiment,31935575,10.1016/j.chemosphere.2020.125879,NA,"Liu W, Zhou Y, Yong Li Y, Qin L, Yu R, Li Y, Chen Y , Xu",Effects of PM<sub>2.5</sub> exposure during gestation on maternal gut microbiota and pregnancy outcomes,Chemosphere,2020,Experiment 1,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice exposed suspension from extracts of “blank” filter,mice exposed to Pm 2.5 suspension,exposed to PM2.5 suspension,12,12,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,increased,decreased,increased,NA,increased,Signature 2,"Figure 4a, text",7 July 2020,Zyaijah Bailey,WikiWorks743,"the most differentially abundant taxa between the two groups were identified through the LDA score which was generated from LEfSe analysis (phylum to genus: p, phylum; c, class; o, order; f, family; g, genus)",decreased,"k__Bacteria|p__Acidobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Gemmatimonadetes|c__Gemmatimonadetes|o__Gemmatimonadales,k__Bacteria|p__Gemmatimonadetes|c__Gemmatimonadetes,k__Bacteria|p__Gemmatimonadetes|c__Gemmatimonadetes|o__Gemmatimonadales|f__Gemmatimonadaceae|g__Gemmatimonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Gemmatimonadetes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales,k__Bacteria|p__Deferribacteres,k__Bacteria|p__Deferribacteres|c__Deferribacteres,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Mucispirillum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|57723;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|351;2|1239|91061;2|1224|1236;2|1224|1236|72274;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|142182|219685|219686;2|142182|219685;2|142182|219685|219686|219687|173479;2|1224|28216|80840|80864|80865;2|142182;2|1239|91061|186826|1300;2|1239|91061|1385;2|201174|1760|85006|85023;2|1239|91061|186826|1300|1301;2|1239|91061|1385|186817|1386;2|201174|1760|85006|85023|55968;2|200930|68337|191393|191394;2|200930|68337|191393;2|200930;2|200930|68337;2|200930|68337|191393|191394|248038;2|976|200643|171549|1853231|283168,Complete,NA
Study 345,case-control,30366118,10.1016/j.anaerobe.2018.10.009,NA,"Maya-Lucas O, Murugesan S, Nirmalkar K, Alcaraz LD, Hoyo-Vadillo C, Pizano-Zárate ML , García-Mena J",The gut microbiome of Mexican children affected by obesity,Anaerobe,2019,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal,obese,unrelated children between 9 and 11 years,10,10,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 4A,8 July 2020,Mst Afroza Parvin,WikiWorks743,"Significant bacteria, path abundance-coverage, gene families found in the gut microbiome and association with metadata. Figure shows graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial genera, families or species;",increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,2|1239|909932|909929|1843491|158846,Complete,NA
Study 345,case-control,30366118,10.1016/j.anaerobe.2018.10.009,NA,"Maya-Lucas O, Murugesan S, Nirmalkar K, Alcaraz LD, Hoyo-Vadillo C, Pizano-Zárate ML , García-Mena J",The gut microbiome of Mexican children affected by obesity,Anaerobe,2019,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal,obese,unrelated children between 9 and 11 years,10,10,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 4A,8 July 2020,Mst Afroza Parvin,WikiWorks743,"Significant bacteria, path abundance-coverage, gene families found in the gut microbiome and association with metadata. Figure shows graphs of linear discriminant analysis (LDA) scores for differentially abundant bacterial genera, families or species;",decreased,"k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides faecis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae",2|1224|28221;2|1224|28221|213115|194924;2|1224|28221|213115;2|1239|91061|186826|1300|1301|1308;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|186803|207244;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572;2|1239|526524|526525|128827|61170;2|976|200643|171549|815|816|674529;2|1224|28221|213115|194924|35832|35833;2|976|200643|171549|815|816|291644;2|976|200643|171549|815|816|371601;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816;2|976|200643|171549|815,Complete,NA
Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,mild depression,severe depression,"psychiatric inpatients diagnosed by DSM-IV Disorders, SCID-I and SCID-II interviews, CSSR-S, SLEQ and GAD-7",NA,NA,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1a,1b",8 July 2020,Fatima Zohra,WikiWorks743,Bacterial biomarkers associated with depression severity with genus and species level resolution at admission,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|946234|292800,Complete,NA
Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,mild depression,severe depression,"psychiatric inpatients diagnosed by DSM-IV Disorders, SCID-I and SCID-II interviews, CSSR-S, SLEQ and GAD-7",NA,NA,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1a,1b",8 July 2020,Fatima Zohra,WikiWorks743,Bacterial biomarkers associated with depression severity with genus and species level resolution at admission,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes",2|201174;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|171550|239759|1288121;2|1224|28216|80840|75682|846|847,Complete,NA
Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,unipolar depression,EFO:0003761,mild depression,moderate depression,"psychiatric inpatients diagnosed by DSM-IV Disorders, SCID-I and SCID-II interviews, CSSR-S, SLEQ and GAD-7",NA,NA,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1a,1b",8 July 2020,Fatima Zohra,WikiWorks743,Bacterial biomarkers associated with depression severity with genus and species level resolution at admission,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum",2|1239|186801|186802|216572|946234;2|1239|91061|186826|1300|1301|1328;2|1239|186801|186802|186803|33042|116085;2|1239|186801|186802|186803|1506553|1512,Complete,NA
Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,anxiety disorder,EFO:0006788,mild anxiety,severe anxiety,"psychiatric inpatients diagnosed by DSM-IV Disorders, SCID-I and SCID-II interviews, CSSR-S, SLEQ and GAD-7",NA,NA,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1c, 1d",8 July 2020,Fatima Zohra,WikiWorks743,Bacterial biomarkers associated with anxiety severity with genus and species level resolution at admission,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,2|1239|91061|186826|1300|1301|1328,Complete,NA
Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,anxiety disorder,EFO:0006788,mild anxiety,severe anxiety,"psychiatric inpatients diagnosed by DSM-IV Disorders, SCID-I and SCID-II interviews, CSSR-S, SLEQ and GAD-7",NA,NA,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 1c, 1d",8 July 2020,Fatima Zohra,WikiWorks743,Bacterial biomarkers associated with anxiety severity with genus and species level resolution at admission,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus",2|1239;2|1239|186801|186802;2|1239|186801;2|201174|1760|85007|1653;2|201174|1760|85007;2|201174|1760;2|201174;2|201174|1760|85007|2805586|1847725;2|976|200643|171549|171550|239759|28117;2|201174|1760|85004|31953|1678|1680;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|186803|841|301301;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|186803|33042|116085,Complete,NA
Study 346,prospective cohort,32056780,10.1016/j.jad.2019.12.020,NA,"Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM , Petrosino JF",The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness,Journal of affective disorders,2020,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,anxiety disorder,EFO:0006788,mild anxiety,moderate anxiety,"psychiatric inpatients diagnosed by DSM-IV Disorders, SCID-I and SCID-II interviews, CSSR-S, SLEQ and GAD-7",NA,NA,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 1c, 1d",8 July 2020,Fatima Zohra,WikiWorks743,Bacterial biomarkers associated with anxiety severity with genus and species level resolution at admission,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,2|1239|91061|186826|1300|1357|1358,Complete,NA
Study 347,case-control,30267022,10.1038/s41598-018-32730-6,NA,"Gao X, Jia R, Xie L, Kuang L, Feng L , Wan C",A study of the correlation between obesity and intestinal flora in school-age children,Scientific reports,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control,obese,School children,38,39,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 1,"Figure 1, Table2, Table 3, Text",8 July 2020,Mst Afroza Parvin,WikiWorks743,Box-plot of α diversity of the obesity group and the control group. Comparisons of relative abundance of gut bacteria between the obesity and control groups at the level of Phylum & Species,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella|s__Allisonella histaminiformans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella stercorea,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter|s__Oxalobacter formigenes",2|976;2|976|200643|171549|815|909656|310297;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|2005525|375288|823;2|1224|28221|213115|194924|35832|35833;2|1239|186801|186802|186803|1506553|1512;2|1239|909932|909929|1843491|158846|437897;2|1239|909932|1843489|31977|209879|209880;2|976|200643|171549|171552|838|363265;2|1224|28216|80840|75682|846|847,Complete,NA
Study 347,case-control,30267022,10.1038/s41598-018-32730-6,NA,"Gao X, Jia R, Xie L, Kuang L, Feng L , Wan C",A study of the correlation between obesity and intestinal flora in school-age children,Scientific reports,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control,obese,School children,38,39,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,increased,NA,decreased,Signature 2,"Figure 1, Table2, Table 3, Text",8 July 2020,Mst Afroza Parvin,"WikiWorks743,Lwaldron",Box-plot of α diversity of the obesity group and the control group. Comparisons of relative abundance of gut bacteria between the obesity and control groups at the level of Phylum & Species,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes caccae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia luti,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__Erysipelatoclostridium ramosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] sporosphaeroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] sulci,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes butyraticus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus cecorum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor|s__Lactonifactor longoviformis",2|201174;2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171552|1283313|671218;2|1239|186801|186802|186803|207244|105841;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|818;2|1239|186801|186802|186803|572511|89014;2|1239|186801|186802|186803|572511|418240;2|95818;2|1239|526524|526525|128827|1505663|1547;2|1239|186801|186802|216572|216851|853;2|1239;2|201174|84998|1643822|1643826|644652|471189;2|1239|526524|526525|128827|123375|102148;2|1239|91061|186826|1300|1301|76860;2|1239|91061|186826|1300|1301|1304;2|74201;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|1549;2|1239|186801|186802|543314|143393;2|1239|186801|186802|186803|207244|645466;2|1239|91061|186826|81852|1350|44008;2|1239|186801|186802|31979|420345|341220,Complete,NA
Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,Experiment 1,Brazil,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,obese,Healthy children,30,30,3 months,16S,NA,RT-qPCR,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,9 July 2020,Mst Afroza Parvin,WikiWorks743,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",2|976|200643|171549|815|816|817;2|1239|91061|186826|33958|1578|1591,Complete,NA
Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,Experiment 1,Brazil,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,obese,Healthy children,30,30,3 months,16S,NA,RT-qPCR,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,9 July 2020,Mst Afroza Parvin,WikiWorks743,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,2|201174|1760|85004|31953|1678|41200,Complete,NA
Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,Experiment 2,Brazil,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,overweight,Healthy children,30,24,3 months,16S,NA,RT-qPCR,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,9 July 2020,Mst Afroza Parvin,WikiWorks743,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",2|976|200643|171549|815|816|817;2|1239|91061|186826|33958|1578|1591,Complete,NA
Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,Experiment 2,Brazil,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,overweight,Healthy children,30,24,3 months,16S,NA,RT-qPCR,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,9 July 2020,Mst Afroza Parvin,WikiWorks743,"Bacterial prevalence and quantification verified in faeces of obese, overweight and lean children by quantitative PCR",decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,2|201174|1760|85004|31953|1678|41200,Complete,NA
Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,Experiment 3,Brazil,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,obese,Healthy children,30,30,3 months,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table 6,9 July 2020,Mst Afroza Parvin,WikiWorks743,Factors associated with body mass index based on multiple logistic regression (logistic regression analysis using quantitative PCR results,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,2|976|200643|171549|815|816|817,Complete,NA
Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,Experiment 3,Brazil,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,obese,Healthy children,30,30,3 months,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Table 6,9 July 2020,Mst Afroza Parvin,WikiWorks743,Factors associated with body mass index based on multiple logistic regression (logistic regression analysis using quantitative PCR results,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,2|201174|1760|85004|31953|1678|41200,Complete,NA
Study 348,"cross-sectional observational, not case-control",26551842,10.1016/j.cmi.2015.10.031,NA,"Ignacio A, Fernandes MR, Rodrigues VA, Groppo FC, Cardoso AL, Avila-Campos MJ , Nakano V",Correlation between body mass index and faecal microbiota from children,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2016,Experiment 4,Brazil,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,overweight,Healthy children,30,24,3 months,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Table 6,9 July 2020,Mst Afroza Parvin,WikiWorks743,Factors associated with body mass index based on multiple logistic regression (logistic regression analysis using quantitative PCR results,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,NA
Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,Experiment 1,Norway,Homo sapiens,endocervix,UBERON:0000458,cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before prcocedure,women with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,100,89,long-term antibiotic use,16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 July 2020,Cynthia Anderson,WikiWorks743,The cervical microbiota in the LEEP group and the Reference group,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2895623|2895509|2098;2|544448|31969|2085|2092|2129|134821,Complete,NA
Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,Experiment 2,Norway,Homo sapiens,endocervix,UBERON:0000458,cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before prcocedure,women with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,99,89,long-term antibiotic use,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,"age,contraception,marital status,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Table 5,10 July 2020,Cynthia Anderson,WikiWorks743,The cervical microbiota in the LEEP group and the Reference group,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|31969|2085|2092|2129|134821,Complete,NA
Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,Experiment 3,Norway,Homo sapiens,endocervix,UBERON:0000458,cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before prcocedure,women <46 years old with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,48,75,long-term antibiotic use,16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 1,10 July 2020,Cynthia Anderson,WikiWorks743,The cervical microbiota in the LEEP group and the Reference group in women aged < 46 years,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2895623|2895509|2098;2|544448|31969|2085|2092|2129|134821,Complete,NA
Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,Experiment 4,Norway,Homo sapiens,endocervix,UBERON:0000458,cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group before prcocedure,women <46 years old with suspected high grade cervical dysplasia planning for their first Loop Electrosurgical Excision Procedure,48,75,long-term antibiotic use,16S,NA,RT-qPCR,Logistic Regression,0.05,FALSE,NA,NA,"age,contraception,marital status,smoking behavior",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 1,10 July 2020,Cynthia Anderson,WikiWorks743,The cervical microbiota in the LEEP group and the Reference group in women aged < 46 years,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|31969|2085|2092|2129|134821,Complete,NA
Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,Experiment 5,Norway,Homo sapiens,endocervix,UBERON:0000458,cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group 6 months prcocedure,women 6 months after Loop Electrosurgical Excision Procedure,100,77,long-term antibiotic use,16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 2,10 July 2020,Cynthia Anderson,WikiWorks743,The cervical microbiota six months post treatment in the LEEP group and the cervical microbiota in the Reference group,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2895623|2895509|2098;2|544448|31969|2085|2092|2129|134821,Complete,NA
Study 349,time series / longitudinal observational,30728029,10.1186/s12905-019-0727-0,NA,"Wiik J, Sengpiel V, Kyrgiou M, Nilsson S, Mitra A, Tanbo T, Monceyron Jonassen C, Møller Tannæs T , Sjøborg K","Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study",BMC women's health,2019,Experiment 6,Norway,Homo sapiens,endocervix,UBERON:0000458,cervical glandular intraepithelial neoplasia,EFO:1000165,normal,LEEP group 12 months prcocedure,women 12 months after Loop Electrosurgical Excision Procedure,100,72,long-term antibiotic use,16S,NA,RT-qPCR,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table 3,10 July 2020,Cynthia Anderson,WikiWorks743,The cervical microbiota 12 months post treatment in the LEEP group and the cervical microbiota in the Reference group,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma hominis,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma|s__Ureaplasma parvum",2|201174|1760|85004|31953|2701|2702;2|544448|2790996|2895623|2895509|2098;2|544448|31969|2085|2092|2129|134821,Complete,NA
Study 350,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L, Cornejo-Granados F, García-López R, Valdez-Lara A, Bikel S, Canizales-Quinteros S, López-Contreras BE, Mendoza-Vargas A, Nielsen H , Ochoa-Leyva A","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,children aged 7-10 years old,7,10,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,1,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2,10 July 2020,Mst Afroza Parvin,WikiWorks743,Differentially abundant taxa in association with groups and their distribution in the samples.,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii",2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|171551|836;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853,Complete,NA
Study 350,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L, Cornejo-Granados F, García-López R, Valdez-Lara A, Bikel S, Canizales-Quinteros S, López-Contreras BE, Mendoza-Vargas A, Nielsen H , Ochoa-Leyva A","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,children aged 7-10 years old,7,10,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,1,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2,10 July 2020,Mst Afroza Parvin,WikiWorks743,Differentially abundant taxa in association with groups and their distribution in the samples.,decreased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,2|1239|909932|1843488|909930|33024,Complete,NA
Study 350,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L, Cornejo-Granados F, García-López R, Valdez-Lara A, Bikel S, Canizales-Quinteros S, López-Contreras BE, Mendoza-Vargas A, Nielsen H , Ochoa-Leyva A","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,Experiment 2,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obesity with metabolic syndrome,children aged 7-10 years old,7,10,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,1,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2,10 July 2020,Mst Afroza Parvin,WikiWorks743,Differentially abundant taxa in association with groups and their distribution in the samples.,increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Proteobacteria",2|201174|84998;2|201174|1760|85007;2|201174|84998|84999|84107;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|1239;2|1239|91061;2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186803|33042;2|1239|526524;2|1239|526524|526525;2|1239|526524|526525|128827;2|1239|526524|526525|2810280|135858;2|1224,Complete,NA
Study 350,case-control,32143621,10.1186/s12934-020-01319-y,NA,"Gallardo-Becerra L, Cornejo-Granados F, García-López R, Valdez-Lara A, Bikel S, Canizales-Quinteros S, López-Contreras BE, Mendoza-Vargas A, Nielsen H , Ochoa-Leyva A","Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children",Microbial cell factories,2020,Experiment 2,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obesity with metabolic syndrome,children aged 7-10 years old,7,10,3 months,16S,4,Illumina,LEfSe,0.05,FALSE,1,"age,sex",NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2,10 July 2020,Mst Afroza Parvin,WikiWorks743,Differentially abundant taxa in association with groups and their distribution in the samples.,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia",2|976;2|976|200643|171549;2|976|200643,Complete,NA
Study 351,"cross-sectional observational, not case-control",31934770,10.1089/chi.2019.0280,NA,"Da Silva CC, Monteil MA , Davis EM",Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota,Childhood obesity (Print),2020,Experiment 1,Trinidad and Tobago,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal,overweight/obesity,school aged children (6-14 years),30,21,3 months,16S,NA,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Table 2 & 3,10 July 2020,Mst Afroza Parvin,WikiWorks743,The Relative Abundance (%) of the Most Dominant Bacterial Families & genus from Stool Samples at Varying Demographic and Anthropometric Measure,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 351,"cross-sectional observational, not case-control",31934770,10.1089/chi.2019.0280,NA,"Da Silva CC, Monteil MA , Davis EM",Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota,Childhood obesity (Print),2020,Experiment 1,Trinidad and Tobago,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal,overweight/obesity,school aged children (6-14 years),30,21,3 months,16S,NA,Illumina,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Table 2 & 3,10 July 2020,Mst Afroza Parvin,WikiWorks743,The Relative Abundance (%) of the Most Dominant Bacterial Families & genus from Stool Samples at Varying Demographic and Anthropometric Measure,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678,Complete,NA
Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,Experiment 1,United States of America,Homo sapiens,vagina,UBERON:0000996,"cervical glandular intraepithelial neoplasia,human papilloma virus infection","EFO:1000165,EFO:0001668",Atypical Squamous Cells of Undetermined Significance,Low Grade Squamous Intraepithelial Lesion,low grade squamous intraepithelial lesion,6,18,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Figure 8,13 July 2020,Cynthia Anderson,WikiWorks743,Fungal biomarker signatures in the 58 introitus samples,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae",2759|4751|4890|4891|4892|4893|4930;2759|4751|5204|162481|231213|1799696,Complete,Fatima Zohra
Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,Experiment 2,United States of America,Homo sapiens,vagina,UBERON:0000996,"cervical glandular intraepithelial neoplasia,human papilloma virus infection","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 8,13 July 2020,Cynthia Anderson,WikiWorks743,Fungal biomarker signatures in the 58 introitus samples,increased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,2759|4751|5204|1538075|162474|742845|55193,Complete,Fatima
Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,Experiment 2,United States of America,Homo sapiens,vagina,UBERON:0000996,"cervical glandular intraepithelial neoplasia,human papilloma virus infection","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Figure 8,13 July 2020,Cynthia Anderson,WikiWorks743,Fungal biomarker signatures in the 58 introitus samples,decreased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae,2759|4751|5204|162481|231213|1799696,Complete,Fatima
Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,Experiment 3,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,"cervical glandular intraepithelial neoplasia,human papilloma virus infection","EFO:1000165,EFO:0001668",Atypical Squamous Cells of Undetermined Significance,Low Grade Squamous Intraepithelial Lesion,low grade squamus intraepithelial lesion,6,18,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 8,13 July 2020,Cynthia Anderson,WikiWorks743,Fungal biomarker signatures in the 55 cervical samples,decreased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae,2759|4751|5204|162481|231213|1799696,Complete,Fatima Zohra
Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,Experiment 4,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,"cervical glandular intraepithelial neoplasia,human papilloma virus infection","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure 8,13 July 2020,Cynthia Anderson,WikiWorks743,Fungal biomarker signatures in the 55 cervical samples,increased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,2759|4751|5204|1538075|162474|742845|55193,Complete,Fatima Zohra
Study 352,"cross-sectional observational, not case-control",30405584,10.3389/fmicb.2018.02533,NA,"Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG , Blaser MJ",Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population,Frontiers in microbiology,2018,Experiment 4,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,"cervical glandular intraepithelial neoplasia,human papilloma virus infection","EFO:1000165,EFO:0001668",Low risk-HPV,High risk-HPV,High risk-HPV,3,27,2 months,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Figure 8,13 July 2020,Cynthia Anderson,WikiWorks743,Fungal biomarker signatures in the 55 cervical samples,decreased,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae,2759|4751|5204|162481|231213|1799696,Complete,Fatima Zohra
Study 353,case-control,19849869,10.1017/S0007114509992182,NA,"Balamurugan R, George G, Kabeerdoss J, Hepsiba J, Chandragunasekaran AM , Ramakrishna BS",Quantitative differences in intestinal Faecalibacterium prausnitzii in obese Indian children,The British journal of nutrition,2010,Experiment 1,India,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,non-obese,obese,(Private) School Children,13,15,1 month,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,class/grade level,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,12 July 2020,Mst Afroza Parvin,WikiWorks743,Quantitative PCR of different bacterial groups from the faeces of obese (OB) and non-obese (NOB) participants,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,2|1239|186801|186802|216572|216851|853,Complete,NA
Study 354,case-control,22546742,10.1038/oby.2012.110,NA,"Karlsson CL, Onnerfält J, Xu J, Molin G, Ahrné S , Thorngren-Jerneck K",The microbiota of the gut in preschool children with normal and excessive body weight,"Obesity (Silver Spring, Md.)",2012,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control (BMI at normal range),overweight/obese,pre-school children,20,20,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Table 3,12 July 2020,Mst Afroza Parvin,WikiWorks743,"Concentrations of specific bacterial groups in feces of overweight/obese and normal weight children, detected by qPCR",increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,NA
Study 354,case-control,22546742,10.1038/oby.2012.110,NA,"Karlsson CL, Onnerfält J, Xu J, Molin G, Ahrné S , Thorngren-Jerneck K",The microbiota of the gut in preschool children with normal and excessive body weight,"Obesity (Silver Spring, Md.)",2012,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control (BMI at normal range),overweight/obese,pre-school children,20,20,NA,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Table 3,12 July 2020,Mst Afroza Parvin,WikiWorks743,"Concentrations of specific bacterial groups in feces of overweight/obese and normal weight children, detected by qPCR",decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|74201|203494|48461|1647988|239934|239935;2|1224|28221|213115|194924|872,Complete,NA
Study 355,"cross-sectional observational, not case-control",23631345,10.1186/1757-4749-5-10,NA,"Bervoets L, Van Hoorenbeeck K, Kortleven I, Van Noten C, Hens N, Vael C, Goossens H, Desager KN , Vankerckhoven V",Differences in gut microbiota composition between obese and lean children: a cross-sectional study,Gut pathogens,2013,Experiment 1,Belgium,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control (lean/normal weight),obese (obese/overweight/morbidly obese),Children,27,26,1 month,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,12 July 2020,Mst Afroza Parvin,WikiWorks743,Differences in bacterial genera between O/O and C group.,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,NA
Study 355,"cross-sectional observational, not case-control",23631345,10.1186/1757-4749-5-10,NA,"Bervoets L, Van Hoorenbeeck K, Kortleven I, Van Noten C, Hens N, Vael C, Goossens H, Desager KN , Vankerckhoven V",Differences in gut microbiota composition between obese and lean children: a cross-sectional study,Gut pathogens,2013,Experiment 1,Belgium,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,control (lean/normal weight),obese (obese/overweight/morbidly obese),Children,27,26,1 month,16S,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,12 July 2020,Mst Afroza Parvin,WikiWorks743,Differences in bacterial genera between O/O and C group.,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,2|976|200643|171549|815|909656|821,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 1,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 3,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5 air,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 7a & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1239|186801|186802|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|186803;2|976|200643|171549|171550,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 1,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 3,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5 air,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 7a & text,12 July 2020,Zyaijah Bailey,"WikiWorks743,Lwaldron","LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1239|91061|186826|186827;2|1239|91061|186826|186827|66831;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1239|91061|1385|90964;2|1224|1236|91347|543|1940338,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 2,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 10,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 7b & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales",2|1224|1236|91347|1903414|583;2|201174|1760|85010,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 3,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 21,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 7c & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales",2|1239|91061|1385|539003;2|1239|91061|1385|1378;2|1239|186801|186802|216572|459786;2|1239|186801|186802|186803|841;2|1239|91061|1385,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 3,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 21,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 7c & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus",2|976|200643|171549|815|816;2|976|200643|171549|815;2|1224|28221|213115|194924|872;2|1239|186801|186802|216572|244127,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 4,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR male mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,Signature 1,Figure 7d& text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae",2|1239|91061|186826|1300|1301;2|201174|1760|85011|2062,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 5,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 10,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 7f & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,NA,NA,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 5,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 10,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 7f & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Enterorhabdus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|201174|84998|84999;2|201174|84998|1643822|1643826|580024;2|976|200643|171549|171552,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 6,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 21,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 7g & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae",2|74201|203494;2|74201|203494|48461;2|74201|203494|48461|203557;2|74201;2|1224|28221;2|1224|28221|213115;2|1224|28221|213115|194924,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 6,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 21,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 7g & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 7,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 1,Figure 7h & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|541000,Complete,NA
Study 356,laboratory experiment,32544691,10.1016/j.scitotenv.2020.139982,NA,"Liu W, Zhou Y, Qin Y, Li Y, Yu L, Li R, Chen Y , Xu Y",Sex-specific effects of PM<sub>2.5</sub> maternal exposure on offspring's serum lipoproteins and gut microbiota,The Science of the total environment,2020,Experiment 7,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice dams exposed to filtered blanks PND 35,ICR female mice exposed to PM 2.5,ICR mice exposed to PM 2.5,8,8,NA,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,unchanged,unchanged,NA,increased,Signature 2,Figure 7h & text,12 July 2020,Zyaijah Bailey,WikiWorks743,"LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.",decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,2|1239|186801|186802|186804,Complete,NA
Study 357,time series / longitudinal observational,30804895,10.3389/fmicb.2019.00054,NA,"Qin T, Zhang F, Zhou H, Ren H, Du Y, Liang S, Wang F, Cheng L, Xie X, Jin A, Wu Y, Zhao J , Xu J",High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,mucosa,UBERON:0000344,air pollution,ENVO:02500037,pre-smog swabs,post-smog swabs,Vendors in an open-air farer's market who worked in the same place and were exposed to smog over the same business hours,83,83,NA,16S,34,Illumina,LEfSe,0.001,TRUE,4,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,Figure S3,12 July 2020,Victoria Goulbourne,WikiWorks743,Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe),increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216;2|976|200643|171549|171552|838,Complete,NA
Study 357,time series / longitudinal observational,30804895,10.3389/fmicb.2019.00054,NA,"Qin T, Zhang F, Zhou H, Ren H, Du Y, Liang S, Wang F, Cheng L, Xie X, Jin A, Wu Y, Zhao J , Xu J",High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition,Frontiers in microbiology,2019,Experiment 1,China,Homo sapiens,mucosa,UBERON:0000344,air pollution,ENVO:02500037,pre-smog swabs,post-smog swabs,Vendors in an open-air farer's market who worked in the same place and were exposed to smog over the same business hours,83,83,NA,16S,34,Illumina,LEfSe,0.001,TRUE,4,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 2,Figure S3,12 July 2020,Victoria Goulbourne,WikiWorks743,Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe),decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia",2|1239|909932|1843489|31977;2|1239|91061;2|32066|203490|203491|1129771|32067,Complete,NA
Study 358,"cross-sectional observational, not case-control",32546712,10.1038/s41598-020-66607-4,NA,"Tango CN, Seo SS, Kwon M, Lee DO, Chang HK , Kim MK",Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development,Scientific reports,2020,Experiment 1,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,"cervical glandular intraepithelial neoplasia,cervical cancer","EFO:1000165,MONDO:0002974",Healthy controls,CIN2/3-CC,patients diagnosed with CIN2/3 or cervical cancer during screening of the cervical tract,50,42,antibiotic therapy within 3 months,16S,NA,Roche454,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,increased,unchanged,NA,increased,Signature 1,figure 2,14 July 2020,Cynthia Anderson,WikiWorks743,Diferences in relative abundances of microbial taxa (genus and species) between groups by LEfSe analysis,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus sakei,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus fornicalis,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter|s__Enhydrobacter aerosaccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella koreensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium striatum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia|s__Massilia alkalitolerans",2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300|1301|1313;2|976|200643|171549|171552|838|419005;2|1239|91061|186826|33958|2767885|1599;2|1224|28211|356|212791;2|1239|91061|186826|33958|1578|88164;2|1224|28211|356|212791|225324;2|1239|91061|186826|33958|46255;2|1239|91061|186826|33958|46255|165096;2|1239|91061|1385|90964|1279;2|201174|1760|85009|31957|1912216;2|201174|1760|85009|31957|1912216|1747;2|201174|1760|85006|1268|1269;2|201174|1760|85006|1268|1269|1270;2|201174|1760|85007|1653|1716|43770;2|32066|203490|203491|203492|848|851;2|1224|28216|80840|75682|149698|286638,Complete,NA
Study 359,meta-analysis,27015003,10.1038/ismej.2016.37,NA,"Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, Ma Y, Purdue MP, Jacobs EJ, Gapstur SM, Li H, Alekseyenko AV, Hayes RB , Ahn J",Cigarette smoking and the oral microbiome in a large study of American adults,The ISME journal,2016,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,former smoker,current smoker,participants who developed head and neck or pancreatic cancer at any point after collection of the oral wash samples,521,112,NA,16S,34,Roche454,Kruskall-Wallis,0.001,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,14 July 2020,Victoria Goulbourne,WikiWorks743,Median relative abundances of selected taxa according to smoking status in four data sets,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia",2|201174;2|201174|84998,Complete,NA
Study 359,meta-analysis,27015003,10.1038/ismej.2016.37,NA,"Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, Ma Y, Purdue MP, Jacobs EJ, Gapstur SM, Li H, Alekseyenko AV, Hayes RB , Ahn J",Cigarette smoking and the oral microbiome in a large study of American adults,The ISME journal,2016,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,former smoker,current smoker,participants who developed head and neck or pancreatic cancer at any point after collection of the oral wash samples,521,112,NA,16S,34,Roche454,Kruskall-Wallis,0.001,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 2,14 July 2020,Victoria Goulbourne,WikiWorks743,Median relative abundances of selected taxa according to smoking status in four data sets,decreased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia",2|1224;2|1224|28216;2|1224|1236;2|976|117743,Complete,NA
Study 359,meta-analysis,27015003,10.1038/ismej.2016.37,NA,"Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, Ma Y, Purdue MP, Jacobs EJ, Gapstur SM, Li H, Alekseyenko AV, Hayes RB , Ahn J",Cigarette smoking and the oral microbiome in a large study of American adults,The ISME journal,2016,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,former smoker,current smoker,participants who developed head and neck or pancreatic cancer at any point after collection of the oral wash samples,521,112,NA,16S,34,Roche454,Kruskall-Wallis,0.001,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 3,Supplementary Table 4,14 July 2020,Victoria Goulbourne,WikiWorks743,q-vales for comparison of medican relative abundances of oral bacterial genera according to smoke status,increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301,Complete,NA
Study 359,meta-analysis,27015003,10.1038/ismej.2016.37,NA,"Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, Ma Y, Purdue MP, Jacobs EJ, Gapstur SM, Li H, Alekseyenko AV, Hayes RB , Ahn J",Cigarette smoking and the oral microbiome in a large study of American adults,The ISME journal,2016,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,former smoker,current smoker,participants who developed head and neck or pancreatic cancer at any point after collection of the oral wash samples,521,112,NA,16S,34,Roche454,Kruskall-Wallis,0.001,TRUE,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 4,Supplementary Table 4,14 July 2020,Victoria Goulbourne,WikiWorks743,q-vales for comparison of medican relative abundances of oral bacterial genera according to smoke status,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|1224|1236|135625|712|416916;2|976|117743|200644|49546|1016;2|201174|1760|85007|1653|1716;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|32067;2|1239|186801|186802|186804|1257;2|1239|91061|186826|186827|46123;2|1239|909932|909929|1843491|970,Complete,NA
Study 360,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch MN, Phillippi D, Zhang Y, Lucero J, Pandey RS, Liu J, Brower J, Allen MS, Campen MJ, McDonald JD , Lund AK","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,Experiment 1,United States of America,Mus musculus,small intestine,UBERON:0002108,air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to MVE,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 10 & text,14 July 2020,Zyaijah Bailey,WikiWorks743,"Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",increased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|526524|526525|2810281|191303;2|1239|186801|186802|31979|1485,Complete,NA
Study 360,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch MN, Phillippi D, Zhang Y, Lucero J, Pandey RS, Liu J, Brower J, Allen MS, Campen MJ, McDonald JD , Lund AK","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,Experiment 1,United States of America,Mus musculus,small intestine,UBERON:0002108,air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to MVE,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 10 & text,14 July 2020,Zyaijah Bailey,WikiWorks743,"Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|186801|186802|216572|119852;2|1239|91061|186826|33958|1578,Complete,NA
Study 360,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch MN, Phillippi D, Zhang Y, Lucero J, Pandey RS, Liu J, Brower J, Allen MS, Campen MJ, McDonald JD , Lund AK","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,Experiment 2,United States of America,Mus musculus,small intestine,UBERON:0002108,air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to WS,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 10 & text,14 July 2020,Zyaijah Bailey,WikiWorks743,"Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",increased,NA,NA,Complete,NA
Study 360,laboratory experiment,31753468,10.1016/j.envres.2019.108913,NA,"Fitch MN, Phillippi D, Zhang Y, Lucero J, Pandey RS, Liu J, Brower J, Allen MS, Campen MJ, McDonald JD , Lund AK","Effects of inhaled air pollution on markers of integrity, inflammation, and microbiota profiles of the intestines in Apolipoprotein E knockout mice",Environmental research,2020,Experiment 2,United States of America,Mus musculus,small intestine,UBERON:0002108,air pollution,ENVO:02500037,mice exposed to Filtered Air,mice exposed to WS,male ApoE−/- mice exposed to  mixed diesel and gasoline engine emissions (MVE) or Wood Smoke (WS),20,20,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 10 & text,14 July 2020,Zyaijah Bailey,WikiWorks743,"Effects of inhaled filtered air (FA), wood-smoke (WS), and mixed diesel and gasoline vehicle exhaust (MVE) on the relative abundance of gastrointestinal bacteria at the (A) phylum level, and (B) genus level in ApoE−/-mice.",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|186801|186802|216572|119852;2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1578,Complete,NA
Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,Experiment 1,Canada,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,control,male mice exposed to cigarette smoke,"male, female or ovariectomized females mice exposed to smoke",10,10,NA,16S,4,Illumina,LEfSe,0.002,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 2,14 July 2020,Zyaijah Bailey,WikiWorks743,"Differential taxa features identified by LEfSe (LDA score > 3.5) according to smoke exposure; red and blue bars represent taxa features with higher expression in the control and smoke-exposed groups, respectively.",increased,"k__Archaea|p__Candidatus Aenigmarchaeota,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales",2157|743724;2|74201;2|74201|203494;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|1647988;2|1224|28211|204441,Complete,NA
Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,Experiment 1,Canada,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,control,male mice exposed to cigarette smoke,"male, female or ovariectomized females mice exposed to smoke",10,10,NA,16S,4,Illumina,LEfSe,0.002,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 2,14 July 2020,Zyaijah Bailey,WikiWorks743,"Differential taxa features identified by LEfSe (LDA score > 3.5) according to smoke exposure; red and blue bars represent taxa features with higher expression in the control and smoke-exposed groups, respectively.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|976|200643|171549|171550|239759;2|976|200643|171549|171550;2|976|200643|171549|2005473,Complete,NA
Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,Experiment 2,Canada,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,control,female mice exposed to cigarette smoke,"male, female or ovariectomized females mice exposed to smoke",10,10,NA,16S,4,Illumina,LEfSe,0.004,TRUE,3.5,NA,NA,decreased,increased,NA,NA,NA,increased,Signature 1,Figure 2,14 July 2020,Zyaijah Bailey,WikiWorks743,"Differential taxa features identified by LEfSe (LDA score > 3.5) according to smoke exposure; red and blue bars represent taxa features with higher expression in the control and smoke-exposed groups, respectively.",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|2005473;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,NA
Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,Experiment 2,Canada,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,control,female mice exposed to cigarette smoke,"male, female or ovariectomized females mice exposed to smoke",10,10,NA,16S,4,Illumina,LEfSe,0.004,TRUE,3.5,NA,NA,decreased,increased,NA,NA,NA,increased,Signature 2,Figure 2,14 July 2020,Zyaijah Bailey,WikiWorks743,"Differential taxa features identified by LEfSe (LDA score > 3.5) according to smoke exposure; red and blue bars represent taxa features with higher expression in the control and smoke-exposed groups, respectively.",decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Heliobacteriaceae|g__Heliobacterium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter",2|1224|29547|213849;2|1239|186801|186802|31984|2697;2|1224|29547|213849|72293;2|976|200643|171549|2005473|1918540;2|976|200643|1970189|1573805;2|976|200643|171549|1853231|283168,Complete,NA
Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,Experiment 3,Canada,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,control,ovariectomized female mice exposed to cigarette smoke,"male, female or ovariectomized females mice exposed to smoke",10,10,NA,16S,4,Illumina,LEfSe,0.003,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 2,14 July 2020,Zyaijah Bailey,WikiWorks743,"Differential taxa features identified by LEfSe (LDA score > 3.5) according to smoke exposure; red and blue bars represent taxa features with higher expression in the control and smoke-exposed groups, respectively.",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio",2|976|200643|171549|171552;2|976|200643|171549|171550|28138;2|1239|186801|186802|186803|830,Complete,NA
Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,Experiment 3,Canada,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,control,ovariectomized female mice exposed to cigarette smoke,"male, female or ovariectomized females mice exposed to smoke",10,10,NA,16S,4,Illumina,LEfSe,0.003,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 2,14 July 2020,Zyaijah Bailey,WikiWorks743,"Differential taxa features identified by LEfSe (LDA score > 3.5) according to smoke exposure; red and blue bars represent taxa features with higher expression in the control and smoke-exposed groups, respectively.",decreased,NA,NA,Complete,NA
Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,Experiment 4,Canada,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,control,mice exposed to smoke,"male, female or ovariectomized females mice exposed to smoke",10,10,NA,16S,4,Illumina,LEfSe,0.001,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 1,Figure 2,14 July 2020,Zyaijah Bailey,WikiWorks743,"Differential taxa features identified by LEfSe (LDA score > 3.5) according to smoke exposure; red and blue bars represent taxa features with higher expression in the control and smoke-exposed groups, respectively.",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia sp.,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|976|200643|171549|815|816;2|976|200643|171549|815;2|74201;2|74201|203494|48461;2|74201|203494|48461|1647988|239934|1872421;2|74201|203494;2|1239|186801|186802|216572|459786,Complete,NA
Study 361,laboratory experiment,32251484,10.1371/journal.pone.0230932,NA,"Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL , Sin DD",Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome,PloS one,2020,Experiment 4,Canada,Mus musculus,caecum,UBERON:0001153,air pollution,ENVO:02500037,control,mice exposed to smoke,"male, female or ovariectomized females mice exposed to smoke",10,10,NA,16S,4,Illumina,LEfSe,0.001,TRUE,3.5,NA,NA,decreased,decreased,NA,NA,NA,decreased,Signature 2,Figure 2,14 July 2020,Zyaijah Bailey,WikiWorks743,"Differential taxa features identified by LEfSe (LDA score > 3.5) according to smoke exposure; red and blue bars represent taxa features with higher expression in the control and smoke-exposed groups, respectively.",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239|186801|186802|186803;2|976|200643|171549|2005473;2|976|200643|171549|171550;2|976|200643|171549|171550|239759,Complete,NA
Study 362,"cross-sectional observational, not case-control",32429742,10.1089/chi.2019.0312,NA,"Aguilar T, Nava GM, Olvera-Ramírez AM, Ronquillo D, Camacho M, Zavala GA, Caamaño MC, Acevedo-Whitehouse K, Rosado JL , García OP",Gut Bacterial Families Are Associated with Body Composition and Metabolic Risk Markers in School-Aged Children in Rural Mexico,Childhood obesity (Print),2020,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight children,obese,School-aged children,56,16,4 months,16S,NA,RT-qPCR,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure A1,15 July 2020,Mst Afroza Parvin,WikiWorks743,"Comparison of mean (ANOVA) between anthropometrical and biochemical variables and their association with the main bacterial families studied. (A) Comparison between normal weight, overweight, and obesity according to BMI for age.",increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,2|1239|91061|186826|33958,Complete,NA
Study 362,"cross-sectional observational, not case-control",32429742,10.1089/chi.2019.0312,NA,"Aguilar T, Nava GM, Olvera-Ramírez AM, Ronquillo D, Camacho M, Zavala GA, Caamaño MC, Acevedo-Whitehouse K, Rosado JL , García OP",Gut Bacterial Families Are Associated with Body Composition and Metabolic Risk Markers in School-Aged Children in Rural Mexico,Childhood obesity (Print),2020,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight children,obese,School-aged children,56,16,4 months,16S,NA,RT-qPCR,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure A1,15 July 2020,Mst Afroza Parvin,WikiWorks743,"Comparison of mean (ANOVA) between anthropometrical and biochemical variables and their association with the main bacterial families studied. (A) Comparison between normal weight, overweight, and obesity according to BMI for age.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|815;2|976|200643|171549|171551;2|976|200643|171549|171552,Complete,NA
Study 363,"cross-sectional observational, not case-control",32341759,10.1080/20002297.2020.1742527,NA,"Sato N, Kakuta M, Uchino E, Hasegawa T, Kojima R, Kobayashi W, Sawada K, Tamura Y, Tokuda I, Imoto S, Nakaji S, Murashita K, Yanagita M , Okuno Y",The relationship between cigarette smoking and the tongue microbiome in an East Asian population,Journal of oral microbiology,2020,Experiment 1,Japan,Homo sapiens,tongue,UBERON:0001723,smoking behavior,EFO:0004318,never smokers,current smokers,participants who underwent tongue-coating analysis in 2016 and 2017,384,144,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,dental caries,number of teeth measurement,peridontal microbiome,sex",NA,decreased,NA,decreased,NA,decreased,Signature 1,Figure 3,15 July 2020,Victoria Goulbourne,WikiWorks743,The result of comparison of bacterial abundance at the genus level,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Paludibacteraceae|g__Paludibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma",2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|201174|84998|84999|1643824|1380;2|1239|909932|1843489|31977|906;2|201174|1760|85007|1653|1716;2|976|200643|171549|2005523|346096;2|1239|186801|186802|543314|109326;2|976|200643|171549|2005525|195950;2|1239|186801|186802|186804|44259;2|544448|31969|2085|2092|2093,Complete,NA
Study 363,"cross-sectional observational, not case-control",32341759,10.1080/20002297.2020.1742527,NA,"Sato N, Kakuta M, Uchino E, Hasegawa T, Kojima R, Kobayashi W, Sawada K, Tamura Y, Tokuda I, Imoto S, Nakaji S, Murashita K, Yanagita M , Okuno Y",The relationship between cigarette smoking and the tongue microbiome in an East Asian population,Journal of oral microbiology,2020,Experiment 1,Japan,Homo sapiens,tongue,UBERON:0001723,smoking behavior,EFO:0004318,never smokers,current smokers,participants who underwent tongue-coating analysis in 2016 and 2017,384,144,NA,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,alcohol drinking,body mass index,dental caries,number of teeth measurement,peridontal microbiome,sex",NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 3,15 July 2020,Victoria Goulbourne,WikiWorks743,The result of comparison of bacterial abundance at the genus level,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella",2|1239|186801|186802|186807|2740;2|976|117743|200644|49546|1016;2|1224|28216|206351|481|482;2|1224|1236|135615|868|2717;2|1224|28216|80840|119060|47670;2|1239|186801|186802|186804|1257;2|1239|186801|186802|186803|43996;2|32066|203490|203491|203492|848;2|976|200643|171549|171552|1283313;2|976|200643|171549|171551|836;2|1239|186801|186802|186803|1164882;2|32066|203490|203491|1129771|32067;2|1239|186801|186802|186803|265975;2|1239|186801|186802|186806|1730;2|1224|29547|213849|72294|194;2|1239|526524|526525|128827|123375;2|1224|1236|135625|712|724;2|1239|186801|186802|186803|1213720;2|1239|91061|1385|1378,Complete,NA
Study 364,meta-analysis,31199220,10.1099/jmm.0.001003,NA,"Karabudak S, Ari O, Durmaz B, Dal T, Basyigit T, Kalcioglu MT , Durmaz R",Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology,Journal of medical microbiology,2019,Experiment 1,Turkey,Homo sapiens,buccal mucosa,UBERON:0006956,smoking behavior,EFO:0004318,non-smoker,smoker,"participants that fulfilled the inclusion criteris for good health: no use of antibiotics in the past 3 months, no respiratory infections, no oral aphthous lesions on buccal mucosa, and absence of dental problems",20,20,3 months,16S,23456789,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,16 July 2020,Victoria Goulbourne,WikiWorks743,Comparison of statistically significant differences between smoker and non-smoker groups at genus and species levels,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella salivae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica",2|201174|1760|2037|2049|1654;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301|113107;2|976|200643|171549|171552|838|228604;2|976|200643|171549|171552|838|28132;2|201174|1760|85006|1268|32207|43675;2|1239|909932|1843489|31977|29465|39777,Complete,NA
Study 365,laboratory experiment,30562947,10.3390/ijms19124079,NA,"Ishii C, Nakanishi Y, Murakami S, Nozu R, Ueno M, Hioki K, Aw W, Hirayama A, Soga T, Ito M, Tomita M , Fukuda S",A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet,International journal of molecular sciences,2018,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,diet,EFO:0002755,mice fed control rodent diet.,mice exposed to American Diet,"C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber",6,5,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3E,15 July 2020,Tahiya Begum,WikiWorks743,"Box plots indicating relative abundance of genera that have absolute LDA score > 2.0, absolute OPLS-DA covariance > 0.11 in OPLS-DA, and FDR < 0.05 based on Mann–Whitney U test and Benjamini-Hochberg correction between the control and AD groups.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|186802|216572|119852;2|1239|186801|186802|186803|33042;2|1239|186801|186802|216572|1263,Complete,NA
Study 365,laboratory experiment,30562947,10.3390/ijms19124079,NA,"Ishii C, Nakanishi Y, Murakami S, Nozu R, Ueno M, Hioki K, Aw W, Hirayama A, Soga T, Ito M, Tomita M , Fukuda S",A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet,International journal of molecular sciences,2018,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,diet,EFO:0002755,mice fed control rodent diet.,mice exposed to American Diet,"C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber",6,5,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3E,16 July 2020,Tahiya Begum,WikiWorks743,"Box plots indicating relative abundance of genera that have absolute LDA score > 2.0, absolute OPLS-DA covariance > 0.11 in OPLS-DA, and FDR < 0.05 based on Mann–Whitney U test and Benjamini-Hochberg correction between the control and AD groups.",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1239|186801|186802|216572|1263;2|976|200643|171549|171552|838;2|976|200643|171549|815|816,Complete,NA
Study 366,case-control,23454028,10.1016/j.cgh.2013.02.015,NA,"Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP , Rioux KP",Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease,Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association,2013,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,healthy controls,nonalcoholic fatty liver disease,Obese patients with a body mass index (BMI) greater than 30 kg/m2 and clinically suspected non-alcoholic fatty liver disease,30,30,3 months,16S,NA,Mass spectrometry,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4,16 July 2020,Rimsha Azhar,WikiWorks743,Significant taxa distinguishing in control and NAFLD,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Kiloniellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea",2|1224|28211|204441|597359;2|1224|1236|135625|712;2|1239|91061|186826|33958;2|1239|909932|1843489|31977;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|588605;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|189330,Complete,NA
Study 366,case-control,23454028,10.1016/j.cgh.2013.02.015,NA,"Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP , Rioux KP",Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease,Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association,2013,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,non-alcoholic fatty liver disease,EFO:0003095,healthy controls,nonalcoholic fatty liver disease,Obese patients with a body mass index (BMI) greater than 30 kg/m2 and clinically suspected non-alcoholic fatty liver disease,30,30,3 months,16S,NA,Mass spectrometry,Metastats,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4,16 July 2020,Rimsha Azhar,WikiWorks743,Significant taxa distinguishing in control and NAFLD,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|1239|186801|186802|541000;2|976|200643|171549|171551;2|1239|186801|186802|216572|459786,Complete,NA
Study 367,"cross-sectional observational, not case-control",25761741,10.1007/s10096-015-2355-4,NA,"Murugesan S, Ulloa-Martínez M, Martínez-Rojano H, Galván-Rodríguez FM, Miranda-Brito C, Romano MC, Piña-Escobedo A, Pizano-Zárate ML, Hoyo-Vadillo C , García-Mena J",Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2015,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,"Unrelated children, 9–11 years old",81,80,3 months,16S,3,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,17 July 2020,Mst Afroza Parvin,WikiWorks743,"Relative abundance of particular bacteria in normal, overweight, and obese Mexican children.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.",2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|186803|572511|1955243;2|1239|186801|186802|186803;2|1239|186801|186802|186803|33042|2049024;2|1224|1236|91347|543;2|1239|186801|186802|186803|841|2049040,Complete,NA
Study 367,"cross-sectional observational, not case-control",25761741,10.1007/s10096-015-2355-4,NA,"Murugesan S, Ulloa-Martínez M, Martínez-Rojano H, Galván-Rodríguez FM, Miranda-Brito C, Romano MC, Piña-Escobedo A, Pizano-Zárate ML, Hoyo-Vadillo C , García-Mena J",Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2015,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,"Unrelated children, 9–11 years old",81,80,3 months,16S,3,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,17 July 2020,Mst Afroza Parvin,WikiWorks743,"Relative abundance of particular bacteria in normal, overweight, and obese Mexican children.",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1224|1236|135624|83763|83770|2053619;2|1224|1236|91347|1903409|551|558;2|1239|186801|186802|216572|119852,Complete,NA
Study 367,"cross-sectional observational, not case-control",25761741,10.1007/s10096-015-2355-4,NA,"Murugesan S, Ulloa-Martínez M, Martínez-Rojano H, Galván-Rodríguez FM, Miranda-Brito C, Romano MC, Piña-Escobedo A, Pizano-Zárate ML, Hoyo-Vadillo C , García-Mena J",Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2015,Experiment 2,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,overweight,"Unrelated children, 9–11 years old",81,29,3 months,16S,3,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,17 July 2020,Mst Afroza Parvin,WikiWorks743,"Relative abundance of particular bacteria in normal, overweight, and obese Mexican children.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.",2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|186803|572511|1955243;2|1239|186801|186802|186803;2|1239|186801|186802|186803|33042|2049024;2|1224|1236|91347|543;2|1239|186801|186802|186803|841|2049040,Complete,NA
Study 367,"cross-sectional observational, not case-control",25761741,10.1007/s10096-015-2355-4,NA,"Murugesan S, Ulloa-Martínez M, Martínez-Rojano H, Galván-Rodríguez FM, Miranda-Brito C, Romano MC, Piña-Escobedo A, Pizano-Zárate ML, Hoyo-Vadillo C , García-Mena J",Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2015,Experiment 2,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,overweight,"Unrelated children, 9–11 years old",81,29,3 months,16S,3,Ion Torrent,ANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,17 July 2020,Mst Afroza Parvin,WikiWorks743,"Relative abundance of particular bacteria in normal, overweight, and obese Mexican children.",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia|s__Erwinia sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1224|1236|135624|83763|83770|2053619;2|1224|1236|91347|1903409|551|558;2|1239|186801|186802|216572|119852,Complete,NA
Study 368,"cross-sectional observational, not case-control",32640977,10.1186/s12866-020-01883-8,NA,"Halboub E, Al-Ak'hali MS, Alamir AH, Homeida HE, Baraniya D, Chen T , Al-Hebshi NN",Tongue microbiome of smokeless tobacco users,BMC microbiology,2020,Experiment 1,Saudi Arabia,Homo sapiens,tongue,UBERON:0001723,smoking behavior,EFO:0004318,non-shammah users,shammah users,participants who used shammah daily for at least one year without a period of cessation and those who had no history of shammah use,23,29,3 months,16S,123,Illumina,LEfSe,0.015,TRUE,NA,sex,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3 a & b,17 July 2020,Victoria Goulbourne,WikiWorks743,Differentially abundant taxa,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus gastricus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flava,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|419014;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|1300|1301|1306;2|201174|1760|2037|2049|2529408|52773;2|201174|1760|85004|31953|419014|419015;2|1239|91061|186826|33958|2742598|227942;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1343;2|1224|1236|135625|712|724|249188;2|1224|28216|206351|481|482|484;2|1239|909932|1843489|31977|29465|29466;2|1224|28216|206351|481|482|34026;2|32066|203490|203491|1129771|32067|554406;2|201174|1760|2037|2049|1654|29317;2|1239|91061|186826|1300|1301|1305;2|1224|28216|206351|481|482|495,Complete,NA
Study 368,"cross-sectional observational, not case-control",32640977,10.1186/s12866-020-01883-8,NA,"Halboub E, Al-Ak'hali MS, Alamir AH, Homeida HE, Baraniya D, Chen T , Al-Hebshi NN",Tongue microbiome of smokeless tobacco users,BMC microbiology,2020,Experiment 1,Saudi Arabia,Homo sapiens,tongue,UBERON:0001723,smoking behavior,EFO:0004318,non-shammah users,shammah users,participants who used shammah daily for at least one year without a period of cessation and those who had no history of shammah use,23,29,3 months,16S,123,Illumina,LEfSe,0.015,TRUE,NA,sex,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3 a & b,17 July 2020,Victoria Goulbourne,WikiWorks743,Differentially abundant taxa,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium asaccharolyticum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Myxococcales|f__Archangiaceae|g__Archangium",2|1224|28216|206351|481|538;2|1239|186801|186802|186804|1257;2|1239|186801|186802|186803|265975;2|1224|28216|206351|481|538|539;2|1239|91061|186826|1300|1301|1306;2|1239|186801|186802|186803|265975|1501332;2|1239|186801|186802|186803|265975|237576;2|32066|203490|203491|1129771|32067|104608;2|1224|28221|29|39|47,Complete,NA
Study 369,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S, Guenther K, Turroni S, Wolters M, Veidebaum T, Kourides Y, Molnár D, Lissner L, Benitez-Paez A, Sanz Y, Fraterman A, Michels N, Brigidi P, Candela M , Ahrens W",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,Experiment 1,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,children aged 2-9 years,34,36,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Table 2,17 July 2020,Mst Afroza Parvin,WikiWorks743,Microbial taxa significantly different across the four groups of children,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|841,Complete,NA
Study 369,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S, Guenther K, Turroni S, Wolters M, Veidebaum T, Kourides Y, Molnár D, Lissner L, Benitez-Paez A, Sanz Y, Fraterman A, Michels N, Brigidi P, Candela M , Ahrens W",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,Experiment 1,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,children aged 2-9 years,34,36,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Table 2,17 July 2020,Mst Afroza Parvin,WikiWorks743,Microbial taxa significantly different across the four groups of children,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|976|200643|171549|171552;2|1239|186801|186802|990719;2|1239|1737404|1737405|1737406;2|201174|84998|1643822|1643826|84108;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|119852,Complete,NA
Study 369,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S, Guenther K, Turroni S, Wolters M, Veidebaum T, Kourides Y, Molnár D, Lissner L, Benitez-Paez A, Sanz Y, Fraterman A, Michels N, Brigidi P, Candela M , Ahrens W",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,Experiment 2,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,before onset of obesity,after onset of obesity,children aged 2-9 years,36,36,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 1,Table 2,17 July 2020,Mst Afroza Parvin,WikiWorks743,Microbial taxa significantly different across the four groups of children,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224;2|1239|526524|526525|2810280|135858;2|1224|28216|80840|506;2|1224|28216|80840|995019|40544,Complete,NA
Study 369,time series / longitudinal observational,30534614,10.1038/s42003-018-0221-5,NA,"Rampelli S, Guenther K, Turroni S, Wolters M, Veidebaum T, Kourides Y, Molnár D, Lissner L, Benitez-Paez A, Sanz Y, Fraterman A, Michels N, Brigidi P, Candela M , Ahrens W",Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity,Communications biology,2018,Experiment 2,"Cyprus,Estonia,Germany,Hungary,Sweden",Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,before onset of obesity,after onset of obesity,children aged 2-9 years,36,36,14 days,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,unchanged,Signature 2,Table 2,17 July 2020,Mst Afroza Parvin,WikiWorks743,Microbial taxa significantly different across the four groups of children,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|91061|186826|33958;2|1239|186801|186802|31979;2|1239|186801|186802|541000;2|1239|186801|186802|216572|1263,Complete,NA
Study 370,time series / longitudinal observational,27836847,10.1128/AEM.02149-16,NA,"Stanaway IB, Wallace JC, Shojaie A, Griffith WC, Hong S, Wilder CS, Green FH, Tsai J, Knight M, Workman T, Vigoren EM, McLean JS, Thompson B , Faustman EM",Human Oral Buccal Microbiomes Are Associated with Farmworker Status and Azinphos-Methyl Agricultural Pesticide Exposure,Applied and environmental microbiology,2017,Experiment 1,United States of America,Homo sapiens,buccal mucosa,UBERON:0006956,air pollution,ENVO:02500037,non-farmworker exposure,farmworker exposure,self-identified Hispanic farmworkers in apple and pear orchads and Hispanic non-farmworker community members,NA,101,NA,16S,56,Ion Torrent,Mann-Whitney (Wilcoxon),0.01,TRUE,NA,NA,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Table 1,18 July 2020,Victoria Goulbourne,"WikiWorks743,Lwaldron",Wilcoxon's rank sum test of azinphos-methyl blood detection groups for compositional pertubation,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|1385|1378;2|1239|91061|186826|186828|117563;2|1224|1236|135625|712|724;2|1224|1236|135619|28256|2745;2|1239|91061|186826|1300|1301,Complete,NA
Study 371,case-control,23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,obese,"hospitalized patients and outpatients who were overweight, obese or anorexic.",15,43,6 months,WMS,NA,RT-qPCR,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,18 July 2020,Mst Afroza Parvin,WikiWorks743,The presence of each taxa according to each weight category,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,NA
Study 371,case-control,23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,Experiment 2,France,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,obese,"hospitalized patients and outpatients who were overweight, obese or anorexic.",55,80,6 months,WMS,NA,RT-qPCR,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,18 July 2020,Mst Afroza Parvin,WikiWorks743,The presence of each taxa according to each weight category,decreased,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,2157|28890|183925|2158|2159|2172|2173,Complete,NA
Study 371,case-control,23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,Experiment 3,France,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,obese,"hospitalized patients and outpatients who were overweight, obese or anorexic.",32,32,6 months,WMS,NA,RT-qPCR,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,18 July 2020,Mst Afroza Parvin,WikiWorks743,The presence of each taxa according to each weight category,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,2|1224|1236|91347|543|561|562,Complete,NA
Study 371,case-control,23459324,10.1038/ijo.2013.20,NA,"Million M, Angelakis E, Maraninchi M, Henry M, Giorgi R, Valero R, Vialettes B , Raoult D","Correlation between body mass index and gut concentrations of Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli",International journal of obesity (2005),2013,Experiment 4,France,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,lean,obese,"hospitalized patients and outpatients who were overweight, obese or anorexic.",5,24,6 months,WMS,NA,RT-qPCR,NA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 1,18 July 2020,Mst Afroza Parvin,WikiWorks743,The presence of each taxa according to each weight category,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,2|1239|91061|186826|33958|2742598|1598,Complete,NA
Study 372,laboratory experiment,31559135,10.1002/advs.201900972,NA,"Li X, Sun H, Li B, Zhang X, Cui J, Yun J, Yang Y, Zhang L, Meng Q, Wu S, Duan J, Yang H, Wu J, Sun Z, Zou Y , Chen R",Probiotics Ameliorate Colon Epithelial Injury Induced by Ambient Ultrafine Particles Exposure,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2019,Experiment 1,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice exposed to FRA,Diesel exhaust particle (DEP) exposed mice,mice exposed to Diesel exhaust particles (DEP),30,37,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C & text,18 July 2020,Zyaijah Bailey,WikiWorks743,LEfSe histogram of fecal microbiota profiling from DEPs group (fecal samples from male n = 20 and female n = 17) and FRA group (fecal samples from male n = 15 and female n = 15) following 7‐day exposure.,increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061;2|1239|91061|186826;2|1239|91061|186826|33958|1578,Complete,NA
Study 372,laboratory experiment,31559135,10.1002/advs.201900972,NA,"Li X, Sun H, Li B, Zhang X, Cui J, Yun J, Yang Y, Zhang L, Meng Q, Wu S, Duan J, Yang H, Wu J, Sun Z, Zou Y , Chen R",Probiotics Ameliorate Colon Epithelial Injury Induced by Ambient Ultrafine Particles Exposure,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2019,Experiment 1,China,Mus musculus,colon,UBERON:0001155,air pollution,ENVO:02500037,mice exposed to FRA,Diesel exhaust particle (DEP) exposed mice,mice exposed to Diesel exhaust particles (DEP),30,37,NA,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2C & text,18 July 2020,Zyaijah Bailey,WikiWorks743,LEfSe histogram of fecal microbiota profiling from DEPs group (fecal samples from male n = 20 and female n = 17) and FRA group (fecal samples from male n = 15 and female n = 15) following 7‐day exposure.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia",2|976|200643|171549|815;2|976|200643|171549|815|816;2|1239;2|1239|186801|186802|186803;2|1239|186801,Complete,NA
Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,Experiment 1,Estonia,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight children,overweight,Children and adults,9,9,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, Table S2",19 July 2020,Mst Afroza Parvin,WikiWorks743,Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,2|201174|1760|85004|31953|1678|1681,Complete,NA
Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,Experiment 1,Estonia,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight children,overweight,Children and adults,9,9,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, Table S2",19 July 2020,Mst Afroza Parvin,WikiWorks743,Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|976|200643|171549|815|909656|821;2|976|200643|171549|815|816|820;2|1239|186801|186802|186803|207244|649756;2|976|200643|171549|815|816|28116;2|74201|203494|48461|1647988|239934|239935,Complete,NA
Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,Experiment 2,Estonia,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight adult,overweight,Children and adults,9,7,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 3, Table S2",19 July 2020,Mst Afroza Parvin,WikiWorks743,Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium mitsuokai,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis",2|1239|186801|186802|186803|572511|418240;2|201174|1760|85004|31953|1678|28026;2|1239|526524|526525|2810280|135858|100886;2|201174|1760|85004|31953|1678|1680,Complete,NA
Study 373,case-control,29935270,10.1016/j.anaerobe.2018.06.009,NA,"Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T , Alamäe T","Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans",Anaerobe,2018,Experiment 2,Estonia,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight adult,overweight,Children and adults,9,7,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 3, Table S2",19 July 2020,Mst Afroza Parvin,WikiWorks743,Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level.,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,2|1239|186801|186802|186803|189330|88431,Complete,NA
Study 374,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M, Seo SS, Kim MK, Lee DO , Lim MC",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,Experiment 1,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,normal control,cervical intraepithelial neoplasia cases,histology proven CIN2/3,18,17,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,19 July 2020,Cynthia Anderson,"WikiWorks743,Cynthia Anderson,LGeistlinger","Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus,k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia",2|1239|186801|186802|31979|114627;2|200918|188708|2419|188709|1643951;2|1224|28211|766|942|953,Complete,NA
Study 374,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M, Seo SS, Kim MK, Lee DO , Lim MC",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,Experiment 1,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,cervical glandular intraepithelial neoplasia,EFO:1000165,normal control,cervical intraepithelial neoplasia cases,histology proven CIN2/3,18,17,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,19 July 2020,Cynthia Anderson,WikiWorks743,"Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Psychrobacter",2|1224|1236|135622|267888|53246;2|1224|1236|2887326|468|497,Complete,NA
Study 374,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M, Seo SS, Kim MK, Lee DO , Lim MC",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,Experiment 2,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,cervical cancer,MONDO:0002974,normal control,cervical cancer cancer,histology proven cervical cancer,18,12,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 1,19 July 2020,Cynthia Anderson,WikiWorks743,"Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus,k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__Anaplasmataceae|g__Wolbachia",2|1239|186801|186802|31979|114627;2|200918|188708|2419|188709|1643951;2|1224|28211|766|942|953,Complete,NA
Study 374,case-control,30841606,10.3390/cancers11030309,NA,"Kwon M, Seo SS, Kim MK, Lee DO , Lim MC",Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing,Cancers,2019,Experiment 2,South Korea,Homo sapiens,uterine cervix,UBERON:0000002,cervical cancer,MONDO:0002974,normal control,cervical cancer cancer,histology proven cervical cancer,18,12,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2.5,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 1,19 July 2020,Cynthia Anderson,"WikiWorks743,Cynthia Anderson,LGeistlinger","Microbial compositions among normal group, cervical intraepithelial neoplasia 2 or 3, and cervical cancer",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae|g__Candidatus Endolissoclinum",2|1239|91061|186826|33958|1578;2|1239|91061|1385|90964|1279;2|1224|28211|204441|41295|1263978,Complete,NA
Study 375,"cross-sectional observational, not case-control",26745497,10.1159/000442479,NA,"Radilla-Vázquez RB, Parra-Rojas I, Martínez-Hernández NE, Márquez-Sandoval YF, Illades-Aguiar B , Castro-Alarcón N",Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects,Obesity facts,2016,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,both sexes aged between 18 to 25 years,32,32,4 weeks,WMS,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,21 July 2020,Mst Afroza Parvin,WikiWorks743,Gut microbiota in obese and normal-weight young subjects,increased,NA,NA,Complete,NA
Study 375,"cross-sectional observational, not case-control",26745497,10.1159/000442479,NA,"Radilla-Vázquez RB, Parra-Rojas I, Martínez-Hernández NE, Márquez-Sandoval YF, Illades-Aguiar B , Castro-Alarcón N",Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects,Obesity facts,2016,Experiment 1,Mexico,Homo sapiens,feces,UBERON:0001988,obesity,EFO:0001073,normal weight,obese,both sexes aged between 18 to 25 years,32,32,4 weeks,WMS,NA,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,21 July 2020,Mst Afroza Parvin,WikiWorks743,Gut microbiota in obese and normal-weight young subjects,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",2|976|200643|171549|171552|838;2|1224|1236|91347|543|561|562,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took amoxiclav,took amoxiclav for 7 days,7,7,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes",2|976|200643;2|976|200643|171549|815|816;2|976,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took amoxiclav,took amoxiclav for 7 days,7,7,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took levofloxacin/Metronidazole,took levofloxacin/Metronidazole for 7 days,9,9,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",2|976|200643|171549|815|816;2|976|200643|171549|815|909656|310297,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took levofloxacin/Metronidazole,took levofloxacin/Metronidazole for 7 days,9,9,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 3,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took Piperacilin/Tazobactam,took Piperacilin/Tazobactam for 7 days,1,1,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 3,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took Piperacilin/Tazobactam,took Piperacilin/Tazobactam for 7 days,1,1,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 4,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took Ceftriaxone/Azithromycin,took Ceftriaxone/Azithromycin for 7 days,3,3,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes",2|976|200643|171549|815|816;2|976,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 4,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took Ceftriaxone/Azithromycin,took Ceftriaxone/Azithromycin for 7 days,3,3,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 5,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took Ciprofloxacin,took Ciprofloxacin for 7 days,1,1,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes",2|976|200643|171549|815|816;2|976,Complete,NA
Study 376,time series / longitudinal observational,24748167,10.1371/journal.pone.0095476,NA,"Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F , Manichanh C",Short-term effect of antibiotics on human gut microbiota,PloS one,2014,Experiment 5,Spain,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,before antibiotic exposure,patients that took Ciprofloxacin,took Ciprofloxacin for 7 days,1,1,NA,16S,4,RT-qPCR,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Text-Results,21 July 2020,Gina Celentano,WikiWorks743,Human gut microbiota before and after antibiotics exposure,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 377,prospective cohort,32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,E-cigarette smoker,never smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers, non-smokers, or e-cigarette users",39,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure S2,21 July 2020,Victoria Goulbourne,WikiWorks743,Linear discriminant analysis (LDA) at species level combined with effect size measurements (LefSe) revealed differentially altered taxa in the saliva samples of (A) NS and ES; (B) NS and CS; (C) ES and CS cohorts,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.",2|1239|91061|186826|1300|1301|1303;2|976|200643|171549|171551|836;2|32066|203490|203491|203492|848|860;2|976|200643|171549|171552|838|59823;2|1224|28216|80840|119060|47670|47671;2|1239|186801|186802|186803|1164882|979627;2|1239|186801|186802|186803|265975|1501329;2|32066|203490|203491|203492|848|68766;2|1239|186801|186802|186807|2740|2049038,Complete,NA
Study 377,prospective cohort,32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,E-cigarette smoker,never smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers, non-smokers, or e-cigarette users",39,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure S2,21 July 2020,Victoria Goulbourne,WikiWorks743,Linear discriminant analysis (LDA) at species level combined with effect size measurements (LefSe) revealed differentially altered taxa in the saliva samples of (A) NS and ES; (B) NS and CS; (C) ES and CS cohorts,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multisaccharivorax,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas dianae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oris,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar",2|976|200643|171549|171552|838|310514;2|1224|28216|206351|481|482|267212;2|1239|909932|909929|1843491|970|671224;2|1239|909932|909929|1843491|970|135079;2|1239|909932|909929|1843491|52225|2049034;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838|59823;2|201174|1760|85004|31953|419014|419015;2|201174|84998|1643822|1643826|84108|84109;2|976|200643|171549|171551|836|281920;2|508458|649775|649776|649777|1434006|651822;2|1239|91061|186826|1300|1357|1358;2|1239|186801|186802;2|1239|1737404|1737405|1570339|543311|33033;2|1239|186801|186802|186804|44259|143361;2|1239|186801|186802|186803|265975|1969407;2|976|200643|171549|171552|838|28135;2|32066|203490|203491|203492|848|851;2|976|200643|171549|171551|836|28124;2|1239|91061|1385|90964|1279|29388;2|1239|909932|1843489|31977|29465|39778,Complete,NA
Study 377,prospective cohort,32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,cigarette smoker,never smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers, non-smokers, or e-cigarette users",39,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure S2,21 July 2020,Victoria Goulbourne,WikiWorks743,Linear discriminant analysis (LDA) at species level combined with effect size measurements (LefSe) revealed differentially altered taxa in the saliva samples of (A) NS and ES; (B) NS and CS; (C) ES and CS cohorts,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Ottowia|s__Ottowia sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.",2|976|200643|171549|171551|836|1583331;2|32066|203490|203491|203492|848|860;2|1239|909932|1843489|31977|29465|423477;2|1224|28216|80840|119060|47670|47671;2|976|200643|171549|171552|838|59823;2|1224|1236|135625|712|724|735;2|1239|186801|186802|186803|265975|1501329;2|1239|91061|186826|186828|117563|137732;2|976|117743|200644|49546|1016|1019;2|1224|28216|206351|481|482|1107316;2|1239|186801|186802|186803|1164882|979627;2|1239|91061|186826|186827|46123|46125;2|1224|1236|135625|712|724|726;2|976|117743|200644|49546|1016|327575;2|1239|186801|186802|186804|1257|341694;2|1239|186801|186802|186803|43996|43997;2|1239|526524|526525|128827|123375|102148;2|1239|91061|186826|1300|1301|1303;2|1239|186801|186802|541000;2|976|117743|200644|49546|1016|1017;2|1224|1236|135615|868|2717|2718;2|976|117743|200644|49546|1016|45243;2|1224|28216|80840|80864|219181|1898956;2|201174|1760|85007|1653|1716|61592;2|1239|186801|186802|186807|2740|2049038;2|201174|1760|85006|1268|32207|43675;2|1224|1236|135625|712|724|740;2|1224|28216|206351|481|538|539;2|201174|1760|2037|2049|1654|52769;2|1224|28216|206351|481|482|192066,Complete,NA
Study 377,prospective cohort,32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,cigarette smoker,never smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers, non-smokers, or e-cigarette users",39,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure S2,21 July 2020,Victoria Goulbourne,"WikiWorks743,Lwaldron",Linear discriminant analysis (LDA) at species level combined with effect size measurements (LefSe) revealed differentially altered taxa in the saliva samples of (A) NS and ES; (B) NS and CS; (C) ES and CS cohorts,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobulbaceae|g__Desulfobulbus|s__Desulfobulbus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus lactis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella sp.,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella maculosa,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multisaccharivorax,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oralis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oulorum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella veroralis,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas dianae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|201174|1760|2037|2049|1654|114702;2|201174|1760|85004|31953|419014|419015;2|1224|28221|213118|213121|893|895;2|1239|186801|186802;2|1239|186801|186802|186804|44259|143361;2|508458|649775|649776|649777|1434006|651822;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|1300|1357|1358;2|1239|909932|1843489|31977|906|187326;2|1239|909932|1843489|31977|906|2023260;2|1239|909932|909929|1843491|52225|2049034;2|544448|31969;2|1239|186801|186802|186803|265975|1969407;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|439703;2|976|200643|171549|171552|838|310514;2|976|200643|171549|171552|838|28134;2|976|200643|171549|171552|838|28135;2|976|200643|171549|171552|838|28136;2|976|200643|171549|171552|838|59823;2|976|200643|171549|171552|838|28137;2|508458|649775|649776|649777|638847|638849;2|201174|1760|85004|31953|196081|230143;2|1239|909932|909929|1843491|970|671224;2|1239|909932|909929|1843491|970|135079;2|201174|84998|1643822|1643826|84108|84109;2|1239|91061|186826|1300|1301|1318;2|203691|203692|136|2845253|157|158;2|203691|203692|136|2845253|157|51160;2|203691|203692|136|2845253|157|166;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|1926307;2|1239|909932|1843489|31977,Complete,NA
Study 377,prospective cohort,32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,Experiment 3,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,cigarette smoker,E-cigarette smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers, non-smokers, or e-cigarette users",40,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure S2,21 July 2020,Victoria Goulbourne,WikiWorks743,Linear discriminant analysis (LDA) at species level combined with effect size measurements (LefSe) revealed differentially altered taxa in the saliva samples of (A) NS and ES; (B) NS and CS; (C) ES and CS cohorts,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella rogosae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria oralis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus|s__Peptococcus sp.",2|1239|909932|1843489|31977|29465|423477;2|976|200643|171549|171551|836|1583331;2|32066|203490|203491|203492|848|860;2|1224|28216|80840|119060|47670|47671;2|1239|186801|186802|541000;2|976|117743|200644|49546|1016|1019;2|1224|28216|206351|481|482|1107316;2|976|117743|200644|49546|1016|1017;2|976|200643|171549|171552|838|59823;2|1224|1236|135625|712|724|726;2|1239|186801|186802|186804|1257|341694;2|1224|1236|135615|868|2717|2718;2|1239|186801|186802|186803|43996|43997;2|1224|28216|206351|481|538|539;2|1224|28216|206351|481|482|192066;2|976|117743|200644|49546|1016|45243;2|201174|1760|85006|1268|32207|43675;2|201174|1760|85007|1653|1716|61592;2|1224|1236|135625|712|724|740;2|1239|186801|186802|186807|2740|2049038,Complete,NA
Study 377,prospective cohort,32105635,10.1016/j.isci.2020.100884,NA,"Pushalkar S, Paul B, Li Q, Yang J, Vasconcelos R, Makwana S, González JM, Shah S, Xie C, Janal MN, Queiroz E, Bederoff M, Leinwand J, Solarewicz J, Xu F, Aboseria E, Guo Y, Aguallo D, Gomez C, Kamer A, Shelley D, Aphinyanaphongs Y, Barber C, Gordon T, Corby P, Li X , Saxena D",Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection,iScience,2020,Experiment 3,United States of America,Homo sapiens,mouth,UBERON:0000165,smoking behavior,EFO:0004318,cigarette smoker,E-cigarette smoker,"participants who were 21 years or older, healthy, diagnosed with periodontal disease, and current smokers, non-smokers, or e-cigarette users",40,40,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure S2,21 July 2020,Victoria Goulbourne,WikiWorks743,Linear discriminant analysis (LDA) at species level combined with effect size measurements (LefSe) revealed differentially altered taxa in the saliva samples of (A) NS and ES; (B) NS and CS; (C) ES and CS cohorts,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfobotulus|s__Desulfobotulus sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces lingnae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|201174|1760|85004|31953|419014|419015;2|1224|28221|213118|213119|48001|1940337;2|201174|1760|2037|2049|1654|114702;2|1239|909932|1843489|31977|906|187326;2|976|200643|171549|171552|838|59823;2|1239|91061|186826|1300|1301|1318,Complete,NA
Study 378,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M, Nicolis I, Robin M, Michonneau D, Delannoye J, Mayeur C, Kapel N, Berçot B, Butel MJ, Le Goff J, Socié G , Rousseau C",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,non acute graft-versus-host-disease,Severe acute graft-versus-host-disease,patients who are diagnosis with mild gut acute graft- versus-host disease (less than or equal 2) or severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 4),35,35,NA,16S,34,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,"Figure 1B, 1D, text, Figure 2B",21 July 2020,William Lam,WikiWorks743,"Potential biomarkers of the microbiota characterizing patients with severe acute graft-versus- host disease (stage 2-3), using Linear Discriminant Analysis (LDA) effect size to identify bacterial taxa enriched in each group of patients.",increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1224|28216|80840|119060|47670;2|1224|1236|135614|32033;2|1224|1236|135614|32033|40323;2|1224|1236|135614;2|1239|91061|186826|1300|1357,Complete,NA
Study 378,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M, Nicolis I, Robin M, Michonneau D, Delannoye J, Mayeur C, Kapel N, Berçot B, Butel MJ, Le Goff J, Socié G , Rousseau C",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,non acute graft-versus-host-disease,Severe acute graft-versus-host-disease,patients who are diagnosis with mild gut acute graft- versus-host disease (less than or equal 2) or severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 4),35,35,NA,16S,34,Illumina,LEfSe,0.01,TRUE,4,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,"Figure 1B, 1D, text, Figure 2B",21 July 2020,William Lam,WikiWorks743,"Potential biomarkers of the microbiota characterizing patients with severe acute graft-versus- host disease (stage 2-3), using Linear Discriminant Analysis (LDA) effect size to identify bacterial taxa enriched in each group of patients.",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium",2|1239|186801|186802;2|1239|186801;2|1239|186801|186802|186803;2|1239|186801|186802|541000;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|1769710;2|1239|91061|1385|1378;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|459786;2|1224|28211;2|1224|28211|204441;2|1239|526524|526525|128827|1505663;2|1239|186801|186802|186803|207244;2|1239|186801|186802|1392389;2|1239|186801|186802|216572|1508657,Complete,NA
Study 378,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M, Nicolis I, Robin M, Michonneau D, Delannoye J, Mayeur C, Kapel N, Berçot B, Butel MJ, Le Goff J, Socié G , Rousseau C",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,Experiment 2,France,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,non acute graft-versus-host-disease,Severe acute graft-versus-host-disease,patients who are diagnosis with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 3),35,15,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,4,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 1,"Figure 1B, 1D, text, Figure 2C",21 July 2020,William Lam,WikiWorks743,"Genera with a cumulative relative abundance in the cohort of at least 5% and present in .10 patients were selected, and relative abundance was compared between controls and severe acute graft-versus- host disease patients.",increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,2|1224|1236|135614|32033|40323,Complete,NA
Study 378,case-control,32353108,10.1182/bloodadvances.2020001531,NA,"Payen M, Nicolis I, Robin M, Michonneau D, Delannoye J, Mayeur C, Kapel N, Berçot B, Butel MJ, Le Goff J, Socié G , Rousseau C",Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity,Blood advances,2020,Experiment 2,France,Homo sapiens,feces,UBERON:0001988,graft versus host disease,MONDO:0013730,non acute graft-versus-host-disease,Severe acute graft-versus-host-disease,patients who are diagnosis with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 3),35,15,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.01,TRUE,4,NA,NA,NA,NA,decreased,decreased,NA,decreased,Signature 2,"Figure 1B, 1D, text, Figure 2C",21 July 2020,William Lam,WikiWorks743,"Genera with a cumulative relative abundance in the cohort of at least 5% and present in .10 patients were selected, and relative abundance was compared between controls and severe acute graft-versus- host disease patients.",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium",2|1239|186801|186802|186803;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|1769710;2|1239|186801|186802|216572|946234;2|1239|526524|526525|128827|1505663,Complete,NA
Study 379,prospective cohort,31489128,10.1080/20002297.2019.1650597,NA,"Yang Y, Cai Q, Zheng W, Steinwandel M, Blot WJ, Shu XO , Long J",Oral microbiome and obesity in a large study of low-income and African-American populations,Journal of oral microbiology,2019,Experiment 1,United States of America,Homo sapiens,mouth,UBERON:0000165,obesity,EFO:0001073,obese,non-obese,"participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer",647,969,1 year,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,"age,race,sex,smoking behavior","age,race,sex,smoking behavior",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 2,22 July 2020,Victoria Goulbourne,WikiWorks743,Probiotic bacterial taxa showing a significantly higher prevelance in non-obese than obese individuals,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium scardovii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium subtile,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus panis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus ultunensis",2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|158787;2|201174|1760|85004|31953|1678|77635;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|47493;2|1239|91061|186826|33958|1578|227945,Complete,NA
Study 379,prospective cohort,31489128,10.1080/20002297.2019.1650597,NA,"Yang Y, Cai Q, Zheng W, Steinwandel M, Blot WJ, Shu XO , Long J",Oral microbiome and obesity in a large study of low-income and African-American populations,Journal of oral microbiology,2019,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,obesity,EFO:0001073,non-obese,obese,"participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer",969,647,1 year,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,"age,race,sex,smoking behavior","age,race,sex,smoking behavior",NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Table 3,22 July 2020,Victoria Goulbourne,WikiWorks743,Common bacterial taxa showing a significantly higher prevelance in obese than in non-obese individuals,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.",2|1239|91061|1385|1378;2|1239|91061|186826|186828;2|1239|91061|186826|186828|117563;2|1239|91061|186826|186828|117563|46124;2|201174|1760|2037|2049|1654|29317,Complete,NA
Study 379,prospective cohort,31489128,10.1080/20002297.2019.1650597,NA,"Yang Y, Cai Q, Zheng W, Steinwandel M, Blot WJ, Shu XO , Long J",Oral microbiome and obesity in a large study of low-income and African-American populations,Journal of oral microbiology,2019,Experiment 2,United States of America,Homo sapiens,mouth,UBERON:0000165,obesity,EFO:0001073,non-obese,obese,"participants who were selected for four nested case-control studies to investigate the oral microbiome and those diagnosed after mouth rinse sample colection with type 2 diabetes, lung cancer, upper aero-digestive tract cancer, and colorectal cancer",969,647,1 year,16S,4,Illumina,Logistic Regression,0.05,TRUE,NA,"age,race,sex,smoking behavior","age,race,sex,smoking behavior",NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Table 4,22 July 2020,Victoria Goulbourne,WikiWorks743,Rare taxa showing a significantly higher prevelance in obese or non-obese individuals,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus",2|201174|1760|85004|31953|419014;2|1239|909932|1843489|31977|156454,Complete,NA
Study 380,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z, Peled JU, Li S, Mahabamunuge J, Dagher Z, Slingerland AE, Del Rio C, Valles B, Kempner ME, Smith M, Brown J, Dey BR, El-Jawahri A, McAfee SL, Spitzer TR, Ballen KK, Sung AD, Dalton TE, Messina JA, Dettmer K, Liebisch G, Oefner P, Taur Y, Pamer EG, Holler E, Mansour MK, van den Brink MRM, Hohmann E, Jenq RR , Chen YB",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,response to allogeneic hematopoietic stem cell transplant,EFO:0007044,patients post allogenic hematopoietic cell transplant/pre Fecal Microbiota Transplant,patients preallogenic hematopoietic cell transplant,patients who received Fecal Microbiome Transplant,5,13,48 hours,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,transplant conditioning",NA,NA,NA,NA,increased,NA,Signature 1,Figure 4B,22 June 2020,Nadine Ulysse,WikiWorks743,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Rimsha Azhar
Study 380,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z, Peled JU, Li S, Mahabamunuge J, Dagher Z, Slingerland AE, Del Rio C, Valles B, Kempner ME, Smith M, Brown J, Dey BR, El-Jawahri A, McAfee SL, Spitzer TR, Ballen KK, Sung AD, Dalton TE, Messina JA, Dettmer K, Liebisch G, Oefner P, Taur Y, Pamer EG, Holler E, Mansour MK, van den Brink MRM, Hohmann E, Jenq RR , Chen YB",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,response to allogeneic hematopoietic stem cell transplant,EFO:0007044,post fecal mircobiota day 180,post allogenic hematopoietic cell transplant/ pre Fecal microbiota transplant,patients who received Fecal Microbiome Transplant,5,13,48 hours,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,transplant conditioning",NA,NA,NA,NA,unchanged,NA,Signature 1,Figure 4B,22 June 2020,Nadine Ulysse,WikiWorks743,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Rimsha Azhar
Study 380,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z, Peled JU, Li S, Mahabamunuge J, Dagher Z, Slingerland AE, Del Rio C, Valles B, Kempner ME, Smith M, Brown J, Dey BR, El-Jawahri A, McAfee SL, Spitzer TR, Ballen KK, Sung AD, Dalton TE, Messina JA, Dettmer K, Liebisch G, Oefner P, Taur Y, Pamer EG, Holler E, Mansour MK, van den Brink MRM, Hohmann E, Jenq RR , Chen YB",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,response to allogeneic hematopoietic stem cell transplant,EFO:0007044,post fecal mircobiota day 7,post allogenic hematopoietic cell transplant/ pre Fecal microbiota transplant,patients who received Fecal Microbiome Transplant,5,13,48 hours,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,transplant conditioning",NA,NA,NA,NA,decreased,NA,Signature 1,Figure 5,22 June 2020,Nadine Ulysse,WikiWorks743,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Rimsha Azhar
Study 380,time series / longitudinal observational,29592876,10.1182/bloodadvances.2018017731,NA,"DeFilipp Z, Peled JU, Li S, Mahabamunuge J, Dagher Z, Slingerland AE, Del Rio C, Valles B, Kempner ME, Smith M, Brown J, Dey BR, El-Jawahri A, McAfee SL, Spitzer TR, Ballen KK, Sung AD, Dalton TE, Messina JA, Dettmer K, Liebisch G, Oefner P, Taur Y, Pamer EG, Holler E, Mansour MK, van den Brink MRM, Hohmann E, Jenq RR , Chen YB",Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity,Blood advances,2018,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,response to allogeneic hematopoietic stem cell transplant,EFO:0007044,post fecal mircobiota day 30,post allogenic hematopoietic cell transplant/ pre Fecal microbiota transplant,patients who received Fecal Microbiome Transplant,5,13,48 hours,16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,age,"HLA match,acute graft vs. host disease,age,transplant conditioning",NA,NA,NA,NA,decreased,NA,Signature 1,Figure 5,22 June 2020,Nadine Ulysse,WikiWorks743,Third-party fecal microbiota transplantation (FMT) may restore intestinal microbiome diversity after allogeneic hematopoietic cell transplantation (allo-HCT),decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,Rimsha Azhar
Study 381,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña JR, Peterson CB, Malik F, Sahasrabhojane PV, Shah DP, Brumlow CE, Carlin LG, Chemaly RF, Im JS, Rondon G, Felix E, Veillon L, Lorenzi PL, Alousi AM, Jenq RR, Kontoyiannis DP, Shpall EJ, Shelburne SA , Okhuysen PC","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,response to allogeneic hematopoietic stem cell transplant,EFO:0007044,healthy volunteers,hematopoietic stem cell transplant recipients,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,18,50,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Text, Figure 1",9 July 2020,Nadine Ulysse,WikiWorks743,Clinical and Microbime Predictors of Acute GastroIntestinal Graft-vs- Host Disease,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,2|1239|91061|186826|81852|1350,Complete,Fatima Zohra
Study 381,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña JR, Peterson CB, Malik F, Sahasrabhojane PV, Shah DP, Brumlow CE, Carlin LG, Chemaly RF, Im JS, Rondon G, Felix E, Veillon L, Lorenzi PL, Alousi AM, Jenq RR, Kontoyiannis DP, Shpall EJ, Shelburne SA , Okhuysen PC","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,response to allogeneic hematopoietic stem cell transplant,EFO:0007044,healthy volunteers,hematopoietic stem cell transplant recipients,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,18,50,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Text, Figure 1",9 July 2020,Nadine Ulysse,WikiWorks743,Clinical and Microbime Predictors of Acute GastroIntestinal Graft-vs- Host Disease,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|186801|186802|186803|46205;2|1239|186801|186802|216572|292632,Complete,Fatima Zohra
Study 381,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña JR, Peterson CB, Malik F, Sahasrabhojane PV, Shah DP, Brumlow CE, Carlin LG, Chemaly RF, Im JS, Rondon G, Felix E, Veillon L, Lorenzi PL, Alousi AM, Jenq RR, Kontoyiannis DP, Shpall EJ, Shelburne SA , Okhuysen PC","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,response to allogeneic hematopoietic stem cell transplant,EFO:0007044,low fecal butyrate levels,high fecal butyrate levels,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,50,50,NA,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure 3, Supplemental figure 2",9 July 2020,Nadine Ulysse,WikiWorks743,Differences in fecal metabolites among hemapoietic stem cell transplant (HSCT) recipients at baseline,increased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium",2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186803;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|541000;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|572511;2|1239|526524;2|1239|526524|526525;2|1239|526524|526525|128827;2|1239|186801|186802|186803|46205;2|1239|526524|526525|128827|1505663,Complete,Fatima Zohra
Study 381,time series / longitudinal observational,31065565,10.1093/ofid/ofz173,NA,"Galloway-Peña JR, Peterson CB, Malik F, Sahasrabhojane PV, Shah DP, Brumlow CE, Carlin LG, Chemaly RF, Im JS, Rondon G, Felix E, Veillon L, Lorenzi PL, Alousi AM, Jenq RR, Kontoyiannis DP, Shpall EJ, Shelburne SA , Okhuysen PC","Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study",Open forum infectious diseases,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,response to allogeneic hematopoietic stem cell transplant,EFO:0007044,low fecal butyrate levels,high fecal butyrate levels,patients undergoing T cell repleted allogeneic hematopoietic stem cell transplantation,50,50,NA,16S,4,Illumina,LEfSe,0.05,FALSE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure 3, Supplemental figure 2",9 July 2020,Nadine Ulysse,WikiWorks743,Differences in fecal metabolites among hemapoietic stem cell transplant (HSCT) recipients at baseline,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|91061|186826;2|1239|91061,Complete,Fatima Zohra
Study 382,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M, Filardo S, Porpora MG, Recine N, Latino MA , Sessa R",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,Experiment 1,Italy,Homo sapiens,endocervix,UBERON:0000458,Chlamydia trachomatis infectious disease,EFO:0007205,healthy control,patient with chlamydia infection,patient with Chlamydia infection,7,7,Current,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,23 July 2020,Cynthia Anderson,WikiWorks743,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus christensenii",2|1239|91061|186826|186827|1375;2|1239|91061|186826|186827;2|1239|91061|186826|186827|1375|87541,Complete,Fatima Zohra
Study 382,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M, Filardo S, Porpora MG, Recine N, Latino MA , Sessa R",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,Experiment 1,Italy,Homo sapiens,endocervix,UBERON:0000458,Chlamydia trachomatis infectious disease,EFO:0007205,healthy control,patient with chlamydia infection,patient with Chlamydia infection,7,7,Current,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,23 July 2020,Cynthia Anderson,WikiWorks743,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli",2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239;2|1239|91061,Complete,Fatima Zohra
Study 382,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M, Filardo S, Porpora MG, Recine N, Latino MA , Sessa R",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,Experiment 2,Italy,Homo sapiens,endocervix,UBERON:0000458,"human papilloma virus infection,Chlamydophila infectious disease","EFO:0001668,EFO:1000863",HPV positive women,patient with chlamydia infection,patient with Chlamydia infection,7,8,Current,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,23 July 2020,Cynthia Anderson,WikiWorks743,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,increased,"k__Bacteria|p__Chlamydiae,k__Bacteria|p__Chlamydiae|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae,k__Bacteria|p__Chlamydiae|c__Chlamydiia,k__Bacteria|p__Chlamydiae|c__Chlamydiia|o__Chlamydiales,k__Bacteria|p__Chlamydiae|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacteria|p__Chlamydiae|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis",2|204428;2|204428|204429|51291|809;2|204428|204429;2|204428|204429|51291;2|204428|204429|51291|809|810;2|204428|204429|51291|809|810|813,Complete,Fatima Zohra
Study 382,"cross-sectional observational, not case-control",29313867,NA,NA,"Di Pietro M, Filardo S, Porpora MG, Recine N, Latino MA , Sessa R",HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women,The new microbiologica,2018,Experiment 2,Italy,Homo sapiens,endocervix,UBERON:0000458,"human papilloma virus infection,Chlamydophila infectious disease","EFO:0001668,EFO:1000863",HPV positive women,patient with chlamydia infection,patient with Chlamydia infection,7,8,Current,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,23 July 2020,Cynthia Anderson,WikiWorks743,LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239|91061|186826;2|1239,Complete,Fatima Zohra
Study 383,prospective cohort,28632934,10.1111/all.13232,NA,"Savage JH, Lee-Sarwar KA, Sordillo J, Bunyavanich S, Zhou Y, O'Connor G, Sandel M, Bacharier LB, Zeiger R, Sodergren E, Weinstock GM, Gold DR, Weiss ST , Litonjua AA",A prospective microbiome-wide association study of food sensitization and food allergy in early childhood,Allergy,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,no food sensitization,child with food sensitization,"child with serum-specific IgE to milk, egg, peanut, soy, wheat, and walnut greater than 0.35 kU/L at age 3",131,85,1 week,16S,345,Roche454,NA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2a,31 July 2020,Lucy Mellor,WikiWorks743,Significant associations between food sensitization and bacterial genera. The log2 fold change is plotted for each bacterial genus significantly associated with food sensitization,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|189330;2|1239|186801|186802|31979|1485,Complete,NA
Study 383,prospective cohort,28632934,10.1111/all.13232,NA,"Savage JH, Lee-Sarwar KA, Sordillo J, Bunyavanich S, Zhou Y, O'Connor G, Sandel M, Bacharier LB, Zeiger R, Sodergren E, Weinstock GM, Gold DR, Weiss ST , Litonjua AA",A prospective microbiome-wide association study of food sensitization and food allergy in early childhood,Allergy,2018,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,food allergy,EFO:1001890,no food allergy,child with food allergy,"child with healthcare provider-diagnosed allergy to milk, egg, peanut, wheat, soy, or other nut allergy prior to age 3 years with evidence of IgE sensitization to that food (>0.1 kU/L) at age 3 years",202,14,1 week,16S,345,Roche454,NA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2b,31 July 2020,Lucy Mellor,WikiWorks743,Significant associations between food allergy and bacterial genera. The log2 fold change is plotted for each bacterial genus significantly associated with food allergy,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea",2|1224|1236|91347|543|544;2|1239|186801|186802|216572|119852;2|1239|91061|186826|1300|1357;2|1239|186801|186802|186803|189330,Complete,NA
Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,FSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",69,40,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,12 August 2020,Fatima Zohra,WikiWorks743,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales|f__Victivallaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|186801|186802|990719;2|1224|1236|91347|543;2|256845|1313211|278082|255528;2|1239|91061|186826|81852;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|909932|1843489|31977|29465,Complete,NA
Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,FSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",69,40,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,12 August 2020,Fatima Zohra,WikiWorks743,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",2|1224|1236|135625|712;2|1224|1236|135624|83763,Complete,NA
Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",69,85,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,12 August 2020,Fatima Zohra,WikiWorks743,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|186801|186802|990719;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|1224|1236|91347|543|561;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",69,85,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3,12 August 2020,Fatima Zohra,WikiWorks743,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,2|1224|1236|135625|712,Complete,NA
Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,FSCZ,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",40,85,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 3,12 August 2020,Fatima Zohra,WikiWorks743,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|186804;2|1239|909932|1843489|31977;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|1224|1236|91347|543|561;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|906;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1224|1236|91347|543|620;2|1239|91061|186826|1300|1301,Complete,NA
Study 384,case-control,32065949,10.1016/j.jpsychires.2020.02.005,NA,"Ma X, Asif H, Dai L, He Y, Zheng W, Wang D, Ren H, Tang J, Li C, Jin K, Li Z , Chen X",Alteration of the gut microbiome in first-episode drug-naïve and chronic medicated schizophrenia correlate with regional brain volumes,Journal of psychiatric research,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,FSCZ,TSCZ,"first-episode drug naive schizophrenia(FSCZ) diagnosed according to the DSM IV criteria and PANSS having illness duration <=12 months and no treatment with antipsycotic medications before, anti-psycotic treated schizophrenia (TSCZ) having illness duration >12 months and received antipsychotic treatment for at least past 3 months",40,85,1 month,16S,4,Illumina,DESeq2,0.05,TRUE,NA,demographics,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 3,12 August 2020,Fatima Zohra,WikiWorks743,"Compositional differences in gut microbiota between first-episode drug naive schizophrenia (FSCZ), anti-psychotic treated schizophrenia (TSCZ) patients and healthy controls (HC)",decreased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,NA
Study 385,case-control,30619779,10.3389/fcimb.2018.00433,NA,"Hu YL, Pang W, Huang Y, Zhang Y , Zhang CJ",The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics,Frontiers in cellular and infection microbiology,2018,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric adenocarcinoma,EFO:0000503,superficial gastritis (SG),gastric adenocarcinoma (GC),SG patients with mild to moderate epigastric discomfort. The disgnosis of malignancy was based on patological analysis of tissue biopsies,5,6,6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figure 2B,16 August 2020,Rimsha Azhar,WikiWorks743,LDA score for differentially abundant taxonomix geatures between GC and SG groups,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pneumoniae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|1224|28216|206351|481|482|490;2|1224|1236|135625|712|416916;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303;2|1239|91061|186826|1300|1301|1313;2|1224|1236|135625|712;2|1224|1236;2|1224|28216|206351|481|482;2|976|200643|171549|171552|1283313,Complete,NA
Study 385,case-control,30619779,10.3389/fcimb.2018.00433,NA,"Hu YL, Pang W, Huang Y, Zhang Y , Zhang CJ",The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics,Frontiers in cellular and infection microbiology,2018,Experiment 1,China,Homo sapiens,stomach,UBERON:0000945,gastric adenocarcinoma,EFO:0000503,superficial gastritis (SG),gastric adenocarcinoma (GC),SG patients with mild to moderate epigastric discomfort. The disgnosis of malignancy was based on patological analysis of tissue biopsies,5,6,6 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,"age,body mass index,sex",NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figure 2B,16 August 2020,Rimsha Azhar,WikiWorks743,LDA score for differentially abundant taxonomix geatures between GC and SG groups,decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium|s__Sphingobium yanoikuyae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Blastomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingobium|s__Sphingobium xenophagum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|1224|28211;2|1224|28211|204457|41297;2|1224|28211|204457|41297|165695;2|1224|28211|204457|41297|165695|13690;2|1224|28211|204457|41297|150203;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|45634;2|1239|91061|186826|1300|1301|1305;2|201174|1760|85006|1268|32207|43675;2|201174|1760|85004|31953;2|201174|1760|2037|2049|1654;2|1224|1236|91347|543|561;2|1239|91061|186826|1300|1301|113107;2|201174|1760|2037|2049|1654|55565;2|1224|28211|204457|41297|165695|121428;2|1239|186801|186802|186803;2|976|200643|171549|171552|838|28129;2|1239|91061|186826|1300|1301|1318,Complete,NA
Study 386,case-control,31001490,10.3389/fcimb.2019.00090,NA,"Hu Y, Feng Y, Wu J, Liu F, Zhang Z, Hao Y, Liang S, Li B, Li J, Lv N, Xu Y, Zhu B , Sun Z",The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,pulmonary tuberculosis,EFO:1000049,healthy controls,Tuberculosis (TB) patients,"patients diagnosed with TB by assessing symptoms, including the results of acid-fast bacilli (AFB) smear microscopy, culture, the T-SPOT.TB test and a chest radiograph.",31,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"Figure 2A, Text (results)",17 August 2020,Yu Wang,WikiWorks743,Alterations in the structure and metabolic pathways of the gut microbiota in clinical pulmonary TB patients,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,2|1239|186801|186802|186803|2719313|208479,Complete,NA
Study 386,case-control,31001490,10.3389/fcimb.2019.00090,NA,"Hu Y, Feng Y, Wu J, Liu F, Zhang Z, Hao Y, Liang S, Li B, Li J, Lv N, Xu Y, Zhu B , Sun Z",The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients,Frontiers in cellular and infection microbiology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,pulmonary tuberculosis,EFO:1000049,healthy controls,Tuberculosis (TB) patients,"patients diagnosed with TB by assessing symptoms, including the results of acid-fast bacilli (AFB) smear microscopy, culture, the T-SPOT.TB test and a chest radiograph.",31,30,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,"Figure 2A, Text (results)",17 August 2020,Yu Wang,"WikiWorks743,Lwaldron",Alterations in the structure and metabolic pathways of the gut microbiota in clinical pulmonary TB patients,decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas funiformis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas rupellensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp. ART55/1",2|74201|203494|48461|1647988|239934|239935;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|28026;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|189330|88431;2|1224|1236|135625|712|724|729;2|1239|186801|186802|186803|28050|39485;2|1239|909932|909929|1843491|158846|437897;2|1239|909932|909929|1843491|158846|158847;2|1239|909932|909929|1843491|158846|491921;2|1239|186801|186802|186803|841|301301;2|1239|186801|186802|186803|841|166486;2|1239|186801|186802|186803|841|360807;2|1224|28216|80840|995019|40544|40545;2|1239|186801|186802|186803|2316020|46228;2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|186803|39491;2|1239|186801|186802|186803|33042|751585,Complete,NA
Study 387,randomized controlled trial,25922405,10.1093/cid/civ137,NA,"Rashid MU, Zaura E, Buijs MJ, Keijser BJ, Crielaard W, Nord CE , Weintraub A",Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2015,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,after antibiotic exposure,Before ciprofloxacin exposure,"""healthy"" adults between the ages of 18-45 years old with normal medical histories and physical examinations",10,10,3 months,16S,567,Roche454,Mann-Whitney (Wilcoxon),NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Text (results),17 August 2020,Gina Celentano,WikiWorks743,Human normal intestinal microbiota before verus after antibotic administration,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 387,randomized controlled trial,25922405,10.1093/cid/civ137,NA,"Rashid MU, Zaura E, Buijs MJ, Keijser BJ, Crielaard W, Nord CE , Weintraub A",Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2015,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,after antibiotic exposure,Before ciprofloxacin exposure,"""healthy"" adults between the ages of 18-45 years old with normal medical histories and physical examinations",10,10,3 months,16S,567,Roche454,Mann-Whitney (Wilcoxon),NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Text (results),18 August 2020,Gina Celentano,WikiWorks743,Human normal intestinal microbiota before verus after antibotic administration,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|216572|216851;2|976|200643|171549|171550|239759;2|1239|186801|186802;2|976|200643|171549;2|1239|526524|526525|128827,Complete,NA
Study 387,randomized controlled trial,25922405,10.1093/cid/civ137,NA,"Rashid MU, Zaura E, Buijs MJ, Keijser BJ, Crielaard W, Nord CE , Weintraub A",Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2015,Experiment 2,Sweden,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,after antibiotic exposure,Before clindamycin exposure,"""healthy"" adults between the ages of 18-45 years old with normal medical histories and physical examinations",10,10,3 months,16S,567,Roche454,Mann-Whitney (Wilcoxon),NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Text (results),20 August 2020,Gina Celentano,WikiWorks743,Human normal intestinal microbiota before verus after antibotic administration,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales",2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803;2|1239|186801|186802,Complete,NA
Study 388,"cross-sectional observational, not case-control",32753953,10.2147/CMAR.S251021,NA,"Zhou J, Wang L, Yuan R, Yu X, Chen Z, Yang F, Sun G , Dong Q",Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model,Cancer management and research,2020,Experiment 1,China,Homo sapiens,"mouth,skin of cheek,tongue,gingiva,oropharynx","UBERON:0000165,UBERON:0008803,UBERON:0001723,UBERON:0001828,UBERON:0001729",oral squamous cell carcinoma,EFO:0000199,paracancerous tissues,cancerous  lesions,patients at different stages of OSCC were enrolled in the study,24,24,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2A,20 August 2020,Rimsha Azhar,WikiWorks743,Relative abundance of genera enriched in cancerous tissues,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1239|186801|186802|186804|44259;2|976|200643|171549|2005525|195950;2|1239|1737404|1737405|1570339|543311;2|1239|91061|186826|186828|2747;2|1239|186801|186802|186804|1257;2|1239|91061|186826|1300|1301;2|203691|203692|136|2845253|157;2|32066|203490|203491|203492|848,Complete,NA
Study 388,"cross-sectional observational, not case-control",32753953,10.2147/CMAR.S251021,NA,"Zhou J, Wang L, Yuan R, Yu X, Chen Z, Yang F, Sun G , Dong Q",Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model,Cancer management and research,2020,Experiment 1,China,Homo sapiens,"mouth,skin of cheek,tongue,gingiva,oropharynx","UBERON:0000165,UBERON:0008803,UBERON:0001723,UBERON:0001828,UBERON:0001729",oral squamous cell carcinoma,EFO:0000199,paracancerous tissues,cancerous  lesions,patients at different stages of OSCC were enrolled in the study,24,24,2 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2A,20 August 2020,Rimsha Azhar,WikiWorks743,Relative abundance of genera enriched in cancerous tissues,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Mucispirillum,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas",2|201174|1760|85006|1268|1663;2|200930|68337|191393|191394|248038;2|1224|28221|213115|194924|872;2|201174|1760|85006|85023|33882;2|1239|91061|1385|186822|44249;2|1224|28211|204458|76892|41275,Complete,NA
Study 389,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R, Prandovszky E, Severance EG, Hatfield G , Dickerson F",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,schizophrenia,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,121,NA,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,nicotine dependence,race,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, figure 3, figure 4, figure 5, figure 6",31 August 2020,Fatima Zohra,WikiWorks743,"Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 389,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R, Prandovszky E, Severance EG, Hatfield G , Dickerson F",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,schizophrenia,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,121,NA,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,nicotine dependence,race,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, figure 3, figure 4, figure 5, figure 6",31 August 2020,Fatima Zohra,WikiWorks743,"Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482|28449;2|976|117743|200644|49546;2|976|200643|171549|171552|838,Complete,NA
Study 389,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R, Prandovszky E, Severance EG, Hatfield G , Dickerson F",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,schizophrenia,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,62,NA,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,nicotine dependence,race,sex",NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, figure 3, figure 4, figure 5, figure 6",31 August 2020,Fatima Zohra,WikiWorks743,"Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Schlegelella",2|1239|91061|186826|1300|1301;2|1224|28216|80840|80864|215579,Complete,NA
Study 389,"cross-sectional observational, not case-control",32334937,10.1016/j.schres.2020.03.010,NA,"Yolken R, Prandovszky E, Severance EG, Hatfield G , Dickerson F",The oropharyngeal microbiome is altered in individuals with schizophrenia and mania,Schizophrenia research,2020,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,schizophrenia,"patients met DSM-IV criteria for schizophrenia, mania participants with symptoms of mania or hypermania could have diagnosis of Bipolar I disorder, single manic episode, most recent episode, mixed Bipolar II episode, most recent episode mixed,or Schizoaffective disorder., bipolar type (manic, hypomanic or mixed state)",85,62,NA,16S,34,Illumina,Wald Test,0.05,TRUE,NA,NA,"age,body mass index,nicotine dependence,race,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, figure 3, figure 4, figure 5, figure 6",31 August 2020,Fatima Zohra,WikiWorks743,"Levels of oral microbiome compared to controls adjusted for age, sex, race, cigarette smoking and BMI among individuals with schizophrenia and mania",decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|28216|206351|481|482|28449;2|976|117743|200644|49546;2|976|200643|171549|171552|838,Complete,NA
Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,acute schizphrenia,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2,1 September 2020,Fatima Zohra,WikiWorks743,Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetanaerobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|1239|186801|186802|186804|1505657;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|258514;2|1239|186801|186802|216572|244127;2|201174|1760|2037;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|1224|28221;2|1224|28221|213115;2|1224|28221|213115|194924|35832,Complete,NA
Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,acute schizphrenia,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2,1 September 2020,Fatima Zohra,WikiWorks743,Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenisphaera",2|1239|186801|186802|186803|1432051;2|1239|186801|186802|1392389;2|1239|526524|526525|128827|1774107,Complete,NA
Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,scizophrenia during remission,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 2,1 September 2020,Fatima Zohra,WikiWorks743,Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|186801|186802|31979|1485;2|1239|186801|186802|186804|1505657;2|976|200643|171549|2005525|375288;2|1239|526524|526525|2810281|191303,Complete,NA
Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,healthy controls,scizophrenia during remission,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2,1 September 2020,Fatima Zohra,WikiWorks743,Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella",2|1239|186801|186802|31979|580596;2|976|200643|171549|171552|577309;2|1239|186801|186802|186803|1432051,Complete,NA
Study 390,case-control,32763534,10.1016/j.psychres.2020.113260,NA,"Pan R, Zhang X, Gao J, Yi W, Wei Q , Su H",Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study,Psychiatry research,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,symptomatic remission,acute schizphrenia,"patients who complied with diagnostic criteria for SCZ in the Diagnostic and Statistical Manual of Mental DIsorders Fourth Edition, Positive and negative syndrome scale, PANSS<60; No change in antipsychotic regimen (within two weeks)",29,29,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,1 September 2020,Fatima Zohra,WikiWorks743,Characterization of fecal microbiota to to distinguish toxigenic types by lineear discriminant anlysis method,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|1239|186801|186802|31979|1485;2|1239|186801|186802|186804,Complete,NA
Study 391,case-control,31841737,10.1016/j.jneuroim.2019.577126,NA,"Shi Z, Qiu Y, Wang J, Fang Y, Zhang Y, Chen H, Du Q, Zhao Z, Yan C, Yang M , Zhou H",Dysbiosis of gut microbiota in patients with neuromyelitis optica spectrum disorders: A cross sectional study,Journal of neuroimmunology,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,neuromyelitis optica,EFO:0004256,healthy controls,neuromyelitis optica spectrum disorder,Each patient met the 2015 international diagnostic criteria for NMOSD and tested positive for serum AQP4-IgG using cell-based assays,20,20,currently taking antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 3,31 August 2020,Rimsha Azhar,WikiWorks743,Abundance of gut microbiota between the NMOSD and HS groups,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1224|1236|91347;2|1224|1236|91347|543;2|1224;2|1224|1236;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1239|91061;2|1239|91061|1385;2|1239|91061|186826;2|1239|186801|186802|186803|265975;2|1239|186801|186802|216572|1486725;2|1239|909932|1843489|31977|156454;2|1239|186801|186802|216572|946234;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300,Complete,NA
Study 391,case-control,31841737,10.1016/j.jneuroim.2019.577126,NA,"Shi Z, Qiu Y, Wang J, Fang Y, Zhang Y, Chen H, Du Q, Zhao Z, Yan C, Yang M , Zhou H",Dysbiosis of gut microbiota in patients with neuromyelitis optica spectrum disorders: A cross sectional study,Journal of neuroimmunology,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,neuromyelitis optica,EFO:0004256,healthy controls,neuromyelitis optica spectrum disorder,Each patient met the 2015 international diagnostic criteria for NMOSD and tested positive for serum AQP4-IgG using cell-based assays,20,20,currently taking antibiotics,16S,34,Illumina,LEfSe,0.05,TRUE,3,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 3,31 August 2020,Rimsha Azhar,WikiWorks743,Abundance of gut microbiota between the NMOSD and HS groups,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia",2|1224|28216|80840|995019|40544;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186804;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552;2|1239|186801|186802;2|1239|186801,Complete,NA
Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,healthy controls,non-IgE mediated cow's milk allergy,"diagnosis of non-IgE mediated cow's milk allergy based on clinical history, negative result of skin prick test, and/or negative level of IgE serum-specific anti-cow's milk proteins",23,23,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,9 September 2020,Lucy Mellor,WikiWorks743,Comparative relative abundance (% of total reads) for the genera identified as significantly different between cow's milk allergy non IgE patients at diagnosis and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Sarcina,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239|186801|186802|31979|1266;2|976|200643|171549|815|816;2|976|200643|171549|171550|239759,Complete,NA
Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy at diagnosis,infant with non-IgE-mediated cow's milk allergy treated with EHCF,infant with non-IgE mediated cow's milk allergy treated with EHCF,23,9,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,9 September 2020,Lucy Mellor,WikiWorks743,Comparative relative abundance (% of total reads) for the genera identified as significantly different between non-IgE-Mediated cow's milk allergy treated with EHCF and non-IgE mediated cow's milk allergy at diagnosis,decreased,"k__Archaea|p__candidate phylum NAG2,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2157|1448937;2|976|200643|171549|815|816,Complete,NA
Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,Experiment 3,Italy,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy at diagnosis,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,23,14,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,9 September 2020,Lucy Mellor,WikiWorks743,Comparative relative abundance (% of total reads) for the genera identified as significantly different between non-IgE-Mediated cow's milk allergy treated with EHCF + LGG and non-IgE mediated cow's milk allergy at diagnosis,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae|g__Streptomyces",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|201174|1760|85011|2062|1883,Complete,NA
Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,Experiment 4,Italy,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy treated with EHCF,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,9,14,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Supplemental Table S1,9 September 2020,Lucy Mellor,WikiWorks743,Comparative relative abundance (% of total reads) for the genera identified as significantly different between non-IgE-Mediated cow's milk allergy treated with EHCF + LGG and non-IgE mediated cow's milk allergy treated with EHCF,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|186801|186802|216572|119852;2|1239|186801|186802|186803|28050;2|1239|186801|186802|216572|1263;2|1239|91061|186826|33958|1578,Complete,NA
Study 392,"cross-sectional observational, not case-control",30131575,10.1038/s41598-018-30428-3,NA,"Berni Canani R, De Filippis F, Nocerino R, Paparo L, Di Scala C, Cosenza L, Della Gatta G, Calignano A, De Caro C, Laiola M, Gilbert JA , Ercolini D",Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy,Scientific reports,2018,Experiment 4,Italy,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy treated with EHCF,infant with non-IgE-mediated cow's milk allergy treated with EHCF+LGG,infant with non-IgE mediated cow's milk allergy treated with EHCF+LGG,9,14,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Supplemental Table S1,9 September 2020,Lucy Mellor,WikiWorks743,Comparative relative abundance (% of total reads) for the genera identified as significantly different between non-IgE-Mediated cow's milk allergy treated with EHCF + LGG and non-IgE mediated cow's milk allergy treated with EHCF,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|39948,Complete,NA
Study 393,prospective cohort,30314304,10.3390/nu10101481,NA,"Díaz M, Guadamuro L, Espinosa-Martos I, Mancabelli L, Jiménez S, Molinos-Norniella C, Pérez-Solis D, Milani C, Rodríguez JM, Ventura M, Bousoño C, Gueimonde M, Margolles A, Díaz JJ , Delgado S",Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet,Nutrients,2018,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,infant with non-IgE-mediated cow's milk allergy non-tolerant to cow's milk protein,infant with non-IgE-mediated cow's milk allergy tolerant to cow's milk protein,infant with non-IgE mediated cow's milk allergy tolerant to cow's milk after a period of six months dairy-free diet,3,14,4 weeks,16S,34,Illumina,Metastats,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,13 September 2020,Lucy Mellor,WikiWorks743,"Significant differences in fecal microbial abundances (%) between tolerant and non-tolerant infants with non-IgE mediated cow’s milk protein allergy (NIM-CMPA) after
a period with a diet free of cow’s milk protein (CMP)",increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174;2|201174|1760|85004|31953;2|201174|84998|84999|84107;2|201174|1760|85004|31953|1678,Complete,NA
Study 393,prospective cohort,30314304,10.3390/nu10101481,NA,"Díaz M, Guadamuro L, Espinosa-Martos I, Mancabelli L, Jiménez S, Molinos-Norniella C, Pérez-Solis D, Milani C, Rodríguez JM, Ventura M, Bousoño C, Gueimonde M, Margolles A, Díaz JJ , Delgado S",Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet,Nutrients,2018,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,healthy control,infant with non-IgE-mediated cow's milk allergy,"infant with cow's milk protein allergy confirmed by a negative skin prick test, values lower than 0.35 kU/L cow’s milk-specific IgE determined in their blood, and a clear positive standardized oral challenge (SOC), performed under medical supervision",10,17,4 weeks,16S,34,Illumina,Metastats,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2,13 September 2020,Lucy Mellor,WikiWorks743,Differences in relative abundances (%) of sequences in fecal samples of infants with non-IgE mediated cow’s milk protein allergy (NIM-CMPA) and non-allergic control infants,increased,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,2|201174|84998|84999|84107,Complete,NA
Study 393,prospective cohort,30314304,10.3390/nu10101481,NA,"Díaz M, Guadamuro L, Espinosa-Martos I, Mancabelli L, Jiménez S, Molinos-Norniella C, Pérez-Solis D, Milani C, Rodríguez JM, Ventura M, Bousoño C, Gueimonde M, Margolles A, Díaz JJ , Delgado S",Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet,Nutrients,2018,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,healthy control,infant with non-IgE-mediated cow's milk allergy,"infant with cow's milk protein allergy confirmed by a negative skin prick test, values lower than 0.35 kU/L cow’s milk-specific IgE determined in their blood, and a clear positive standardized oral challenge (SOC), performed under medical supervision",10,17,4 weeks,16S,34,Illumina,Metastats,0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,13 September 2020,Lucy Mellor,WikiWorks743,Differences in relative abundances (%) of sequences in fecal samples of infants with non-IgE mediated cow’s milk protein allergy (NIM-CMPA) and non-allergic control infants,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976;2|976|200643|171549|815;2|976|200643|171549|815|816,Complete,NA
Study 394,prospective cohort,31676759,10.1038/s41467-019-12989-7,NA,"Thorsen J, Rasmussen MA, Waage J, Mortensen M, Brejnrod A, Bønnelykke K, Chawes BL, Brix S, Sørensen SJ, Stokholm J , Bisgaard H",Infant airway microbiota and topical immune perturbations in the origins of childhood asthma,Nature communications,2019,Experiment 1,Denmark,Homo sapiens,hypopharynx,UBERON:0001051,asthma,MONDO:0004979,healthy control,child with asthma at age 6,"asthma at age 6 years diagnosed using a pre-defined validated quantitative symptom algorithm based on parental registration of troublesome lung symptoms on structured daily diary cards from birth, verified by study pediatricians at each clinic visit",438,135,NA,16S,4,Illumina,Cox Proportional-Hazards Regression,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Supplemental Table 1,14 September 2020,Lucy Mellor,WikiWorks743,"Associations between log-relative abundances at one month and asthma development by age six years, assessed with Cox proportional hazards regression",increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838,Complete,NA
Study 395,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J, Vehaskari VM, Stewart T, Ferris M, Zhang Q, Wang G, Blanchard EE, Taylor CM, Kallash M, Greenbaum LA , Aviles DH",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,"chronic kidney disease,stage 5 chronic kidney disease","EFO:0003884,EFO:0009909",healthy controls,peritoneal dialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",13,8,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Figure 2,15 September 2020,Rimsha Azhar,WikiWorks743,Relative abundance of the four dominant phyla of the intestinal microbiota,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 395,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J, Vehaskari VM, Stewart T, Ferris M, Zhang Q, Wang G, Blanchard EE, Taylor CM, Kallash M, Greenbaum LA , Aviles DH",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,"chronic kidney disease,stage 5 chronic kidney disease","EFO:0003884,EFO:0009909",healthy controls,hemodialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",13,8,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 2,15 September 2020,Rimsha Azhar,WikiWorks743,Relative abundance of the four dominant phyla of the intestinal microbiota,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Actinobacteria",2|976;2|201174,Complete,NA
Study 395,"cross-sectional observational, not case-control",27640125,10.1186/s40168-016-0195-9,NA,"Crespo-Salgado J, Vehaskari VM, Stewart T, Ferris M, Zhang Q, Wang G, Blanchard EE, Taylor CM, Kallash M, Greenbaum LA , Aviles DH",Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study,Microbiome,2016,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,"chronic kidney disease,stage 5 chronic kidney disease","EFO:0003884,EFO:0009909",peritoneal dialysis,hemodialysis,"4 groups of pediatric patients (age 2-18), hemodialysis, peritoneal dialysis, kidney transplant, healthy controls",8,8,1 month,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,age,NA,NA,NA,increased,NA,NA,increased,Signature 1,Figure 2,15 September 2020,Rimsha Azhar,WikiWorks743,Relative abundance of the four dominant phyla of the intestinal microbiota,decreased,k__Bacteria|p__Proteobacteria,2|1224,Complete,NA
Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child between the age of 3 months-5 years with moderate to severe atopic dermatitis defined as an investigator’s global assessment (IGA) score of 3 or 4 (0–4 scale),11,21,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7a,17 September 2020,Lucy Mellor,WikiWorks743,Differentiating taxa between baseline atopic dermatitis lesional sites verses control skin at the class level,increased,k__Bacteria|p__Firmicutes|c__Bacilli,2|1239|91061,Complete,NA
Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child between the age of 3 months-5 years with moderate to severe atopic dermatitis defined as an investigator’s global assessment (IGA) score of 3 or 4 (0–4 scale),11,21,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7a,17 September 2020,Lucy Mellor,WikiWorks743,Differentiating taxa between baseline atopic dermatitis lesional sites verses control skin at the class level,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Actinobacteria|c__Rubrobacteria,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Actinobacteria|c__Actinomycetia",2|1239|186801;2|1224|28211;2|201174|84995;2|74201|203494;2|201174|84998;2|1224|28216;2|1239|526524;2|976|200643;2|201174|1760,Complete,NA
Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child between the age of 3 months-5 years with moderate to severe atopic dermatitis defined as an investigator’s global assessment (IGA) score of 3 or 4 (0–4 scale),11,21,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 7b,17 September 2020,Lucy Mellor,WikiWorks743,Differentiating taxa between baseline atopic dermatitis lesional sites verses control skin at the genus level,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,Experiment 1,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child between the age of 3 months-5 years with moderate to severe atopic dermatitis defined as an investigator’s global assessment (IGA) score of 3 or 4 (0–4 scale),11,21,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,Figure 7b,17 September 2020,Lucy Mellor,WikiWorks743,Differentiating taxa between baseline atopic dermatitis lesional sites verses control skin at the genus level,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus",2|1224|28216|80840|119060|47670;2|1224|28216|80840|119060|106589,Complete,NA
Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,Experiment 2,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS + Bleach,child with moderate to severe atopic dermatitis after treatment with TCS + bleach,9,9,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7c,17 September 2020,Lucy Mellor,WikiWorks743,Differentiating taxa for children with atopic dermatitis randomized to the TCS + bleach treatment group at baseline and after treatment,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|201174|1760|85007|1653|1716;2|1224|1236|2887326|468|469;2|976|200643|171549|171552|838,Complete,NA
Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,Experiment 2,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS + Bleach,child with moderate to severe atopic dermatitis after treatment with TCS + bleach,9,9,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7c,17 September 2020,Lucy Mellor,WikiWorks743,Differentiating taxa for children with atopic dermatitis randomized to the TCS + bleach treatment group at baseline and after treatment,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,Experiment 3,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS,child with moderate to severe atopic dermatitis after treatment with TCS,9,9,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 7d,17 September 2020,Lucy Mellor,WikiWorks743,Differentiating taxa for children with atopic dermatitis randomized to the TCS only treatment group at baseline and after treatment,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|201174|1760|85007|1653|1716;2|1224|1236|2887326|468|469;2|976|200643|171549|171552|838,Complete,NA
Study 396,randomized controlled trial,27543211,10.1016/j.jaad.2016.04.066,NA,"Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV , Blaser MJ",Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis,Journal of the American Academy of Dermatology,2016,Experiment 3,United States of America,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,baseline,atopic dermatitis after treatment with TCS,child with moderate to severe atopic dermatitis after treatment with TCS,9,9,2 weeks,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 7d,17 September 2020,Lucy Mellor,WikiWorks743,Differentiating taxa for children with atopic dermatitis randomized to the TCS only treatment group at baseline and after treatment,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 397,case-control,31152265,10.1007/s10096-019-03598-9,NA,"Zheng Y, Wang Q, Ma L, Chen Y, Gao Y, Zhang G, Cui S, Liang H, He C , Song L",Alterations in the skin microbiome are associated with disease severity and treatment in the perioral zone of the skin of infants with atopic dermatitis,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2019,Experiment 1,China,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,healthy control,severe atopic dermatitis,child with severe atopic dermatitis based on eczema area and severity index (EASI) local rating method,20,20,1 month,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,increased,NA,decreased,Signature 1,"Table 2, Table 3",20 September 2020,Lucy Mellor,WikiWorks743,Different genera of average relative abundance >=0.1% in healthy and severe atopic dermatitis groups,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Tepidimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium simulans,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae",2|1239|91061|1385|90964|1279;2|201174|1760|85007|85025|1827;2|1239|91061|186826|186828|1651;2|1224|28216|80840|114248;2|1239|91061|1385|90964|1279|1280;2|201174|1760|85007|1653|1716|146827;2|1224|28211|204457|41297|13687|172044,Complete,NA
Study 397,case-control,31152265,10.1007/s10096-019-03598-9,NA,"Zheng Y, Wang Q, Ma L, Chen Y, Gao Y, Zhang G, Cui S, Liang H, He C , Song L",Alterations in the skin microbiome are associated with disease severity and treatment in the perioral zone of the skin of infants with atopic dermatitis,European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology,2019,Experiment 1,China,Homo sapiens,skin of body,UBERON:0002097,atopic eczema,EFO:0000274,healthy control,severe atopic dermatitis,child with severe atopic dermatitis based on eczema area and severity index (EASI) local rating method,20,20,1 month,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,increased,NA,decreased,Signature 2,"Table 2, Table 3",20 September 2020,Lucy Mellor,WikiWorks743,Different genera of average relative abundance >=0.1% in healthy and severe atopic dermatitis groups,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Limnobacter,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Agrobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838;2|976|200643|171549|171551|836;2|1224|28216|80840|119060|131079;2|32066|203490|203491|1129771|32067;2|1224|28211|356|82115|357;2|201174|84998|84999|1643824|1380;2|201174|1760|85006|1268|32207|43675;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|425941,Complete,NA
Study 398,prospective cohort,27609659,10.1016/j.jaci.2016.07.029,NA,"Kennedy EA, Connolly J, Hourihane JO, Fallon PG, McLean WHI, Murray D, Jo JH, Segre JA, Kong HH , Irvine AD",Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year,The Journal of allergy and clinical immunology,2017,Experiment 1,Ireland,Homo sapiens,skin of forearm,UBERON:0003403,atopic eczema,EFO:0000274,healthy control,atopic dermatitis,child with atopic dermatis at month 12 diagnosed by experienced health care personnel using the UK Working Party Diagnostic Criteria,10,10,NA,16S,123,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 4b,21 September 2020,Lucy Mellor,WikiWorks743,Relative abundance of major taxa in antecubital fossa at month 2 between subjects that went on to be affected with atopic dermatits at month 12 and those who went on to be unaffected,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,2|1239|91061|1385|90964|1279,Complete,NA
Study 399,case-control,31620923,10.1007/s11357-019-00098-8,NA,"Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE , Pieper R",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,Experiment 1,United States of America,Homo sapiens,saliva,UBERON:0001836,age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 1a, Figure 2, Supplemental File S2",24 September 2020,Yu Wang,WikiWorks743,Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977|29465,Complete,NA
Study 399,case-control,31620923,10.1007/s11357-019-00098-8,NA,"Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE , Pieper R",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,Experiment 1,United States of America,Homo sapiens,saliva,UBERON:0001836,age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 1a, Figure 2, Supplemental File S2",24 September 2020,Yu Wang,WikiWorks743,Oral cavity microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|32066|203490|203491|203492|848;2|976|117743|200644|49546|1016,Complete,NA
Study 399,case-control,31620923,10.1007/s11357-019-00098-8,NA,"Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE , Pieper R",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Figure 4a, Figure 5, Supplemental File S2",24 September 2020,Yu Wang,WikiWorks743,Gut microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,NA
Study 399,case-control,31620923,10.1007/s11357-019-00098-8,NA,"Singh H, Torralba MG, Moncera KJ, DiLello L, Petrini J, Nelson KE , Pieper R",Gastro-intestinal and oral microbiome signatures associated with healthy aging,GeroScience,2019,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,age,EFO:0000246,healthy aging (HA),non-healthy aging (NHA),"participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.",33,32,6 weeks,16S,123,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Figure 4a, Figure 5, Supplemental File S2",24 September 2020,Yu Wang,WikiWorks743,Gut microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts,decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|74201|203494|48461|1647988|239934;2|976|200643|171549|815|816;2|1239|526524|526525|128827;2|1239|186801|186802|186803,Complete,NA
Study 400,case-control,31206804,10.1111/pai.13096,NA,"Chiu CY, Cheng ML, Chiang MH, Kuo YL, Tsai MH, Chiu CC , Lin G",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,healthy control,asthma,child age 4-7 years with physician diagnosed asthma,24,34,4 weeks,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Text",27 September 2020,Lucy Mellor,WikiWorks743,Differential expression of genera of bacteria between children with asthma and health controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium",2|1224|1236|91347|543|561;2|1239|91061|186826|81852|1350;2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186806|1730,Complete,NA
Study 400,case-control,31206804,10.1111/pai.13096,NA,"Chiu CY, Cheng ML, Chiang MH, Kuo YL, Tsai MH, Chiu CC , Lin G",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,healthy control,asthma,child age 4-7 years with physician diagnosed asthma,24,34,4 weeks,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Text",27 September 2020,Lucy Mellor,WikiWorks743,Differential expression of genera of bacteria between children with asthma and health controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|841;2|1239|909932|1843489|31977|39948;2|1239,Complete,NA
Study 400,case-control,31206804,10.1111/pai.13096,NA,"Chiu CY, Cheng ML, Chiang MH, Kuo YL, Tsai MH, Chiu CC , Lin G",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,child age 4-7 years with physician diagnosed allergic rhinitis,24,27,4 weeks,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2a, Text",27 September 2020,Lucy Mellor,WikiWorks743,Differential expression of genera of bacteria between children with allergic rhinitis and health controls,increased,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,2|201174|84998|1643822|1643826|447020,Complete,NA
Study 400,case-control,31206804,10.1111/pai.13096,NA,"Chiu CY, Cheng ML, Chiang MH, Kuo YL, Tsai MH, Chiu CC , Lin G",Gut microbial-derived butyrate is inversely associated with IgE responses to allergens in childhood asthma,Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,child age 4-7 years with physician diagnosed allergic rhinitis,24,27,4 weeks,16S,34,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2a, Text",27 September 2020,Lucy Mellor,WikiWorks743,Differential expression of genera of bacteria between children with allergic rhinitis and health controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes",2|1239|186801|186802|186803|189330;2|1239|909932|1843489|31977|39948;2|1239,Complete,NA
Study 401,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF , Chung IF",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,asthma,MONDO:0004979,healthy control,asthma,"child age 3-5 diagnosed as ever having asthma with the occurrence of recurrent wheeze in the last 12 months, or current use of asthma medication",32,32,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Table 2,27 September 2020,Lucy Mellor,WikiWorks743,Differences and comparisons of bacteria in phlya and genera among children with asthma and health controls,increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,2|1239|909932|909929|1843491|970,Complete,NA
Study 401,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF , Chung IF",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,asthma,MONDO:0004979,healthy control,asthma,"child age 3-5 diagnosed as ever having asthma with the occurrence of recurrent wheeze in the last 12 months, or current use of asthma medication",32,32,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Table 2,27 September 2020,Lucy Mellor,WikiWorks743,Differences and comparisons of bacteria in phlya and genera among children with asthma and health controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|1239|186801|186802|186803|830;2|1239|1737404|1737405|1570339|543311,Complete,NA
Study 401,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF , Chung IF",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,Experiment 2,China,Homo sapiens,throat,UBERON:0000341,allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,"child age 3-5 diagnosed as having symptoms such as sneezing, nasal congestion, itching, and rhinorrhea in the last 12 months",32,23,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Table 2, Text",27 September 2020,Lucy Mellor,WikiWorks743,Differences and comparisons of bacteria in phlya and genera among children with allergic rhinitis and health controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria",2|1224|1236|2887326|468|475;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|32066|203490|203491|203492|848;2|976|200643|171549|171551|836;2|1224,Complete,NA
Study 401,case-control,28500319,10.1038/s41598-017-02067-7,NA,"Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF , Chung IF",Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood,Scientific reports,2017,Experiment 2,China,Homo sapiens,throat,UBERON:0000341,allergic rhinitis,EFO:0005854,healthy control,allergic rhinitis,"child age 3-5 diagnosed as having symptoms such as sneezing, nasal congestion, itching, and rhinorrhea in the last 12 months",32,23,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,"Table 2, Text",27 September 2020,Lucy Mellor,WikiWorks743,Differences and comparisons of bacteria in phlya and genera among children with allergic rhinitis and health controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella",2|1239|186801|186802|186803|830;2|1224|1236|135625|712|416916;2|1239|186801|186802|186803|437755,Complete,NA
Study 402,case-control,25944283,10.1111/cea.12566,NA,"West CE, Rydén P, Lundin D, Engstrand L, Tulic MK , Prescott SL",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,Experiment 1,Australia,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,IgE associated eczema,Infants with typical skin lesions responsive to topical steroids diagnosed with eczema and with severity determined using the SCORAD index,8,6,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"delivery procedure,medical procedure",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Table 2,28 September 2020,Lucy Mellor,WikiWorks743,"Relative abundance >1% of dominant phyla, classes, families and genera in stool samples at 1 week of age infants that remained non-allergic (controls) and in infants developing IgE-associated eczema",decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,2|1239|186801|186802|541000,Complete,NA
Study 402,case-control,25944283,10.1111/cea.12566,NA,"West CE, Rydén P, Lundin D, Engstrand L, Tulic MK , Prescott SL",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,Experiment 2,Australia,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,mothers whose infants remained non-allergic,Mothers whose infants developed IgE associated eczema,Mothers whose infants developed typical skin lesions responsive to topical steroids diagnosed with eczema and with severity determined using the SCORAD index,10,9,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"delivery procedure,medical procedure",NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,Table 2,28 September 2020,Lucy Mellor,WikiWorks743,"Relative abundance >1% of dominant phyla, classes, families and genera in stool samples of mothers who's infants that remained non-allergic (controls) or infants developed IgE-associated eczema",increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,NA
Study 402,case-control,25944283,10.1111/cea.12566,NA,"West CE, Rydén P, Lundin D, Engstrand L, Tulic MK , Prescott SL",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,Experiment 3,Australia,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginally delivered infant,caesarean delivered infant,infant born by caesarean section,7,7,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1a, Text",28 September 2020,Lucy Mellor,WikiWorks743,Median relative abundances (%) of the most abundant phyla in vaginally delivered infants and caesarean delivered infants at 1 week,increased,k__Bacteria|p__Proteobacteria,2|1224,Complete,NA
Study 402,case-control,25944283,10.1111/cea.12566,NA,"West CE, Rydén P, Lundin D, Engstrand L, Tulic MK , Prescott SL",Gut microbiome and innate immune response patterns in IgE-associated eczema,Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology,2015,Experiment 3,Australia,Homo sapiens,feces,UBERON:0001988,cesarean section,EFO:0009636,vaginally delivered infant,caesarean delivered infant,infant born by caesarean section,7,7,NA,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1a, Text",28 September 2020,Lucy Mellor,WikiWorks743,Median relative abundances (%) of the most abundant phyla in vaginally delivered infants and caesarean delivered infants at 1 week,decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,NA
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3a,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia",2|1239|186801|186802|186803|841;2|1224|1236|91347|1903409|551,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3a,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|547,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3b,29 September 2020,Lucy Mellor,"WikiWorks743,Lwaldron",Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,increased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium neonatale",2|1239|186801;2|1239|186801|186802;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|31979|1485|137838,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3b,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age groups 0-3 years,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Proteobacteria",2|201174;2|201174|1760;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|216816|1679;2|1224,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3c,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,2|1224|1236|91347|1903409|551,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3c,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|28050,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3d,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis",2|1239|909932|1843489|31977|29465|29466;2|976|200643|171549|815|816|817,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0-0.5 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3d,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 0-0.5 years,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,2|201174|1760|85004|31953|1678|1681,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3e,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years,increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,2|1224|1236|91347|1903409|551,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3e,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",2|201174|1760|85004|31953|1678;2|1239|91061|186826|1300|1301;2|1224|29547|213849|72294|194,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 6,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 0.5-1 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3f,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 0.5-1 years,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|201174;2|201174|1760;2|201174|1760|85004|31953|1678;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|216816|1679;2|1224|1236|91347|543|547,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 7,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 1-2 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 1-2 years,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter",2|201174|1760|85004|31953|1678;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|1224|1236|91347|543|570;2|1224|1236|91347|543|547,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 8,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 1-2 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3h,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 1-2 years,decreased,k__Bacteria|p__Actinobacteria,2|201174,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 9,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 2-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3i,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 2-3 years,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila",2|201174|1760|85004|31953|1678;2|1224|28216|80840|995019|40544;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1224|28221|213115|194924|35832,Complete,Lwaldron
Study 403,case-control,30860574,10.1093/femsle/fnz020,NA,"Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y , Li S",Variations in early gut microbiome are associated with childhood eczema,FEMS microbiology letters,2019,Experiment 10,China,Homo sapiens,feces,UBERON:0001988,Eczema,HP:0000964,healthy control,child with eczema,"children age 2-3 with eczema diagnosed by pediatrician based on clinical criteria such as dry, desquamation skin, increased temperature on the local skin, and oozing or crusting",123,49,NA,16S,34,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3j,29 September 2020,Lucy Mellor,WikiWorks743,Significantly diverse bacterial communities between healthy and eczema groups in age group 2-3 years,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria",2|1239|186801|186802|186803;2|201174;2|201174|1760;2|201174|1760|85004;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1224,Complete,Lwaldron
Study 404,case-control,26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age <1 year diagnosed with atopic dermatitis based on the SCORAD scoring system,5,15,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Supplemental Figure E1",30 September 2020,Lucy Mellor,WikiWorks743,Bacterial genera that are distinctive between the AD and the non-AD children age <1 year old,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes",2|1239|186801|186802|216572|1263;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|292632;2|1239|186801|186802|186803|140625;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|186803|207244;2|976|200643|171549|171550|239759,Complete,NA
Study 404,case-control,26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age <1 year diagnosed with atopic dermatitis based on the SCORAD scoring system,5,15,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1, Supplemental Figure E1",30 September 2020,Lucy Mellor,WikiWorks743,Bacterial genera that are distinctive between the AD and the non-AD children age <1 year old,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|543|561;2|1224|1236|91347|543|620;2|1224|1236|91347|543,Complete,NA
Study 404,case-control,26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age 1-6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,15,58,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Supplemental Figure E1",30 September 2020,Lucy Mellor,WikiWorks743,Bacterial genera that are distinctive between the AD and the non-AD children age 1-6 years old,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,2|1239|186801|186802|216572|1263,Complete,NA
Study 404,case-control,26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age 1-6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,15,58,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1, Supplemental Figure E1",30 September 2020,Lucy Mellor,WikiWorks743,Bacterial genera that are distinctive between the AD and the non-AD children age 1-6 years old,decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810280|100883,Complete,NA
Study 404,case-control,26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age >6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,22,17,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Figure 1, Supplemental Figure E1",30 September 2020,Lucy Mellor,WikiWorks743,Bacterial genera that are distinctive between the AD and the non-AD children age >6 years old,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|1239|186801|186802|186803|588605;2|1239|186801|186802|186804,Complete,NA
Study 404,case-control,26431583,10.1016/j.jaci.2015.08.021,NA,"Song H, Yoo Y, Hwang J, Na YC , Kim HS",Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis,The Journal of allergy and clinical immunology,2016,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,atopic eczema,EFO:0000274,healthy control,patient with atopic dermatitis,patient age >6 years diagnosed with atopic dermatitis based on the SCORAD scoring system,22,17,6 months,16S,12,Roche454,Random Forest Analysis,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Figure 1, Supplemental Figure E1",30 September 2020,Lucy Mellor,WikiWorks743,Bacterial genera that are distinctive between the AD and the non-AD children age >6 years old,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania",2|976|200643|171549|171551;2|976|200643|171549|171552|577309;2|1239|186801|186802|216572|244127;2|976|200643|171549|1853231|574697;2|1239|186801|186802|541000;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186803|33042;2|1239|186801|186802;2|1239|526524|526525|128827|61170,Complete,NA
Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment",531,58,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,1 October 2020,Lucy Mellor,WikiWorks743,Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in all children,increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,NA
Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment",531,58,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,1 October 2020,Lucy Mellor,WikiWorks743,Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in all children,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",2|1239|186801|186802|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|946234,Complete,NA
Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,Experiment 2,Denmark,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers with asthma,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment and mother with asthma",122,25,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 3,1 October 2020,Lucy Mellor,WikiWorks743,Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to asthmatic mothers,increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,NA
Study 405,prospective cohort,29321519,10.1038/s41467-017-02573-2,NA,"Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ , Bisgaard H",Maturation of the gut microbiome and risk of asthma in childhood,Nature communications,2018,Experiment 2,Denmark,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,no asthma at 5 years old,child with asthma at 5 years old among mothers with asthma,"child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment and mother with asthma",122,25,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 3,1 October 2020,Lucy Mellor,WikiWorks743,Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to asthmatic mothers,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|1239|186801|186802|216572|216851;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|841;2|976|200643|171549|171550|239759;2|1239|186801|186802|216572|1263;2|1239|909932|1843489|31977|39948,Complete,NA
Study 406,prospective cohort,30524957,10.3389/fonc.2018.00520,NA,"Yang J, Mu X, Wang Y, Zhu D, Zhang J, Liang C, Chen B, Wang J, Zhao C, Zuo Z, Heng X, Zhang C , Zhang L",Dysbiosis of the Salivary Microbiome Is Associated With Non-smoking Female Lung Cancer and Correlated With Immunocytochemistry Markers,Frontiers in oncology,2018,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,lung cancer,MONDO:0008903,healthy controls,non-smoking female lung cancer patients,female and have confirmed diagnosis of non-small-cell lung cancer,172,75,NA,16S,12,Illumina,LEfSe,0.05,FALSE,3,age,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 5,30 September 2020,Rimsha Azhar,"WikiWorks743,WikiWorks753,WikiWorks",Most differently abundant taxa between lung cancer and control groups,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Blastomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae",2|1224;2|1224|28211|204457|41297;2|1224|28211|204457;2|976|117743|200644;2|976|117743;2|1224|28211|204457|41297|13687;2|1224|28216|206389|75787;2|1224|28211|204457|41297|150203;2|1224|28216|80840|75682|963;2|1224|28216|80840|75682,Complete,NA
Study 406,prospective cohort,30524957,10.3389/fonc.2018.00520,NA,"Yang J, Mu X, Wang Y, Zhu D, Zhang J, Liang C, Chen B, Wang J, Zhao C, Zuo Z, Heng X, Zhang C , Zhang L",Dysbiosis of the Salivary Microbiome Is Associated With Non-smoking Female Lung Cancer and Correlated With Immunocytochemistry Markers,Frontiers in oncology,2018,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,lung cancer,MONDO:0008903,healthy controls,non-smoking female lung cancer patients,female and have confirmed diagnosis of non-small-cell lung cancer,172,75,NA,16S,12,Illumina,LEfSe,0.05,FALSE,3,age,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 5,30 September 2020,Rimsha Azhar,WikiWorks743,Most differently abundant taxa between lung cancer and control groups,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|s__Azotobacter group,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter",2|1224|28216|80840|80864|283;2|1224|28216|80840|80864;2|1224|1236|135614|32033;2|1224|1236|72274|135621|351;2|1224|1236|135614;2|976|117743|200644|2762318|59732;2|1224|28216|80840;2|1224|28216;2|976;2|1239|91061;2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|91061|186826;2|1239;2|1224|1236|91347;2|1224|1236|91347|543;2|1224|1236|2887326|468|469,Complete,NA
Study 407,prospective cohort,32733243,10.3389/fphar.2020.01000,NA,"Wang B, Zhang Y, Zhao Q, Yan Y, Yang T, Xia Y , Chen H",Patients With Reflux Esophagitis Possess a Possible Different Oral Microbiota Compared With Healthy Controls,Frontiers in pharmacology,2020,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,peptic esophagitis,EFO:1001095,healthy controls,reflux esophagus patients,symptoms such as heartburn and regurgitation were in accordance with the endoscopic criteria of Los Angeles Grade and taken no drugs as treatment,51,55,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 3,30 September 2020,Rimsha Azhar,WikiWorks743,Bacterial taxa diversities between Reflux Esophigitis (RE) and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes",2|1239|526524|526525|128827|123375;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186803|265975;2|1239|186801|186802|186803|1164882;2|1239|186801|186802|186804;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|186804|1257;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803;2|1224|28211|356|119045;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|976|200643|171549|171552|838;2|1239|909932;2|1239|909932|909929;2|976|200643;2|976|200643|171549;2|976,Complete,NA
Study 407,prospective cohort,32733243,10.3389/fphar.2020.01000,NA,"Wang B, Zhang Y, Zhao Q, Yan Y, Yang T, Xia Y , Chen H",Patients With Reflux Esophagitis Possess a Possible Different Oral Microbiota Compared With Healthy Controls,Frontiers in pharmacology,2020,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,peptic esophagitis,EFO:1001095,healthy controls,reflux esophagus patients,symptoms such as heartburn and regurgitation were in accordance with the endoscopic criteria of Los Angeles Grade and taken no drugs as treatment,51,55,6 months,16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 3,30 September 2020,Rimsha Azhar,"WikiWorks743,Lwaldron",Bacterial taxa diversities between Reflux Esophigitis (RE) and healthy controls,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales Family X. Incertae Sedis,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Acidobacteria|c__Acidobacteriia|o__Acidobacteriales|f__Acidobacteriaceae|g__Granulicella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hallella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Lactivibrio,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Spirochaetes|c__Spirochaetia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales,k__Bacteria|p__Synergistetes,k__Bacteria|p__Synergistetes|c__Synergistia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Wolinella",2|201174|1760|2037;2|1224|1236|135625|712|416916;2|1239|91061|1385;2|1239|91061|1385|539003;2|1239|91061;2|1224|28216;2|1224|28216|80840;2|1224|29547|213849|72294|194;2|1224|29547|213849|72294;2|1224|29547|213849;2|1239|91061|186826|186828;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|538;2|1224|29547;2|1239|186801|186802|186804|44259;2|201174|1760|85004|31953|2701;2|1239|91061|1385|1378;2|57723|204432|204433|204434|940557;2|976|200643|171549|171552|52228;2|1239|186801|186802|186803|43994;2|508458|649775|649776|649777|1508421;2|1239|91061|186826;2|201174|1760|85006|1268;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|28216|206351;2|1224;2|1239|186801|186802|186806|113286;2|201174|1760|85006|1268|32207;2|203691|203692|136|137;2|203691|203692|136;2|203691;2|203691|203692;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|508458|649775|649776|649777;2|508458|649775|649776;2|508458;2|508458|649775;2|1239|186801|186802|68298;2|203691|203692|136|2845253|157;2|1224|29547|213849|72293|843,Complete,NA
Study 408,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma LT, Arrieta MC, Dimitriu PA, Cheng J, Thorson L, Lefebvre DL, Azad MB, Subbarao P, Mandhane P, Becker A, Sears MR, Kollmann TR, Mohn WW, Finlay BB , Turvey SE",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,healthy controls,asthma at 3 months,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,DESeq2,0.05,TRUE,NA,"antibiotic exposure,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1a,4 October 2020,Lucy Mellor,WikiWorks743,Differentially abundant OTUs Identified by Deseq2 analysis at 3 months,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239;2|1239|186801|186802|31979,Complete,NA
Study 408,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma LT, Arrieta MC, Dimitriu PA, Cheng J, Thorson L, Lefebvre DL, Azad MB, Subbarao P, Mandhane P, Becker A, Sears MR, Kollmann TR, Mohn WW, Finlay BB , Turvey SE",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,healthy controls,asthma at 3 months,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,DESeq2,0.05,TRUE,NA,"antibiotic exposure,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 1a,4 October 2020,Lucy Mellor,WikiWorks743,Differentially abundant OTUs Identified by Deseq2 analysis at 3 months,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,2|1239|186801|186802,Complete,NA
Study 408,case-control,27634868,10.1042/CS20160349,NA,"Stiemsma LT, Arrieta MC, Dimitriu PA, Cheng J, Thorson L, Lefebvre DL, Azad MB, Subbarao P, Mandhane P, Becker A, Sears MR, Kollmann TR, Mohn WW, Finlay BB , Turvey SE",Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma,"Clinical science (London, England : 1979)",2016,Experiment 2,Canada,Homo sapiens,feces,UBERON:0001988,asthma,MONDO:0004979,healthy controls,asthma at 1 year,physician diagnosis of asthma by 4 years of age or was prescribed inhaled asthma medications (inhaled corticosteroids or bronchodilators) from 3 to 4 years of age,37,39,NA,16S,3,Illumina,DESeq2,0.05,TRUE,NA,"antibiotic exposure,feeding practices,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 1b,4 October 2020,Lucy Mellor,WikiWorks743,Differentially abundant OTUs Identified by Deseq2 analysis at 1 year,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239|186801|186802|186803;2|201174|1760|85006|1268|32207,Complete,NA
Study 409,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA , Nagler CR",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,healthy controls,IgE mediated cow's milk allergy,diagnosis of IgE mediated cow's milk allergy based on clinical history and level of IgE serum-specific anti-cow's milk proteins,20,19,4 weeks,16S,4,Illumina,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 1,"Figure 1d, Text, Supplemental Table 2",4 October 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa between healthy and cow's milk allergy pre-treatment groups,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|186802|541000;2|1239|186801|186802|186803;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|216851,Complete,NA
Study 409,randomized controlled trial,26394008,10.1038/ismej.2015.151,NA,"Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA , Nagler CR",Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants,The ISME journal,2016,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,milk allergic reaction,EFO:0007369,healthy controls,IgE mediated cow's milk allergy,diagnosis of IgE mediated cow's milk allergy based on clinical history and level of IgE serum-specific anti-cow's milk proteins,20,19,4 weeks,16S,4,Illumina,Welch's T-Test,0.05,TRUE,NA,"age,body weight,sex",NA,increased,increased,NA,NA,NA,NA,Signature 2,"Figure 1d, Text, Supplemental Table 2",4 October 2020,Lucy Mellor,WikiWorks743,Differentially abundant taxa between healthy and cow's milk allergy pre-treatment groups,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|201174|1760|85004|31953;2|1239|91061|186826|1300;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|201174|1760|85004|31953|1678;2|1224|1236|91347|543|561,Complete,NA
Study 410,"cross-sectional observational, not case-control",28118207,10.1097/QAD.0000000000001409,NA,"Nowak RG, Bentzen SM, Ravel J, Crowell TA, Dauda W, Ma B, Liu H, Blattner WA, Baral SD , Charurat ME","Rectal microbiota among HIV-uninfected, untreated HIV, and treated HIV-infected in Nigeria","AIDS (London, England)",2017,Experiment 1,Nigeria,Homo sapiens,rectum,UBERON:0001052,HIV infection,EFO:0000764,HIV-uninfected MSM,ART-treated HIV infected MSM,Men who have sex with men (MSM) with HIV that has been treated with antiretroviral therapy (ART),55,34,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,"Table 1, Figure 1, Text",5 October 2020,Michael Lutete,WikiWorks743,"Relative abundance of most common rectal genera within 5 phyla, stratified by HIV and ART status",increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter",2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|165779;2|1224|29547|213849|72294|194,Complete,NA
Study 410,"cross-sectional observational, not case-control",28118207,10.1097/QAD.0000000000001409,NA,"Nowak RG, Bentzen SM, Ravel J, Crowell TA, Dauda W, Ma B, Liu H, Blattner WA, Baral SD , Charurat ME","Rectal microbiota among HIV-uninfected, untreated HIV, and treated HIV-infected in Nigeria","AIDS (London, England)",2017,Experiment 1,Nigeria,Homo sapiens,rectum,UBERON:0001052,HIV infection,EFO:0000764,HIV-uninfected MSM,ART-treated HIV infected MSM,Men who have sex with men (MSM) with HIV that has been treated with antiretroviral therapy (ART),55,34,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,"Table 1, Figure 1, Text",5 October 2020,Michael Lutete,WikiWorks743,"Relative abundance of most common rectal genera within 5 phyla, stratified by HIV and ART status",decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
Study 410,"cross-sectional observational, not case-control",28118207,10.1097/QAD.0000000000001409,NA,"Nowak RG, Bentzen SM, Ravel J, Crowell TA, Dauda W, Ma B, Liu H, Blattner WA, Baral SD , Charurat ME","Rectal microbiota among HIV-uninfected, untreated HIV, and treated HIV-infected in Nigeria","AIDS (London, England)",2017,Experiment 2,Nigeria,Homo sapiens,rectum,UBERON:0001052,gonorrhea,NA,MSM with no gonorrhea,MSM with gonorrhea,Men who have sex with men (MSM),95,35,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Text,15 November 2020,Michael Lutete,WikiWorks743,Shifts in microbial composition between men who have sex with men (MSM) with gonorrhea and without gonorrhea,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
Study 411,"cross-sectional observational, not case-control",32258202,10.1093/ofid/ofz463,NA,"Fulcher JA, Li F, Cook RR, Zabih S, Louie A, Okochi H, Tobin NH, Gandhi M, Shoptaw S, Gorbach PM , Aldrovandi GM",Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis,Open forum infectious diseases,2019,Experiment 1,United States of America,Homo sapiens,rectum,UBERON:0001052,HIV/AIDS pre-exposure prophylaxis,GSSO:001787,HIV-negative MSM not on PrEP,HIV-negative MSM on PrEP,HIV-negative Men who have sex with men (MSM) on HIV pre-exposure prophylaxis (PrEP),37,37,NA,16S,4,Illumina,NA,0.1,TRUE,NA,"age,anal intercourse,ethnic group,marijuana,nicotine dependence,obesity,race",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 1, Figure 2, Text",7 October 2020,Michael Lutete,WikiWorks743,Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella",2|1239|91061|186826|1300|1301;2|32066|203490|203491|203492|848;2|1239|909932|909929|1843491|52225,Complete,NA
Study 411,"cross-sectional observational, not case-control",32258202,10.1093/ofid/ofz463,NA,"Fulcher JA, Li F, Cook RR, Zabih S, Louie A, Okochi H, Tobin NH, Gandhi M, Shoptaw S, Gorbach PM , Aldrovandi GM",Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis,Open forum infectious diseases,2019,Experiment 1,United States of America,Homo sapiens,rectum,UBERON:0001052,HIV/AIDS pre-exposure prophylaxis,GSSO:001787,HIV-negative MSM not on PrEP,HIV-negative MSM on PrEP,HIV-negative Men who have sex with men (MSM) on HIV pre-exposure prophylaxis (PrEP),37,37,NA,16S,4,Illumina,NA,0.1,TRUE,NA,"age,anal intercourse,ethnic group,marijuana,nicotine dependence,obesity,race",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 1, Figure 2, Text",7 October 2020,Michael Lutete,WikiWorks743,Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella",2|1224|1236|91347|543|561;2|1224|1236|91347|543|620,Complete,NA
Study 411,"cross-sectional observational, not case-control",32258202,10.1093/ofid/ofz463,NA,"Fulcher JA, Li F, Cook RR, Zabih S, Louie A, Okochi H, Tobin NH, Gandhi M, Shoptaw S, Gorbach PM , Aldrovandi GM",Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis,Open forum infectious diseases,2019,Experiment 2,United States of America,Homo sapiens,rectum,UBERON:0001052,HIV/AIDS pre-exposure prophylaxis,GSSO:001787,HIV-negative MSM not on PrEP,HIV-negative MSM on PrEP,HIV-negative Men who have sex with men (MSM) on HIV pre-exposure prophylaxis (PrEP),37,37,NA,16S,4,Illumina,NA,0.05,TRUE,NA,"age,anal intercourse,ethnic group,marijuana,nicotine dependence,obesity,race",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 2, Text",15 October 2020,Michael Lutete,WikiWorks743,Pre-exposure prophylaxis use associates with differential abundance of specific bacterial genera,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 412,case-control,31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,Experiment 1,United States of America,Homo sapiens,rectum,UBERON:0001052,"HIV infection,methamphetamine dependence","EFO:0000764,EFO:0004701",HIV-positive non-MA users,HIV-positive MA users,HIV-positive Men who have sex with men (MSM) who self-reported methamphetamine (MA) use in the past six months,81,101,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,"age,ethnic group",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Table S2, Figure 3",22 October 2020,Michael Lutete,WikiWorks743,Differential abundance of bacterial genera between HIV-positive MSM and HIV-negative MSM stratified by methamphetamine use,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Mannheimia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|75984;2|1239|909932|1843489|31977|909928;2|32066|203490|203491|1129771|34104,Complete,NA
Study 412,case-control,31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,Experiment 2,United States of America,Homo sapiens,rectum,UBERON:0001052,methamphetamine dependence,EFO:0004701,non-users,Methamphetamine users,MSM who self-reported methamphetamine (MA) use in the past six months,225,156,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,"age,ethnic group",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Table S2",22 October 2020,Michael Lutete,WikiWorks743,Differential abundance of bacterial genera between MA users and non-users,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium",2|1239|1737404|1737405|1570339|1161127;2|1224|1236|135625|712|724;2|1239|186801|186802|186806|1730;2|1239|909932|1843489|31977|29465;2|201174|1760|85007|85029|37914;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|150022;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|1239|186801|186802|186804|1257;2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|543314|86331,Complete,NA
Study 412,case-control,31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,Experiment 2,United States of America,Homo sapiens,rectum,UBERON:0001052,methamphetamine dependence,EFO:0004701,non-users,Methamphetamine users,MSM who self-reported methamphetamine (MA) use in the past six months,225,156,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,"age,ethnic group",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Table S2",22 October 2020,Michael Lutete,WikiWorks743,Differential abundance of bacterial genera between MA users and non-users,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella",2|1239|186801|186802|31979|580596;2|1239|186801|186802|216572|216851;2|976|200643|171549|171552|1283313,Complete,NA
Study 412,case-control,31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,Experiment 3,United States of America,Homo sapiens,rectum,UBERON:0001052,methamphetamine dependence,EFO:0004701,MSM who did not test positive on MA urine drug screening,MSM who tested positive on MA urine drug screening,MSM who tested positive for methamphetamine (MA) use in a urine drug screening,NA,52,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,"age,ethnic group",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Figure 4-6",3 November 2020,Michael Lutete,WikiWorks743,Sensitivity analysis using urine toxicology screening to define MA use,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",2|1239|1737404|1737405|1570339|1161127;2|201174|1760|85007|85029|37914;2|1239|186801|186802|186806|1730;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|32066|203490|203491|203492|848;2|1239|186801|186802|543314|86331;2|1239|186801|186802|186804|1257;2|201174|1760|85007|1653|1716;2|1239|1737404|1737405|1570339|165779,Complete,NA
Study 412,case-control,31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,Experiment 3,United States of America,Homo sapiens,rectum,UBERON:0001052,methamphetamine dependence,EFO:0004701,MSM who did not test positive on MA urine drug screening,MSM who tested positive on MA urine drug screening,MSM who tested positive for methamphetamine (MA) use in a urine drug screening,NA,52,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,"age,ethnic group",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Figure 4-6",3 November 2020,Michael Lutete,WikiWorks743,Sensitivity analysis using urine toxicology screening to define MA use,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Lentisphaerae|c__Oligosphaeria|o__Oligosphaerales|f__Oligosphaeraceae|g__Oligosphaera,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio",2|1239|186801|186802|216572|216851;2|1239|186801|186802|31979|1485;2|1239|91061|186826|33958|1578;2|256845|1313207|1313208|1313209|1313210;2|1224|1236|135624|83763|83770,Complete,NA
Study 412,case-control,31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,Experiment 4,United States of America,Homo sapiens,rectum,UBERON:0001052,"HIV infection,methamphetamine dependence","EFO:0000764,EFO:0004701",HIV-positive men who have sex with men who did not test positive in a methamphetamine drug screening,HIV-positive men who have sex with men who tested positive in a methamphetamine drug screening,HIV-positive Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,NA,NA,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,"age,ethnic group",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Figure 4-6",3 November 2020,Michael Lutete,WikiWorks743,Sensitivity analysis using urine toxicology screening to define MA use in HIV-positive MSM,increased,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,2|32066|203490|203491|1129771|34104,Complete,NA
Study 412,case-control,31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,Experiment 4,United States of America,Homo sapiens,rectum,UBERON:0001052,"HIV infection,methamphetamine dependence","EFO:0000764,EFO:0004701",HIV-positive men who have sex with men who did not test positive in a methamphetamine drug screening,HIV-positive men who have sex with men who tested positive in a methamphetamine drug screening,HIV-positive Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,NA,NA,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,"age,ethnic group",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Figure 4-6",3 November 2020,Michael Lutete,WikiWorks743,Sensitivity analysis using urine toxicology screening to define MA use in HIV-positive MSM,decreased,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,2|1224|28216|80840|75682|846,Complete,NA
Study 412,case-control,31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,Experiment 5,United States of America,Homo sapiens,rectum,UBERON:0001052,"HIV infection,methamphetamine dependence","EFO:0000764,EFO:0004701",HIV-negative MSM who did not test positive in a MA drug screening,HIV-negative MSM who tested positive in a MA drug screening,HIV-negative Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,NA,NA,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,"age,ethnic group",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Text, Supplementary Figure 4-6",3 November 2020,Michael Lutete,WikiWorks743,Sensitivity analysis using urine toxicology screening to define MA use in HIV-negative MSM,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,2|1239|186801|186802|31979|1485,Complete,NA
Study 412,case-control,31619731,10.1038/s41598-019-51142-8,NA,"Cook RR, Fulcher JA, Tobin NH, Li F, Lee DJ, Woodward C, Javanbakht M, Brookmeyer R, Shoptaw S, Bolan R, Aldrovandi GM , Gorbach PM",Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men,Scientific reports,2019,Experiment 5,United States of America,Homo sapiens,rectum,UBERON:0001052,"HIV infection,methamphetamine dependence","EFO:0000764,EFO:0004701",HIV-negative MSM who did not test positive in a MA drug screening,HIV-negative MSM who tested positive in a MA drug screening,HIV-negative Men who have sex with men (MSM) who tested positive in a methamphetamine (MA) drug screening,NA,NA,NA,16S,4,Illumina,NA,0.1,TRUE,NA,NA,"age,ethnic group",NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Text, Supplementary Figure 4-6",3 November 2020,Michael Lutete,WikiWorks743,Sensitivity analysis using urine toxicology screening to define MA use in HIV-negative MSM,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|1239|186801|186802|216572|292632;2|1239|91061|186826|186828|117563;2|976|200643|171549|2005519|397864;2|32066|203490|203491|1129771|34104;2|32066|203490|203491|1129771|168808,Complete,NA
Study 413,"cross-sectional observational, not case-control",32307692,10.1111/acps.13175,NA,"Turna J, Grosman Kaplan K, Anglin R, Patterson B, Soreni N, Bercik P, Surette MG , Van Ameringen M",The gut microbiome and inflammation in obsessive-compulsive disorder patients compared to age- and sex-matched controls: a pilot study,Acta psychiatrica Scandinavica,2020,Experiment 1,Canada,Homo sapiens,feces,UBERON:0001988,obsessive-compulsive disorder,EFO:0004242,healthy controls,OCD,non-depressed medication free individuals or individuals with mild depressive symptoms (MADRS score<16) with a primary DSM-5 diagnosis of OCD as per the MINI or at least moderate OCD (Y-BOCS score >= 20),22,21,8 weeks,16S,3,Illumina,ANCOM,0.05,TRUE,NA,"age,sex",NA,NA,unchanged,unchanged,NA,decreased,unchanged,Signature 1,Figure 3,4 November 2020,Fatima Zohra,WikiWorks743,Relative abundance of gut microbiome in OCD patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes",2|1239|186801|186802|216572|119852;2|976|200643|171549|1853231|283168;2|1239|186801|186802|186803|207244,Complete,Fatima
Study 414,time series / longitudinal observational,30701077,10.1038/s41522-018-0073-2,NA,"Lindefeldt M, Eng A, Darban H, Bjerkner A, Zetterström CK, Allander T, Andersson B, Borenstein E, Dahlin M , Prast-Nielsen S",The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy,NPJ biofilms and microbiomes,2019,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,epilepsy,EFO:0000474,after keto diet,before keto diet,children with therapy resistent inoperabe epilepsy or a diagnosis of a neorometablic disorder in which KD is recommended,12,12,3 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,4 November 2020,Fatima Zohra,WikiWorks743,Statistical changes at all taxonomic levels during dietary interventaion (keto diet) using LEFse method,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rectale CAG:36,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|201174|1760;2|1239|186801|186802|186806|1730|1263079;2|1239|909932|1843489|31977|39948,Complete,NA
Study 414,time series / longitudinal observational,30701077,10.1038/s41522-018-0073-2,NA,"Lindefeldt M, Eng A, Darban H, Bjerkner A, Zetterström CK, Allander T, Andersson B, Borenstein E, Dahlin M , Prast-Nielsen S",The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy,NPJ biofilms and microbiomes,2019,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,epilepsy,EFO:0000474,after keto diet,before keto diet,children with therapy resistent inoperabe epilepsy or a diagnosis of a neorometablic disorder in which KD is recommended,12,12,3 months,WMS,NA,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3,4 November 2020,Fatima Zohra,WikiWorks743,Statistical changes at all taxonomic levels during dietary interventaion (keto diet) using LEFse method,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria",2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|561;2|1224|1236;2|1224|1236|91347|543;2|1224|1236|91347;2|1224,Complete,NA
Study 415,case-control,29808701,10.1089/AID.2017.0200,NA,"Lewy T, Hong BY, Weiser B, Burger H, Tremain A, Weinstock G, Anastos K , George MD","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,Experiment 1,United States of America,Homo sapiens,saliva,UBERON:0001836,HIV infection,EFO:0000764,Age-matched HIV-uninfected women,HIV-positive women who have been taking ART for more than 1 year,HIV-positive women who have been taking antiretroviral therapy (ART) for more than 1 year,3,3,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Text, Supplementary Figure S3, Figure 2",5 November 2020,Michael Lutete,WikiWorks743,Differences in abundance of salivary bacteria between HIV uninfected women and HIV-positive women on ART,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella",2|1239|186801|186802|186803|265975;2|1239|186801|186802|186803|437755,Complete,NA
Study 415,case-control,29808701,10.1089/AID.2017.0200,NA,"Lewy T, Hong BY, Weiser B, Burger H, Tremain A, Weinstock G, Anastos K , George MD","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,Experiment 2,United States of America,Homo sapiens,saliva,UBERON:0001836,"HIV infection,oral candidiasis","EFO:0000764,EFO:0007406",Age-matched HIV-uninfected womenn,HIV-positive women with oral candidiasis,HIV-positive women with oral candidiasis,3,3,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Text, Supplementary Figure S3, Figure 2",5 November 2020,Michael Lutete,WikiWorks743,Differences in abundance of salivary bacteria between HIV uninfected women and HIV-positive women coinfected with oral candidiasis,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|909932|1843489|31977|29465;2|1239|186801|186802|186803,Complete,NA
Study 415,case-control,29808701,10.1089/AID.2017.0200,NA,"Lewy T, Hong BY, Weiser B, Burger H, Tremain A, Weinstock G, Anastos K , George MD","Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy",AIDS research and human retroviruses,2019,Experiment 3,United States of America,Homo sapiens,saliva,UBERON:0001836,age,EFO:0000246,HIV uninfected women who are less than 35 years of age,HIV uninfected women who are 50 years of age or older,HIV-negative women who are 50 years of age or older,4,4,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Text, Supplementary Figure S3, Figure 2",6 November 2020,Michael Lutete,WikiWorks743,Differences in abundance of salivary bacteria between young HIV uninfected women and old HIV uninfected women,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella",2|1239|186801|186802|186803|265975;2|1239|186801|186802|186803|437755,Complete,NA
Study 416,randomized controlled trial,30944164,10.1126/scitranslmed.aav0537,NA,"Bourke CD, Gough EK, Pimundu G, Shonhai A, Berejena C, Terry L, Baumard L, Choudhry N, Karmali Y, Bwakura-Dangarembizi M, Musiime V, Lutaakome J, Kekitiinwa A, Mutasa K, Szubert AJ, Spyer MJ, Deayton JR, Glass M, Geum HM, Pardieu C, Gibb DM, Klein N, Edens TJ, Walker AS, Manges AR , Prendergast AJ",Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation,Science translational medicine,2019,Experiment 1,Zimbabwe,Homo sapiens,feces,UBERON:0001988,"HIV infection,cotrimoxazole",EFO:0000764,stop cotrimoxazole prophylaxis,continue cotrimoxazole prophylaxis,HIV-positive and antiretroviral therapy (ART) treated children who were randomized to continue taking cotrimoxazole prophylaxis,36,36,NA,WMS,NA,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 1,"Text, Figure S3",7 November 2020,Michael Lutete,WikiWorks743,Bacterial species from stool samples that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis based on protein families,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus",2|976|200643|171549|815|816|371601;2|1224|1236|91347|543|561|562;2|976|200643|171549|1853231|283168|28118,Complete,NA
Study 416,randomized controlled trial,30944164,10.1126/scitranslmed.aav0537,NA,"Bourke CD, Gough EK, Pimundu G, Shonhai A, Berejena C, Terry L, Baumard L, Choudhry N, Karmali Y, Bwakura-Dangarembizi M, Musiime V, Lutaakome J, Kekitiinwa A, Mutasa K, Szubert AJ, Spyer MJ, Deayton JR, Glass M, Geum HM, Pardieu C, Gibb DM, Klein N, Edens TJ, Walker AS, Manges AR , Prendergast AJ",Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation,Science translational medicine,2019,Experiment 1,Zimbabwe,Homo sapiens,feces,UBERON:0001988,"HIV infection,cotrimoxazole",EFO:0000764,stop cotrimoxazole prophylaxis,continue cotrimoxazole prophylaxis,HIV-positive and antiretroviral therapy (ART) treated children who were randomized to continue taking cotrimoxazole prophylaxis,36,36,NA,WMS,NA,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 2,"Text, Figure S3",7 November 2020,Michael Lutete,WikiWorks743,Bacterial species from stool samples that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis based on protein families,decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis",2|1239|526524|526525|128827|1573535|1735;2|1224|1236|135625|712|724|729;2|1239|91061|186826|1300|1301|1318,Complete,NA
Study 416,randomized controlled trial,30944164,10.1126/scitranslmed.aav0537,NA,"Bourke CD, Gough EK, Pimundu G, Shonhai A, Berejena C, Terry L, Baumard L, Choudhry N, Karmali Y, Bwakura-Dangarembizi M, Musiime V, Lutaakome J, Kekitiinwa A, Mutasa K, Szubert AJ, Spyer MJ, Deayton JR, Glass M, Geum HM, Pardieu C, Gibb DM, Klein N, Edens TJ, Walker AS, Manges AR , Prendergast AJ",Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation,Science translational medicine,2019,Experiment 1,Zimbabwe,Homo sapiens,feces,UBERON:0001988,"HIV infection,cotrimoxazole",EFO:0000764,stop cotrimoxazole prophylaxis,continue cotrimoxazole prophylaxis,HIV-positive and antiretroviral therapy (ART) treated children who were randomized to continue taking cotrimoxazole prophylaxis,36,36,NA,WMS,NA,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 3,"Text, Figure S2",7 November 2020,Michael Lutete,WikiWorks743,Fecal bacterial species that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides goldsteinii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|2005525|375288|328812;2|976|200643|171549|2005525|375288|387661;2|1239|186801|186802|186803|841|166486,Complete,NA
Study 416,randomized controlled trial,30944164,10.1126/scitranslmed.aav0537,NA,"Bourke CD, Gough EK, Pimundu G, Shonhai A, Berejena C, Terry L, Baumard L, Choudhry N, Karmali Y, Bwakura-Dangarembizi M, Musiime V, Lutaakome J, Kekitiinwa A, Mutasa K, Szubert AJ, Spyer MJ, Deayton JR, Glass M, Geum HM, Pardieu C, Gibb DM, Klein N, Edens TJ, Walker AS, Manges AR , Prendergast AJ",Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation,Science translational medicine,2019,Experiment 1,Zimbabwe,Homo sapiens,feces,UBERON:0001988,"HIV infection,cotrimoxazole",EFO:0000764,stop cotrimoxazole prophylaxis,continue cotrimoxazole prophylaxis,HIV-positive and antiretroviral therapy (ART) treated children who were randomized to continue taking cotrimoxazole prophylaxis,36,36,NA,WMS,NA,Illumina,Zero-Inflated Beta Regression,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,Signature 4,"Text, Figure S2",7 November 2020,Michael Lutete,WikiWorks743,Fecal bacterial species that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis",2|976|200643|171549|171550|239759|328813;2|1239|186801|186802|186804|1505657|261299;2|201174|84998|1643822|1643826|84111|84112;2|1224|1236|135625|712|724|729;2|1239|91061|186826|1300|1301|1309;2|1239|91061|186826|1300|1301|1318;2|1239|91061|186826|1300|1301|1343,Complete,NA
Study 417,"cross-sectional observational, not case-control",30366816,10.1016/j.ebiom.2018.10.037,NA,"Moon JY, Zolnik CP, Wang Z, Qiu Y, Usyk M, Wang T, Kizer JR, Landay AL, Kurland IJ, Anastos K, Kaplan RC, Burk RD , Qi Q","Gut microbiota and plasma metabolites associated with diabetes in women with, or at high risk for, HIV infection",EBioMedicine,2018,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,"diabetes mellitus,HIV infection","EFO:0000400,EFO:0000764",Women without diabetes,Women with diabetes,Women with or at high risk for HIV infection who have diabetes,26,22,NA,16S,4,Illumina,Linear Regression,0.1,TRUE,NA,NA,"HIV infection,age",NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,"Text, Figure 2, Table 2",8 November 2020,Michael Lutete,WikiWorks743,Differentially abundant genera by diabetes status in women with HIV or at high risk for HIV,decreased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus",2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|165779,Complete,NA
Study 418,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D Auria G , Knobel H","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological non-responders assigned to treatment for 12 weeks,HIV-infected immunological non-responders (INR) who received S. boulardii probiotic,11,11,2 months,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure S1",14 November 2020,Michael Lutete,WikiWorks743,Saccharomyces boulardii produces changes in some gut bacterial communities,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|1239|909932|909929|1843491|158846;2|1224|28221|213115|194924|872,Complete,NA
Study 418,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D Auria G , Knobel H","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological non-responders assigned to treatment for 12 weeks,HIV-infected immunological non-responders (INR) who received S. boulardii probiotic,11,11,2 months,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure S1, Figure 3",14 November 2020,Michael Lutete,WikiWorks743,Saccharomyces boulardii produces changes in some gut bacterial communities,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",2|1239|186801|186802|31979;2|1239|526524|526525|2810280|135858,Complete,NA
Study 418,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D Auria G , Knobel H","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological responders assigned to treatment for 12 weeks,HIV-infected immunological responders (IR) who received S. boulardii probiotic,11,11,2 months,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Text, Figure S1",14 November 2020,Michael Lutete,WikiWorks743,Saccharomyces boulardii produces changes in some gut bacterial communities,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|1239|909932|909929|1843491|158846;2|1224|28221|213115|194924|872,Complete,NA
Study 418,randomized controlled trial,28388647,10.1371/journal.pone.0173802,NA,"Villar-García J, Güerri-Fernández R, Moya A, González A, Hernández JJ, Lerma E, Guelar A, Sorli L, Horcajada JP, Artacho A, D Auria G , Knobel H","Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial",PloS one,2017,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,immunological responders assigned to treatment for 12 weeks,HIV-infected immunological responders (IR) who received S. boulardii probiotic,11,11,2 months,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Text, Figure S1, Figure 3",14 November 2020,Michael Lutete,WikiWorks743,Saccharomyces boulardii produces changes in some gut bacterial communities,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",2|1239|186801|186802|31979;2|1239|526524|526525|2810280|135858,Complete,NA
Study 419,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg CJ, Vestad B, Hov JR, Pedersen KK, Jespersen S, Johannesen HH, Holm K, Halvorsen B, Fallentin E, Hansen AE, Lange T, Kjær A, Trøseid M, Fischer BM , Nielsen SD",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,combination antiretroviral therapy treated individuals after taking LGG probiotic for 8 weeks,Persons with HIV,27,27,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Text, Supplementary Figure 3",14 November 2020,Michael Lutete,WikiWorks743,Effect of Probiotic LGG on Gut Microbiota Composition,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|186801|186802|216572|1508657;2|1239|186801|186802|186803,Complete,NA
Study 419,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg CJ, Vestad B, Hov JR, Pedersen KK, Jespersen S, Johannesen HH, Holm K, Halvorsen B, Fallentin E, Hansen AE, Lange T, Kjær A, Trøseid M, Fischer BM , Nielsen SD",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,combination antiretroviral therapy treated individuals after taking LGG probiotic for 8 weeks,Persons with HIV,27,27,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Text, Supplementary Figure 3",14 November 2020,Michael Lutete,WikiWorks743,Effect of Probiotic LGG on Gut Microbiota Composition,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1224|1236|91347|543;2|1239|526524|526525|128827,Complete,NA
Study 419,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg CJ, Vestad B, Hov JR, Pedersen KK, Jespersen S, Johannesen HH, Holm K, Halvorsen B, Fallentin E, Hansen AE, Lange T, Kjær A, Trøseid M, Fischer BM , Nielsen SD",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,Experiment 2,Denmark,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,combination antiretroviral therapy naive individuals after taking LGG probiotic for 8 weeks,Persons with HIV,13,13,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Text, Supplementary Figure 3",14 November 2020,Michael Lutete,WikiWorks743,Effect of Probiotic LGG on Gut Microbiota Composition,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1224|1236|91347|543;2|1239|526524|526525|128827,Complete,NA
Study 419,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg CJ, Vestad B, Hov JR, Pedersen KK, Jespersen S, Johannesen HH, Holm K, Halvorsen B, Fallentin E, Hansen AE, Lange T, Kjær A, Trøseid M, Fischer BM , Nielsen SD",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,Experiment 2,Denmark,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,combination antiretroviral therapy naive individuals after taking LGG probiotic for 8 weeks,Persons with HIV,13,13,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 2,"Text, Supplementary Figure 3",14 November 2020,Michael Lutete,WikiWorks743,Effect of Probiotic LGG on Gut Microbiota Composition,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1224|1236|91347|543;2|1239|526524|526525|128827,Complete,NA
Study 419,prospective cohort,29874201,10.1097/QAI.0000000000001693,NA,"Arnbjerg CJ, Vestad B, Hov JR, Pedersen KK, Jespersen S, Johannesen HH, Holm K, Halvorsen B, Fallentin E, Hansen AE, Lange T, Kjær A, Trøseid M, Fischer BM , Nielsen SD",Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals,Journal of acquired immune deficiency syndromes (1999),2018,Experiment 3,Denmark,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,individuals with no change in uptake,individuals with decreased F-2-fluoro-2-deoxy-D-glucose (F-FDG) uptake on positron emission tomography (PET)/magnetic resonance imaging (MRI),Persons with HIV,7,5,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,"Text, Figure 2",14 November 2020,Michael Lutete,WikiWorks743,Changes in relative abundance of Enterobacteriaceae after LGG supplementation in responders and nonresponders,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,NA
Study 420,randomized controlled trial,26258571,10.1097/QAI.0000000000000784,NA,"Stiksrud B, Nowak P, Nwosu FC, Kvale D, Thalme A, Sonnerborg A, Ueland PM, Holm K, Birkeland SE, Dahm AE, Sandset PM, Rudi K, Hov JR, Dyrhol-Riise AM , Trøseid M",Reduced Levels of D-dimer and Changes in Gut Microbiota Composition After Probiotic Intervention in HIV-Infected Individuals on Stable ART,Journal of acquired immune deficiency syndromes (1999),2015,Experiment 1,"Norway,Sweden",Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,HIV-infected on antiretroviral therapy allocated to probiotic intervention,HIV-infected patients receiving antiretroviral therapy (ART) with HIV-RNA < 50 copies per milliliter for at least 6 months and CD4 count < 500 cell per microliter,11,11,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Text, Supplementary Table 1, Supplementary Figure 3, Figure 3",14 November 2020,Michael Lutete,WikiWorks743,Gut microbiota composition after probiotic intervention in HIV-infected individuals on stable antiretroviral therapy (ART),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia,k__Bacteria|p__Firmicutes",2|201174|1760|85004|31953|1678;2|201174|1760;2|1239,Complete,NA
Study 420,randomized controlled trial,26258571,10.1097/QAI.0000000000000784,NA,"Stiksrud B, Nowak P, Nwosu FC, Kvale D, Thalme A, Sonnerborg A, Ueland PM, Holm K, Birkeland SE, Dahm AE, Sandset PM, Rudi K, Hov JR, Dyrhol-Riise AM , Trøseid M",Reduced Levels of D-dimer and Changes in Gut Microbiota Composition After Probiotic Intervention in HIV-Infected Individuals on Stable ART,Journal of acquired immune deficiency syndromes (1999),2015,Experiment 1,"Norway,Sweden",Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,baseline,HIV-infected on antiretroviral therapy allocated to probiotic intervention,HIV-infected patients receiving antiretroviral therapy (ART) with HIV-RNA < 50 copies per milliliter for at least 6 months and CD4 count < 500 cell per microliter,11,11,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Text, Supplementary Table 1, Supplementary Figure 3, Figure 3",14 November 2020,Michael Lutete,WikiWorks743,Gut microbiota composition after probiotic intervention in HIV-infected individuals on stable antiretroviral therapy (ART),decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes",2|976|200643|171549|815|816;2|976,Complete,NA
Study 420,randomized controlled trial,26258571,10.1097/QAI.0000000000000784,NA,"Stiksrud B, Nowak P, Nwosu FC, Kvale D, Thalme A, Sonnerborg A, Ueland PM, Holm K, Birkeland SE, Dahm AE, Sandset PM, Rudi K, Hov JR, Dyrhol-Riise AM , Trøseid M",Reduced Levels of D-dimer and Changes in Gut Microbiota Composition After Probiotic Intervention in HIV-Infected Individuals on Stable ART,Journal of acquired immune deficiency syndromes (1999),2015,Experiment 2,"Norway,Sweden",Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,nonprobiotic intervention,HIV-infected on antiretroviral therapy allocated to probiotic intervention,HIV-infected patients receiving antiretroviral therapy (ART) with HIV-RNA < 50 copies per milliliter for at least 6 months and CD4 count < 500 cell per microliter,13,11,2 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Text, Supplementary Table 1, Supplementary Figure 3, Figure 3",15 November 2020,Michael Lutete,WikiWorks743,Gut microbiota composition after probiotic intervention in HIV-infected individuals on stable antiretroviral therapy (ART),increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 421,randomized controlled trial,32708743,10.3390/nu12072112,NA,"Sainz T, Gosalbes MJ, Talavera-Rodríguez A, Jimenez-Hernandez N, Prieto L, Escosa L, Guillén S, Ramos JT, Muñoz-Fernández MÁ, Moya A, Navarro ML, Mellado MJ , Serrano-Villar S",Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study,Nutrients,2020,Experiment 1,Spain,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,uninfected siblings or children born to HIV-infected mothers,Vertically HIV-infected children,Vertically HIV-infected children,10,23,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Text (results),26 November 2020,Michael Lutete,WikiWorks743,Comparison of basal samples from vertically HIV-infected children vs. healthy controls,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus",2|32066|203490|203491|203492|848;2|1239|526524|526525|2810280|100883,Complete,NA
Study 421,randomized controlled trial,32708743,10.3390/nu12072112,NA,"Sainz T, Gosalbes MJ, Talavera-Rodríguez A, Jimenez-Hernandez N, Prieto L, Escosa L, Guillén S, Ramos JT, Muñoz-Fernández MÁ, Moya A, Navarro ML, Mellado MJ , Serrano-Villar S",Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study,Nutrients,2020,Experiment 2,Spain,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,uninfected siblings or children born to HIV-infected mothers,Vertically HIV-infected children,Vertically HIV-infected children,12,12,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Text (results),26 November 2020,Michael Lutete,WikiWorks743,Comparison of basal samples from vertically HIV-infected children vs. healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803;2|1239|186801|186802|186803|189330;2|1239|186801|186802|31979|1485;2|1239|91061|186826|1300|1357,Complete,NA
Study 422,case-control,30518941,10.1038/s41598-018-35877-4,NA,"Kaur US, Shet A, Rajnala N, Gopalan BP, Moar P, D H, Singh BP, Chaturvedi R , Tandon R",High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy,Scientific reports,2018,Experiment 1,India,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,uninfected age-matched controls,Perinatally HIV-infected children,Perinatally HIV-infected children,14,29,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,age,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Text, Figure 1, Figure 3, Table S1",26 November 2020,Michael Lutete,WikiWorks743,Perinatally HIV-infected children show a distinct pattern of gut microbiota compared to uninfected controls,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales",2|976;2|203691;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|906;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|909932|909929|1843491|970;2|1239|186801|186802|31979|1485;2|32066|203490|203491|1129771;2|32066|203490|203491|1129771|32067;2|1224|1236|91347|1903409|53335;2|1224|1236|135624|84642;2|32066;2|32066|203490;2|32066|203490|203491,Complete,NA
Study 422,case-control,30518941,10.1038/s41598-018-35877-4,NA,"Kaur US, Shet A, Rajnala N, Gopalan BP, Moar P, D H, Singh BP, Chaturvedi R , Tandon R",High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy,Scientific reports,2018,Experiment 1,India,Homo sapiens,feces,UBERON:0001988,HIV infection,EFO:0000764,uninfected age-matched controls,Perinatally HIV-infected children,Perinatally HIV-infected children,14,29,1 month,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,age,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Text, Figure 1, Figure 3, Table S1",26 November 2020,Michael Lutete,WikiWorks743,Perinatally HIV-infected children show a distinct pattern of gut microbiota compared to uninfected controls,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Cyanobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria,k__Bacteria|p__Lentisphaerae,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales,k__Bacteria|p__Chloroflexi|c__Anaerolineae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Prosthecobacter,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales,k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Longilinea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Dehalobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales",2|1239;2|201174;2|1117;2|976|200643|171549|815;2|1239|186801|186802|541000;2|1239|186801|186802|186803;2|976|200643|171549|171550;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|1263;2|1224|1236|135625|712|724;2|1239|186801|186802|31979;2|256845|1313211;2|256845;2|256845|1313211|278082;2|200795|292625;2|74201|203494|48461|203557|48463;2|1224|28211|766;2|200795|292625|292629|292628|475961;2|1239|186801|186802|186807|51514;2|1239|186801|186802,Complete,NA
Study 423,case-control,32747678,10.1038/s41598-020-69845-8,https://pubmed.ncbi.nlm.nih.gov/32747678/,"Zeng Q, Shen J, Chen K, Zhou J, Liao Q, Lu K, Yuan J , Bi F",The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients,Scientific reports,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,amyotrophic lateral sclerosis,MONDO:0004976,Healthy controls,ALS patients,Patients clinically diagnosed with probably or definite ALS according to the revised El Escorial criteria in the neurology department.,20,20,NA,16S,4,Illumina,LEfSe,0.05,TRUE,4,age,age,NA,increased,increased,NA,NA,increased,Signature 1,Figure 2,14 January 2021,Fatima,Fatima,Biomarkers with differential abundance between Amyotrophic lateral sclerosis (ALS) patients and healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|976|200643|171549;2|976;2|976|200643;2|976|200643|171549|171551,Complete,NA
Study 423,case-control,32747678,10.1038/s41598-020-69845-8,https://pubmed.ncbi.nlm.nih.gov/32747678/,"Zeng Q, Shen J, Chen K, Zhou J, Liao Q, Lu K, Yuan J , Bi F",The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients,Scientific reports,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,amyotrophic lateral sclerosis,MONDO:0004976,Healthy controls,ALS patients,Patients clinically diagnosed with probably or definite ALS according to the revised El Escorial criteria in the neurology department.,20,20,NA,16S,4,Illumina,LEfSe,0.05,TRUE,4,age,age,NA,increased,increased,NA,NA,increased,Signature 2,Figure 2,14 January 2021,Fatima,Fatima,Biomarkers with differential abundance between Amyotrophic lateral sclerosis (ALS) patients and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|909929|1843491|158846;2|1239|909932;2|1239|909932|909929;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977,Complete,NA
Study 424,case-control,31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,Experiment 1,Israel,NA,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,Healthy control,PC,Patients presenting with pancreatic cancer. The diagnosis was verified by histological samples obtained by EUS or by postoperative pathological assessment.,13,30,8 weeks,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2a,4 February 2021,Yu Wang,"Yu Wang,Fatima",Bacterial taxa identified by LEfSe as differentiating between PC patients and healthy control subjects.,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|74201|203494|48461|1647988|239934;2|976|200643|171549;2|1239|909932|1843489|31977|906;2|976|200643|171549|1853231|283168;2|1239|909932|1843489|31977,Complete,NA
Study 424,case-control,31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,Experiment 1,Israel,NA,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,Healthy control,PC,Patients presenting with pancreatic cancer. The diagnosis was verified by histological samples obtained by EUS or by postoperative pathological assessment.,13,30,8 weeks,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2a,4 February 2021,Yu Wang,"Yu Wang,Fatima",Bacterial taxa identified by LEfSe as differentiating between PC patients and healthy control subjects.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|186801|186802|186803|207244;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|186802|541000;2|1239|186801|186802|216572|292632,Complete,NA
Study 424,case-control,31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,Experiment 2,Israel,NA,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,Healthy control,PC,Patients presenting with pancreatic cancer. The diagnosis was verified by histological samples obtained by EUS or by postoperative pathological assessment.,13,30,Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 424,case-control,31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,Experiment 3,Israel,Homo sapiens,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,NBO PC,BO PC,Bile duct-obstructed pancreatic cancer patients.,16,11,Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3b,4 February 2021,Yu Wang,"Yu Wang,Fatima",Taxa identified by LEfSe as differentiating between BO PC and NBO PC patients.,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,2|1239|186801|186802|186803|572511,Complete,NA
Study 424,case-control,31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,Experiment 3,Israel,Homo sapiens,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,NBO PC,BO PC,Bile duct-obstructed pancreatic cancer patients.,16,11,Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3b,4 February 2021,Yu Wang,"Yu Wang,Fatima",Taxa identified by LEfSe as differentiating between BO PC and NBO PC patients.,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1239|909932|909929;2|1239|909932|1843489|31977,Complete,NA
Study 424,case-control,31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,Experiment 4,Israel,NA,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,Healthy control,NBO PC,Non-Bile duct-obstructed pancreatic cancer patients.,13,16,Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3c,4 February 2021,Yu Wang,"Yu Wang,Fatima","Taxa identified by LEfSe as differentiating between healthy controls and “pure”, NBO PC patients.",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1239|186801|186802|216572|216851;2|1239|186801|186802|541000,Complete,NA
Study 424,case-control,31727922,10.1038/s41598-019-53041-4,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856127/,"Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM , Gophna U",Fecal microbiome signatures of pancreatic cancer patients,Scientific reports,2019,Experiment 4,Israel,NA,feces,UBERON:0001988,pancreatic carcinoma,EFO:0002618,Healthy control,NBO PC,Non-Bile duct-obstructed pancreatic cancer patients.,13,16,Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.,16S,NA,Illumina,LEfSe,0.05,FALSE,3,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3c,4 February 2021,Yu Wang,"Yu Wang,Fatima","Taxa identified by LEfSe as differentiating between healthy controls and “pure”, NBO PC patients.",increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|74201|203494|48461|1647988|239934;2|976|200643|171549,Complete,NA
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,34,38,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2c,17 February 2021,Manuela,Manuela,NA,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,34,38,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2c,17 February 2021,Manuela,Manuela,NA,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Verrucomicrobia",2|976;2|74201,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Hypertensive at Middle Altitude (MHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,49,38,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2g,17 February 2021,Manuela,Manuela,NA,decreased,"k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Proteobacteria",2|95818;2|1224,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Hypertensive at Middle Altitude (MHH),Tibetan Hypertensive at High Altitude (HTH),Tibetan participants with hypertension living at high altitudes.,49,38,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2g,17 February 2021,Manuela,Manuela,NA,increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Tibetan Healthy at High Altitude (HTN),Tibetan healthy participants living at high altitudes.,35,34,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2d,17 February 2021,Manuela,Manuela,NA,decreased,"k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria",2|95818;2|32066;2|1224,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Tibetan Healthy at High Altitude (HTN),Tibetan healthy participants living at high altitudes.,35,34,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 2d,17 February 2021,Manuela,Manuela,NA,increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Healthy at Middle Altitude (MHN),Tibetan Healthy at High Altitude (HTN),Tibetan healthy participants living at high altitudes.,35,34,3 months,16S,34,Illumina,T-Test,0.05,FALSE,NA,"age,sex",NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 2h,17 February 2021,Manuela,Manuela,NA,decreased,k__Bacteria|p__Candidatus Saccharibacteria,2|95818,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Han Hypertensive at Middle Altitude (MHH),Han hypertensive participants living at middle altitude.,34,49,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2e,17 February 2021,Manuela,Manuela,NA,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Hypertensive at Low Altitude (LHH),Han Hypertensive at Middle Altitude (MHH),Han hypertensive participants living at middle altitude.,34,49,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2e,17 February 2021,Manuela,Manuela,NA,increased,"k__Bacteria|p__Acidobacteria,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Tenericutes,k__Bacteria|p__Verrucomicrobia",2|57723;2|976;2|95818;2|544448;2|74201,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 6,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Han Healthy at Middle Altitude (MHN),Han healthy participants living at middle altitude.,35,35,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2f,17 February 2021,Manuela,Manuela,NA,increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Lwaldron
Study 425,case-control,33294219,10.1155/2020/1957843,NA,"Zhu LL, Ma ZJ, Ren M, Wei YM, Liao YH, Shen YL, Fan SM, Li L, Wu QX, Gao ZS, Song JF , Ma YL",Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients,Cardiology research and practice,2020,Experiment 6,China,Homo sapiens,feces,UBERON:0001988,hypertension,EFO:0000537,Han Healthy at Low Altitude (LHN),Han Healthy at Middle Altitude (MHN),Han healthy participants living at middle altitude.,35,35,3 months,16S,34,Illumina,T-Test,0.05,NA,NA,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2f,17 February 2021,Manuela,Manuela,NA,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Fusobacteria",2|1239;2|32066,Complete,Lwaldron
Study 426,"cross-sectional observational, not case-control",31201284,10.1136/gutjnl-2018-317836,NA,"Wei Y, Li Y, Yan L, Sun C, Miao Q, Wang Q, Xiao X, Lian M, Li B, Chen Y, Zhang J, Li Y, Huang B, Li Y, Cao Q, Fan Z, Chen X, Fang JY, Gershwin ME, Tang R , Ma X",Alterations of gut microbiome in autoimmune hepatitis,Gut,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Autoimmune Hepatitis,EFO:0005676,healthy controls,autoimmune hepatits cases,The diagnosis of AIH was made if patients conformed with (1) 1999 revised International Autoimmune Hepatitis Group (IAIHG) score ≥10 and/or (2) 2008 IAIHG simplified AIH score ≥6 and/or (3) histological features indicative of AIH.,98,91,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Figure 2,25 February 2021,Valentina,Valentina,LDA effect size analysis of 11 genera was significantly different between AIH and the control group.,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 426,"cross-sectional observational, not case-control",31201284,10.1136/gutjnl-2018-317836,NA,"Wei Y, Li Y, Yan L, Sun C, Miao Q, Wang Q, Xiao X, Lian M, Li B, Chen Y, Zhang J, Li Y, Huang B, Li Y, Cao Q, Fan Z, Chen X, Fang JY, Gershwin ME, Tang R , Ma X",Alterations of gut microbiome in autoimmune hepatitis,Gut,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Autoimmune Hepatitis,EFO:0005676,healthy controls,autoimmune hepatits cases,The diagnosis of AIH was made if patients conformed with (1) 1999 revised International Autoimmune Hepatitis Group (IAIHG) score ≥10 and/or (2) 2008 IAIHG simplified AIH score ≥6 and/or (3) histological features indicative of AIH.,98,91,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Figure 2,3 March 2021,Valentina,Valentina,LDA effect size analysis of 11 genera was significantly different between AIH and the control group.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1239|186801|186802|186803|33042;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288,Complete,NA
Study 426,"cross-sectional observational, not case-control",31201284,10.1136/gutjnl-2018-317836,NA,"Wei Y, Li Y, Yan L, Sun C, Miao Q, Wang Q, Xiao X, Lian M, Li B, Chen Y, Zhang J, Li Y, Huang B, Li Y, Cao Q, Fan Z, Chen X, Fang JY, Gershwin ME, Tang R , Ma X",Alterations of gut microbiome in autoimmune hepatitis,Gut,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,Autoimmune Hepatitis,EFO:0005676,healthy controls,autoimmune hepatits cases,The diagnosis of AIH was made if patients conformed with (1) 1999 revised International Autoimmune Hepatitis Group (IAIHG) score ≥10 and/or (2) 2008 IAIHG simplified AIH score ≥6 and/or (3) histological features indicative of AIH.,98,91,NA,16S,34,Illumina,Logistic Regression,0.05,FALSE,NA,"age,body mass index,sex","age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 427,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW , Ercolini D",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,vegetarians,omnivores,NA,51,51,3 months,16S,123,Roche454,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",NA,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Figure S3A – Microbiota structure in the three diet types.,11 February 2021,Lorakasselman,Lorakasselman,Pie charts of the family level microbiota. Only taxa with an average relative abundance higher than 0.5% are shown and the class level assignment is reported when family level was not reached. Outer circle shows the phylum level assignment,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976;2|976|200643|171549|171552,Complete,NA
Study 427,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW , Ercolini D",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,vegans,omnivores,NA,51,51,3 months,16S,123,Roche454,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",NA,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure S3A – Microbiota structure in the three diet types.,11 February 2021,Lorakasselman,Lorakasselman,"Microbiota structure in the three diet types. Pie charts of the family level
microbiota. Only taxa with an average relative abundance higher than 0.5% are shown
and the class level assignment is reported when family level was not reached. Outer
circle shows the phylum level assignment",decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976;2|976|200643|171549|171552,Complete,NA
Study 427,prospective cohort,26416813,10.1136/gutjnl-2015-309957,NA,"De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW , Ercolini D",High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome,Gut,2016,Experiment 3,Italy,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,vegans,vegetarians,NA,51,51,3 months,16S,123,Roche454,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",NA,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs,78,87,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 2,28 May 2021,Claregrieve1,Claregrieve1,Differential bacterial species abundance between COVID-19 samples and non-COVID-19 samples,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila",2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|909656|821;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186803|2316020|33039;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|47678;2|74201|203494|48461|1647988|239934|239935,Complete,Fatima
Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs,78,87,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 2,28 May 2021,Claregrieve1,Claregrieve1,Differential bacterial species abundance between COVID-19 samples and non-COVID-19 samples,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rectale CAG:36,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus obeum CAG:39,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans",2|201174|1760|85004|31953|1678|1680;2|1239|186801|186802|186806|1730|1263079;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|292632;2|201174|1760|85004|31953|1678|28026;2|1239|186801|186802|216572|216851|853;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|216572|1263|1263107;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|186803|189330|39486,Complete,Fatima
Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs,78,13,Patients whose COVID-19 treatment included antibiotics were excluded,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,30 May 2021,Claregrieve1,Claregrieve1,Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from non-antibiotic-treated patients with COVID-19 after recovery,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum",2|201174|1760|85004|31953|1678|1689;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|186803|2719313|208479;2|1239|91061|186826|33958|2767887|1623;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|2005525|375288|1869337;2|976|200643|171549|171552|838|165179;2|1239|186801|186802|216572|1263|457412;2|1239|91061|186826|1300|1301|1304;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|186803|1506553|1512,Complete,Fatima
Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs,78,13,Patients whose COVID-19 treatment included antibiotics were excluded,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,30 May 2021,Claregrieve1,Claregrieve1,Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from non-antibiotic-treated patients with COVID-19 after recovery,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rectale CAG:36,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus obeum CAG:39,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|976|200643|171549|171550|239759|28117;2|201174|1760|85004|31953|1678|216816|1679;2|201174|1760|85004|31953|1678|28026;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186806|1730|1263079;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|1263|1263107;2|1239|186801|186802|216572|292632,Complete,Fatima
Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,"Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs, treated with antibiotics during course of COVID-19",78,14,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,30 May 2021,Claregrieve1,Claregrieve1,Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from antibiotic-treated patients with COVID-19 after recovery,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus ruminis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula",2|201174|1760|85004|31953|1678|1689;2|1239|91061|186826|33958|2767887|1623;2|976|200643|171549|2005525|375288|823;2|1239|91061|186826|81852|1350|1351;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186803|2719313|208479;2|1239|186801|186802|186803|1506553|1512;2|1239|909932|1843489|31977|29465|29466,Complete,Fatima
Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 cases,"Recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs, treated with antibiotics during course of COVID-19",78,14,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3,30 May 2021,Claregrieve1,Claregrieve1,Differences in gut microbiome bacterial species between feces samples from healthy controls and samples from antibiotic-treated patients with COVID-19 after recovery,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rectale CAG:36,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus obeum CAG:39,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii",2|1239|186801|186802|186806|1730|1263079;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|216851|853;2|201174|1760|85004|31953|1678|28026;2|1239|186801|186802|216572|292632;2|201174|84998|84999|84107|102106|74426;2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|186802|216572|1263|457412;2|1239|186801|186802|216572|1263|1263107;2|976|200643|171549|171552|838|165179;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|189330|88431;2|976|200643|171549|171550|239759|28117;2|1239|91061|186826|1300|1301|1304;2|1239|186801|186802|186803|2569097|39488,Complete,Fatima
Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients treated with antibiotics,"Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs, treated with antibiotics",78,34,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S3,11 June 2021,Claregrieve1,Claregrieve1,Differential bacterial species abundance between COVID-19 samples from patients were treated with antibiotics and non-COVID-19 samples,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus obeum CAG:39,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium leptum CAG:27,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.",2|201174|1760|85004|31953|1678|1680;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|1263|1263107;2|1239|186801|186802|216572|292632|2053618;2|1224|1236|91347|543|570|573;2|201174|84998|1643822|1643826|447020|446660;2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|31979|1485|1263068;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|216572|292632|665956;2|1239|91061|186826|81852|1350|33945;2|1239|186801|186802|186806|1730|39496;2|1224|1236|91347|543|544|1896336,Complete,Fatima
Study 428,case-control,33431578,10.1136/gutjnl-2020-323020,NA,"Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK , Ng SC",Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19,Gut,2021,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients treated with antibiotics,"Laboratory-confirmed SARS-CoV-2 positive by quantitative reverse transcription PCR performed on nasopharyngeal swabs, treated with antibiotics",78,34,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S3,11 June 2021,Claregrieve1,Claregrieve1,Differential bacterial species abundance between COVID-19 samples from patients were treated with antibiotics and non-COVID-19 samples,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia inopinata,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium|s__Cryptobacterium curtum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia|s__Shuttleworthia satelles,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Parascardovia|s__Parascardovia denticolens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus gallinarum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum sp. ICM7,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 078,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella profusa,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides sp.",2|1239|186801|186802|186803|2569097|39488;2|976|200643|171549|815|816|47678;2|976|200643|171549|815|816|28116;2|1239|186801|186802|216572|1263|457412;2|201174|1760|85004|31953|196081|78259;2|201174|1760|85009|31957|1912216|1747;2|201174|84998|1643822|1643826|84162|84163;2|1239|186801|186802|186803|177971|177972;2|201174|1760|85004|31953|196082|78258;2|1239|91061|186826|81852|1350|1353;2|1239|186801|186802|186803|1164882|936594;2|1239|186801|186802|186803|265975|652706;2|1239|186801|186802|186803|658089;2|201174|84998|1643822|1643826|84108|2049041;2|201174|84998|84999|1643824|133925|138595;2|1239|186801|186802|186803|33042|116085;2|201174|84998|84999|1643824|2767353|1383;2|1239|91061|1385|90964|1279|1280;2|201174|1760|85006|1268|32207|172042;2|1239|91061|186826|186827|46123|46125;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|186803|1213720|796942;2|1239|91061|1385|90964|1279|1282;2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|186806|1730|39490;2|201174|1760|85004|31953|196081|230143;2|1224|28216|80840|995019|40544|40545;2|976|200643|171549|171550|239759|328813;2|1239|526524|526525|2810280|100883;2|201174|84998|84999|1643824|133925|133926;2|976|200643|171549|2005525|375288|1869337,Complete,Fatima
Study 430,prospective cohort,32690600,10.1136/gutjnl-2020-322294,NA,"Zuo T, Liu Q, Zhang F, Lui GC, Tso EY, Yeoh YK, Chen Z, Boon SS, Chan FK, Chan PK , Ng SC",Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19,Gut,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Patients with low-to-none SARS CoV-2 infectivity,Patients with high SARS CoV-2 infectivity,SARS CoV-2 infection confirmed by two consecutive RT-OCR tests. High SARS-CoV2 infectivity defined as higher 3' vs 5' end coverage of SARS CoV-2 genome in fecal viral RNA metagenome.,15,15,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,4 March 2021,Fatima,"Fatima,Claregrieve1",Differential bacterial species and functional capacities between feces with high severe acute respiratory syndrome coronavirus 2 infectivity and feces with low to-none SARS-CoV-2 infectivity,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium",2|976|200643|171549|815|816|46506;2|976|200643|171549|2005525|375288|46503;2|1239|186801|186802|186803|1898203,Complete,NA
Study 430,prospective cohort,32690600,10.1136/gutjnl-2020-322294,NA,"Zuo T, Liu Q, Zhang F, Lui GC, Tso EY, Yeoh YK, Chen Z, Boon SS, Chan FK, Chan PK , Ng SC",Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19,Gut,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Patients with low-to-none SARS CoV-2 infectivity,Patients with high SARS CoV-2 infectivity,SARS CoV-2 infection confirmed by two consecutive RT-OCR tests. High SARS-CoV2 infectivity defined as higher 3' vs 5' end coverage of SARS CoV-2 genome in fecal viral RNA metagenome.,15,15,NA,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,4 March 2021,Fatima,"Fatima,Claregrieve1",Differential bacterial species and functional capacities between feces with high severe acute respiratory syndrome coronavirus 2 infectivity and feces with low to-none SARS-CoV-2 infectivity,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella|s__Morganella morganii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella tanakaei",2|201174|84998|84999|84107|102106|74426;2|1224|1236|91347|1903414|581|582;2|1239|91061|186826|1300|1301|68892;2|201174|84998|84999|84107|102106|626935,Complete,NA
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 1,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,persistent HPV+ with LSIL,persistent HPV+ with HSIL,persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3A,18 March 2021,Cynthia Anderson,"Cynthia Anderson,Fatima",Differential florae types in the comparison of the microbiota between high-risk human papillomavirus (HPV) persistent infection higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Commensalibacter,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Pseudoduganella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Actinobacteria|c__Thermoleophilia|o__Solirubrobacterales|f__Solirubrobacteraceae|g__Solirubrobacter,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Stappiaceae|g__Stappia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",2|1224|28216|80840|506|222;2|1224|28216|80840|80864|283;2|1224|28211|204441|433|1079922;2|1239|1737404|1737405|1570339|162290;2|1224|1236|135619|28256|2745;2|1239|91061|186826|1300|1357;2|1239|91061|186826|33958|1243;2|1224|1236|135614|32033|68;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045|407;2|201174|1760|85009|85015|1839;2|1224|28211|204455|31989|265;2|1239|909932|1843488|909930|33024;2|1224|28216|80840|75682|1522432;2|1224|1236|72274|135621|286;2|201174|1497346|588673|320599|207599;2|1224|28211|356|2821832|152161;2|1239|186801|186802|186803|84036;2|1297|188787|68933|188786|270,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 2,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with LSIL,transient HPV+ with HSIL,high-risk HPV transient infection (HPV has regressed within 1 year) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3B,19 March 2021,Cynthia Anderson,Cynthia Anderson,comparison of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] innocuum",2|1224|1236|135614|32033;2|1239|526524|526525|128827|1505663|1522,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 3,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,transient HPV+ with LSIL,high-risk HPV transient infection (HPV has regressed within 1 year) with low grade squamus intraepithelial lesion,31,NA,NA,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3C,19 March 2021,Cynthia Anderson,Cynthia Anderson,Comparison of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group,decreased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] innocuum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella",2|32066|203490|203491|1129771|168808;2|1239|186801|186802|186803|177971;2|1239|909932|1843489|31977|29465;2|1239|526524|526525|128827|1505663|1522;2|1239|909932|1843489|31977|906;2|1224|28211|356|2831106|46913;2|1224|1236|135614|32033;2|201174|1760|85004|31953|2701,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 4,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,persistent HPV+ with HSIL,high-risk HPV persistent infection with high grade squamus intraepithelial lesion,31,NA,NA,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3D,19 March 2021,Cynthia Anderson,"Cynthia Anderson,Fatima",Comparison of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|1239|909932|1843489|31977|906;2|1239|186801|186802|186804|1257;2|1239|186801|186802|186803|177971;2|32066|203490|203491|1129771|168808,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 5,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,persistent HPV+ with LSIL,persistent HPV+ with HSIL,persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4A,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,2|1239|91061|186826|1300|1301|1311,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 5,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,persistent HPV+ with LSIL,persistent HPV+ with HSIL,persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4A,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuberculostearicum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Pseudarthrobacter|s__Pseudarthrobacter oxydans,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Deinococcus-Thermus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Nitrosomonadales|f__Nitrosomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus coxii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|1239|186801|186802|216572|216851;2|1239|91061|1385|186818;2|201174|1760|85007|1653|1716|38304;2|201174|1760|85007|2805586|1847725;2|1239|526524|526525;2|201174|1760|85006|1268;2|201174|1760|85006|1268|1742993|1671;2|201174|1760|85007|1653|1716|169292;2|1239|1737404|1737405|1570339|162289;2|201174|1760|2037|2049;2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|186803|2316020|33039;2|976|200643|171549|171552|838|28130;2|201174|1760|85007|85025;2|1239|909932|1843489|31977|39948;2|1297;2|201174|1760|2037;2|976|200643|171549|171552|838;2|201174|1760|85004|31953|2701;2|1297|188787;2|1239|91061|186826|33958|1243;2|1224|28216|32003|206379;2|1224|1236|135614;2|1239|186801|186802|404402;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289|755172;2|201174|1760|85004|31953|1678|1689;2|1239|91061|1385|90964|1279;2|1239|91061|1385|90964|1279|1280;2|1239|91061|1385|90964;2|1239|91061|1385;2|1239|91061|186826|81852|1350|53345;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852;2|1239|91061|186826|33958|2767887|1624;2|1239|909932|1843489|31977|39948|309120;2|1239|909932|909929;2|1239|909932;2|201174|1760|85004|31953;2|201174|1760|85004;2|1239|91061|186826|1300,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 6,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with HSIL,persistent HPV+ with LSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4B,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,2|1239|186801|186802|186803|2316020|33039,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 6,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with HSIL,persistent HPV+ with LSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4B,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Eukaryota|k__Metazoa|p__Nematoda|c__Enoplea|o__Trichinellida|f__Trichinellidae|g__Trichinella|s__Trichinella pseudospiralis,k__Bacteria|p__Firmicutes|c__Negativicutes|g__Quinella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium gelidilacus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides faecis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Azonexaceae|g__Dechloromonas",2|976|200643|171549|171551|836;2759|33208|6231|119088|6329|6332|6333|6337;2|1239|909932|1567;2|1239|186801|186802|186803|1506577;2|976|117743|200644|49546|237|206041;2|976|200643|171549|2005525|375288|1217282;2|1224|28216|206389|2008795|73029,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 7,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,transient HPV+ with LSIL,transient HPV+ with HSIL,high-risk HPV transient infection with high grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4C,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk HPV transient infection with HSIL group and high-risk HPV transient infection with LSIL group,increased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Rhodanobacteraceae|g__Dyella|s__Dyella koreensis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium|s__Flavobacterium gelidilacus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Rhodanobacteraceae|g__Dyella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides faecis",2|976|117743;2|976|117743|200644;2|976|117743|200644|2762318|501783;2|1239|91061|186826|33958|1578;2|1224|1236|135614|1775411|231454|311235;2|976|117743|200644|49546|237|206041;2|1224|1236|135614|1775411|231454;2|976|200643|171549|2005525|375288|1217282,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 8,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,transient HPV+ with LSIL,high-risk HPV transient infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4D,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group,decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Devosia|s__Devosia riboflavina,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1224|28211|356|2831106|46913|46914;2|95818;2|32066|203490|203491|1129771|168808;2|1239|91061|186826|33958|1578;2|1224|1236|72274|135621|286;2|1239|186801|186802|186803|177971;2|32066|203490|203491|1129771;2|1239|186801|186802|541000;2|1224|1236|72274|135621,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 9,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,persistent HPV+ with HSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4E,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group,increased,"k__Bacteria|p__Actinobacteria|c__Thermoleophilia|o__Solirubrobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella",2|201174|1497346|588673;2|1224|1236|91347|1903414|581,Complete,Fatima
Study 431,"cross-sectional observational, not case-control",33241010,10.21037/atm-20-5832,https://pubmed-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/33241010/,"Liu J, Luo M, Zhang Y, Cao G , Wang S",Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition,Annals of translational medicine,2020,Experiment 9,China,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,HPV-,persistent HPV+ with HSIL,high-risk HPV persistent infection with low grade squamus intraepithelial lesion,NA,NA,NA,16S,NA,Illumina,LEfSe,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4E,19 March 2021,Cynthia Anderson,Cynthia Anderson,Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus equicursoris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|39948;2|1239|91061|186826|33958|1578|420645;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544;2|1239|186801|186802|186804|1257;2|1224|1236|72274|135621|286;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171552|838|28130;2|1239|186801|186802|541000,Complete,Fatima
Study 432,"cross-sectional observational, not case-control",33490017,10.3389/fpubh.2020.587298,NA,"Wei ZT, Chen HL, Wang CF, Yang GL, Han SM , Zhang SL",Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection,Frontiers in public health,2020,Experiment 1,China,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by Hybrid Capture II assay,30,30,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 1,Figure 2E,19 March 2021,Cynthia Anderson,Cynthia Anderson,Bacterial taxa analysis of the HPV-positive and HPV-negative groups.,increased,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,2|544448|31969|2085|2092|2093,Complete,NA
Study 432,"cross-sectional observational, not case-control",33490017,10.3389/fpubh.2020.587298,NA,"Wei ZT, Chen HL, Wang CF, Yang GL, Han SM , Zhang SL",Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection,Frontiers in public health,2020,Experiment 1,China,Homo sapiens,vagina,UBERON:0000996,human papilloma virus infection,EFO:0001668,HPV-,HPV+,HPV+ confirmed by Hybrid Capture II assay,30,30,2 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,unchanged,Signature 2,Figure 2E,19 March 2021,Cynthia Anderson,Cynthia Anderson,Bacterial taxa analysis of the HPV-positive and HPV-negative groups.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Sporolactobacillaceae|g__Sporolactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales",2|1239|91061|1385|186821;2|1239|91061|1385|186821|2077;2|1239|91061;2|1239|91061|186826,Complete,NA
Study 433,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC7912413/,"Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO , Shin JH",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,Experiment 1,South Korea,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,healthy controls,CIN 2+,Patients with cervical intraepithelial neoplasia 2 or higher,7,8,NA,16S,3,Ion Torrent,LEfSe,0.05,FALSE,7,NA,NA,NA,increased,NA,increased,NA,increased,Signature 1,Figure 2F,19 March 2021,Cynthia Anderson,Cynthia Anderson,Comparative analysis of vaginal microbiota profiles,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,2|201174|1760|85004|31953|2701,Complete,NA
Study 433,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC7912413/,"Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO , Shin JH",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,Experiment 1,South Korea,Homo sapiens,vagina,UBERON:0000996,cervical glandular intraepithelial neoplasia,EFO:1000165,healthy controls,CIN 2+,Patients with cervical intraepithelial neoplasia 2 or higher,7,8,NA,16S,3,Ion Torrent,LEfSe,0.05,FALSE,7,NA,NA,NA,increased,NA,increased,NA,increased,Signature 2,Figure 2F,19 March 2021,Cynthia Anderson,Cynthia Anderson,Comparative analysis of vaginal microbiota profiles,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239|91061|186826,Complete,NA
Study 433,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC7912413/,"Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO , Shin JH",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,Experiment 2,South Korea,Homo sapiens,vagina,UBERON:0000996,cervical cancer,MONDO:0002974,healthy controls,cervical cancer,Patients with cervical cancer,7,8,NA,16S,3,Ion Torrent,LEfSe,0.05,FALSE,7,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 1,Figure 2F,19 March 2021,Cynthia Anderson,Cynthia Anderson,Comparative analysis of vaginal microbiota profiles,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia",2|1239|91061|186826|1300|1301;2|1239|91061|186826|1300;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|165779;2|1239|186801;2|1239|1737404|1737405;2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|976|200643|171549;2|976|200643,Complete,NA
Study 433,"cross-sectional observational, not case-control",33572693,10.3390/microorganisms9020294,https://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/pmc/articles/PMC7912413/,"Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO , Shin JH",Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study,Microorganisms,2021,Experiment 2,South Korea,Homo sapiens,vagina,UBERON:0000996,cervical cancer,MONDO:0002974,healthy controls,cervical cancer,Patients with cervical cancer,7,8,NA,16S,3,Ion Torrent,LEfSe,0.05,FALSE,7,NA,NA,NA,unchanged,NA,unchanged,NA,increased,Signature 2,Figure 2F,19 March 2021,Cynthia Anderson,Cynthia Anderson,Comparative analysis of vaginal microbiota profiles,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales",2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239|91061|186826,Complete,NA
Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,Experiment 1,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,human papilloma virus infection,EFO:0001668,healthy control,HPV +,HPV-infected women without CIN confirmed by HPV genotyping test and examination,68,78,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,2|1239|909932|1843489|31977|906,Complete,NA
Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,Experiment 1,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,human papilloma virus infection,EFO:0001668,healthy control,HPV +,HPV-infected women without CIN confirmed by HPV genotyping test and examination,68,78,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae",2|201174|84998|84999|1643824|1380;2|1239|91061;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|201174|1760|2037|2049|2767327|82135,Complete,NA
Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,Experiment 2,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,cervical glandular intraepithelial neoplasia,EFO:1000165,healthy control,LSIL,women with low-grade squamous intraepithelial lesions confirmed by biopsy,78,51,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,2|976|200643|171549|171552|838|419005,Complete,NA
Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,Experiment 2,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,cervical glandular intraepithelial neoplasia,EFO:1000165,healthy control,LSIL,women with low-grade squamous intraepithelial lesions confirmed by biopsy,78,51,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,increased,NA,NA,NA,Signature 2,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups.,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae",2|201174|84998|84999|1643824|1380;2|1239|91061;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|201174|1760|2037|2049|2767327|82135,Complete,NA
Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,Experiment 3,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,cervical glandular intraepithelial neoplasia,EFO:1000165,healthy control,HSIL,women with high-grade squamous intraepithelial lesions confirmed by biopsy,68,23,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis",2|976|200643|171549|171552|838;2|1239|186801;2|1239|186801|186802;2|976|200643|171549|171552;2|1239|186801|186802|186803;2|1239|186801|186802|186803|177971;2|1239|91061|186826|1300;2|976|200643|171549|171552|838|386414,Complete,NA
Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,Experiment 3,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,cervical glandular intraepithelial neoplasia,EFO:1000165,healthy control,HSIL,women with high-grade squamous intraepithelial lesions confirmed by biopsy,68,23,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae",2|201174|84998|84999|1643824|1380;2|1239|91061;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|201174|1760|2037|2049|2767327|82135,Complete,NA
Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,Experiment 4,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,cervical cancer,MONDO:0002974,healthy control,cervical cancer,women with cervical cancer confirmed by biopsy,68,9,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Oceanobacillus|s__Oceanobacillus profundus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis",2|1239|91061|1385;2|32066|203490|203491;2|32066|203490;2|32066;2|1239|91061|1385|186817;2|1224;2|1239|91061|1385|186817|1386;2|976|200643;2|976|200643|171549;2|976;2|1224|28216;2|32066|203490|203491|1129771|168808;2|32066|203490|203491|1129771;2|1224|28216|80840|80864;2|1224|28216|80840;2|1224|28216|80840|80864|12916;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492;2|1239|91061|1385|186817|182709;2|1239|91061|1385|186817|182709|372463;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|1239|909932|1843489|31977;2|1239|909932;2|1239|909932|909929;2|1239|186801|186802;2|1239|1737404|1737405|1570339|165779;2|976|200643|171549|171551|836|281920,Complete,NA
Study 434,"cross-sectional observational, not case-control",32842982,0.1186/s12879-020-05324-9,NA,"Chen Y, Qiu X, Wang W, Li D, Wu A, Hong Z, Di W , Qiu L",Human papillomavirus infection and cervical intraepithelial neoplasia progression are associated with increased vaginal microbiome diversity in a Chinese cohort,BMC infectious diseases,2020,Experiment 4,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,cervical cancer,MONDO:0002974,healthy control,cervical cancer,women with cervical cancer confirmed by biopsy,68,9,14 days,16S,34,Illumina,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,The unique taxa and microbiomarkers for different groups,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae",2|201174|84998|84999|1643824|1380;2|1239|91061;2|201174|84998|84999|84107;2|201174|84998|84999;2|1239;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|201174|1760|2037|2049|2767327|82135,Complete,NA
Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,Experiment 1,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,5,6,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,LEfSe Analysis. A: LDA value distribution histogram,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas leidyi,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprocola,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium papyrosolvens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1224;2|1224|28211;2|201174;2|1239|186801;2|1239|186801|186802;2|1224|28211|356;2|976;2|976|200643;2|1224|1236;2|1224|28211|356|82115;2|1224|28211|356|69277|28100;2|1239|909932|1843489|31977;2|976|200643|171549;2|976|200643|171549|171552;2|1224|28211|204457;2|1224|28211|204457|41297;2|1224|28211|204457|41297|13687;2|1239|1737404|1737405|1570339|165779;2|1224|28211|204457|41297|13687|68569;2|976|200643|171549|171552|838;2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|976|200643|171549|815|909656|310298;2|1224|28216|80840|119060;2|1239|186801|186802|216572|1508657|29362;2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|162289,Complete,NA
Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,Experiment 1,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+ persistence,HPV infection of the same type that lasts for more than 12 months,5,6,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,LEfSe Analysis. A: LDA value distribution histogram,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes",2|1239|91061|186826|33958|1578;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061;2|1239,Complete,NA
Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,Experiment 2,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+ transient,HPV infection cleared within 12 months,5,4,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,LEfSe Analysis. A: LDA value distribution histogram,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,2|1239|91061|186826|33958|1578|147802,Complete,NA
Study 435,"cross-sectional observational, not case-control",33207260,10.1016/j.micpath.2020.104617,NA,"Qingqing B, Jie Z, Songben Q, Juan C, Lei Z , Mu X",Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection,Microbial pathogenesis,2021,Experiment 2,China,Homo sapiens,uterine cervix,UBERON:0000002,human papilloma virus infection,EFO:0001668,HPV-,HPV+ transient,HPV infection cleared within 12 months,5,4,1 month,16S,4,Ion Torrent,LEfSe,0.05,TRUE,4,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5,20 March 2021,Cynthia Anderson,Cynthia Anderson,LEfSe Analysis. A: LDA value distribution histogram,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes",2|1239|91061|186826;2|1239|91061|186826|33958;2|1239|91061|186826|33958|1578;2|1239|91061;2|1239,Complete,NA
Study 436,"cross-sectional observational, not case-control",32941440,10.1371/journal.pone.0238705,NA,"So KA, Yang EJ, Kim NR, Hong SR, Lee JH, Hwang CS, Shim SH, Lee SJ , Kim TJ",Changes of vaginal microbiota during cervical carcinogenesis in women with human papillomavirus infection,PloS one,2020,Experiment 1,South Korea,Homo sapiens,Vaginal fluid,UBERON:0036243,cervical glandular intraepithelial neoplasia,EFO:1000165,healthy control,CIN2+/cervical cancer,patients with cervical intraepithelial neoplasia 2+ or cervical cancer confirmed by biopsy,10,20,NA,16S,34,Illumina,NA,0.05,NA,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 2,21 March 2021,Cynthia Anderson,Cynthia Anderson,The species-specific risk for cervical disease with CIN 2 or 3 and cervical cancer,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea|s__Fannyhessea vaginae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella timonensis",2|201174|1760|2037|2049|2767327|82135;2|1239|909932|1843489|31977|39948|218538;2|1239|1737404|1737405|1570339|150022|1260;2|201174|1760|85004|31953|2701|2702;2|976|200643|171549|171552|838|28127;2|976|200643|171549|171552|838|386414,Complete,NA
Study 437,"cross-sectional observational, not case-control",32656096,10.3389/fcimb.2020.00286,NA,"Yang Q, Wang Y, Wei X, Zhu J, Wang X, Xie X , Lu W",The Alterations of Vaginal Microbiome in HPV16 Infection as Identified by Shotgun Metagenomic Sequencing,Frontiers in cellular and infection microbiology,2020,Experiment 1,China,Homo sapiens,"cervicovaginal secretion,posterior fornix of vagina",UBERON:0016486,human papilloma virus infection,EFO:0001668,healthy control,HPV-16+,Patients with HPV-16 confirmed by HPV genotyping assay,25,27,1 month,WMS,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,21 March 2021,Cynthia Anderson,Cynthia Anderson,Vaginal microbiome as HPV16-infection markers.,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Nocardia|s__Nocardia brevicatena,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter|s__Pedobacter panaciterrae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella corporis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Kytococcaceae|g__Kytococcus|s__Kytococcus sedentarius,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces auratus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia turicensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus|s__Paracoccus denitrificans,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium deltae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Bacteria|p__Chlamydiae|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia trachomatis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas stutzeri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus|s__Mageeibacillus indolicus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus tetradius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella asaccharolytica,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus|s__Mobiluncus curtisii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis",2|201174|1760|85007|85025|1817|37327;2|976|200643|171549|171552|838|28132;2|1239|909932|1843489|31977|39948|218538;2|976|117747|200666|84566|84567|363849;2|201174|84998|84999|1643824|133925|133926;2|976|200643|171549|171552|838|28128;2|201174|1760|85006|2805426|57499|1276;2|32066|203490|203491|203492|848|851;2|201174|1760|85011|2062|1883|114687;2|976|200643|171549|171552|838|419005;2|1239|526524|526525|128827|123375|102148;2|1239|1737404|1737405|1570339|543311|33033;2|976|200643|171549|171552|838|28125;2|976|200643|171549|171552|838|28130;2|201174|1760|2037|2049|2529408|131111;2|1239|1737404|1737405|1570339|162289|54005;2|1224|28211|204455|31989|265|266;2|1239|909932|1843489|31977|39948|309120;2|201174|84998|84999|1643824|1380|1393034;2|1239|909932|1843489|31977|29465|187328;2|204428|204429|51291|809|810|813;2|1224|1236|72274|135621|286|316;2|1239|186801|186802|216572|1637257|884684;2|1239|1737404|1737405|1570339|165779|33036;2|1239|91061|1385|1378|502393;2|1239|1737404|1737405|1570339|162289|33031;2|201174|1760|2037|2049|2050|2051;2|1239|186801|186802|186804|1257|1261;2|201174|1760|85004|31953|2701|2702,Complete,NA
Study 438,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F, Guinane CM, Hussey S, Wall R, Ryan CA, Dempsey EM, Murphy B, Ross RP, Fitzgerald GF, Stanton C , Cotter PD","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,Experiment 1,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Untreated controls (week 4),Antibiotic treated (week 4),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,excluded if they required oral antibiotics (no time frame given),16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,Mmarin,"Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable tags.

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

Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05).  Percentages are based on proportions of assignable reads.",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|543;2|1239|91061|186826|81850;2|1239|186801|186802|186804;2|1224;2|1224|1236|91347|543,Complete,Chloe
Study 438,prospective cohort,22948872,10.1128/AAC.00789-12,NA,"Fouhy F, Guinane CM, Hussey S, Wall R, Ryan CA, Dempsey EM, Murphy B, Ross RP, Fitzgerald GF, Stanton C , Cotter PD","High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin",Antimicrobial agents and chemotherapy,2012,Experiment 1,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Untreated controls (week 4),Antibiotic treated (week 4),Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth,9,9,excluded if they required oral antibiotics (no time frame given),16S,4,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,"Figure 1, Figure 2, Figure 3",7 October 2021,Mmarin,Mmarin,"Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable tags.

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

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

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

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

A statistically significant difference between treated infants at week 4 and week 8 (i.e., the recovery of the treated infants) is indicated by a diamond. Percentages are based on proportions of assignable tags.",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|1224|1236|91347|543;2|1239|186801|186802|186804;2|1224;2|1224|1236|91347|543,Complete,Chloe
Study 439,case-control,32158702,10.3389/fcimb.2020.00063,https://pubmed.ncbi.nlm.nih.gov/32158702/,"Doumatey AP, Adeyemo A, Zhou J, Lei L, Adebamowo SN, Adebamowo C , Rotimi CN",Gut Microbiome Profiles Are Associated With Type 2 Diabetes in Urban Africans,Frontiers in cellular and infection microbiology,2020,Experiment 1,Nigeria,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus; The definition of T2D was based on the American Diabetes Association (ADA) criteria: a fasting plasma glucose concentration (FPG) ≥ 126 mg/dl (7.0 mmol/l) or a 2-h post-load value in the oral glucose tolerance test ≥ 200 mg/dl (11.1 mmol/l) on more than one occasion. Alternatively, a diagnosis of T2D was accepted if an individual was on pharmacological treatment for T2D, and a review of clinical records indicated adequate justification for that therapy.",193,98,NA,16S,4,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Table 3, Table 4",27 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of gut microbial communities in individuals with Type 2 Diabetes,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Cellulosilyticum|s__Cellulosilyticum ruminicola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium butyricum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium paraputrificum,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae",2|1239|186801|186802|186803|698776|425254;2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485|1492;2|1239|186801|186802|31979|1485|29363;2|1239;2|1239|186801|186802|186804,Complete,NA
Study 439,case-control,32158702,10.3389/fcimb.2020.00063,https://pubmed.ncbi.nlm.nih.gov/32158702/,"Doumatey AP, Adeyemo A, Zhou J, Lei L, Adebamowo SN, Adebamowo C , Rotimi CN",Gut Microbiome Profiles Are Associated With Type 2 Diabetes in Urban Africans,Frontiers in cellular and infection microbiology,2020,Experiment 1,Nigeria,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus; The definition of T2D was based on the American Diabetes Association (ADA) criteria: a fasting plasma glucose concentration (FPG) ≥ 126 mg/dl (7.0 mmol/l) or a 2-h post-load value in the oral glucose tolerance test ≥ 200 mg/dl (11.1 mmol/l) on more than one occasion. Alternatively, a diagnosis of T2D was accepted if an individual was on pharmacological treatment for T2D, and a review of clinical records indicated adequate justification for that therapy.",193,98,NA,16S,4,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Table 3, Table 4",15 August 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Terrisporobacter|s__Terrisporobacter glycolicus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976;2|1224|28221|213115|194924|872|901;2157|28890;2|1239|186801|186802|186804|1505652|36841;2|1239|186801|186802|186803|2316020|46228;2|976|200643|171549|171552|838,Complete,NA
Study 440,case-control,31502207,10.1007/s40257-019-00471-5,https://pubmed.ncbi.nlm.nih.gov/31502207/,"Rainer BM, Thompson KG, Antonescu C, Florea L, Mongodin EF, Bui J, Fischer AH, Pasieka HB, Garza LA, Kang S , Chien AL",Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study,American journal of clinical dermatology,2020,Experiment 1,United States of America,Homo sapiens,"nose,skin of cheek","UBERON:0000004,UBERON:0008803",rosacea,EFO:1000760,Healthy controls,Participants with papulopustular rosacea (PPR),Participants with rosacea included individuals with diagnosed papulopustular rosacea (PPR): severity of rosacea assessed using the National Rosacea Society clinical grading system ranged from mild to moderate,19,19,"4 weeks for topical antibiotics, corticosteroids, and other anti-inflammatory medications, within 8 weeks for systemic antibiotics, corticosteroids, and other immunosuppressive agents",16S,34,Illumina,Metastats,0.05,TRUE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table 1,30 May 2021,Madhubani Dey,Madhubani Dey,Significantly enriched species in papulopustular rosacea (PPR) patients,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium kroppenstedtii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Gleimia|s__Gleimia europaea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",2|976|200643|171549|171552|1283313|76122;2|1224|29547|213849|72294|194|827;2|201174|1760|85007|1653|1716|161879;2|201174|1760|2037|2049|2692113|66228;2|976|200643|171549|171552|838|28131,Complete,NA
Study 440,case-control,31502207,10.1007/s40257-019-00471-5,https://pubmed.ncbi.nlm.nih.gov/31502207/,"Rainer BM, Thompson KG, Antonescu C, Florea L, Mongodin EF, Bui J, Fischer AH, Pasieka HB, Garza LA, Kang S , Chien AL",Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study,American journal of clinical dermatology,2020,Experiment 1,United States of America,Homo sapiens,"nose,skin of cheek","UBERON:0000004,UBERON:0008803",rosacea,EFO:1000760,Healthy controls,Participants with papulopustular rosacea (PPR),Participants with rosacea included individuals with diagnosed papulopustular rosacea (PPR): severity of rosacea assessed using the National Rosacea Society clinical grading system ranged from mild to moderate,19,19,"4 weeks for topical antibiotics, corticosteroids, and other anti-inflammatory medications, within 8 weeks for systemic antibiotics, corticosteroids, and other immunosuppressive agents",16S,34,Illumina,Metastats,0.05,TRUE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 2,Table 1,30 May 2021,Madhubani Dey,Madhubani Dey,Significantly depleted species in papulopustular rosacea (PPR) patients,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus|s__Anoxybacillus kestanbolensis,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Azorhizobium|s__Azorhizobium doebereinerae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas|s__Dysgonomonas gadei,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia stuartii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella algae",2|1239|91061|1385|186817|150247|227476;2|1224|28211|356|335928|6|281091;2|201174|1760|85009|31957|1912216|33011;2|976|200643|171549|2005520|156973|156974;2|1224|1236|91347|1903414|586|588;2|1224|1236|135622|267890|22|38313,Complete,NA
Study 440,case-control,31502207,10.1007/s40257-019-00471-5,https://pubmed.ncbi.nlm.nih.gov/31502207/,"Rainer BM, Thompson KG, Antonescu C, Florea L, Mongodin EF, Bui J, Fischer AH, Pasieka HB, Garza LA, Kang S , Chien AL",Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study,American journal of clinical dermatology,2020,Experiment 2,United States of America,Homo sapiens,"nose,skin of cheek","UBERON:0000004,UBERON:0008803",rosacea,EFO:1000760,Healthy controls,Participants with erythematotelangiectatic rosacea,Participants with rosacea included individuals with diagnosed erythematotelangiectatic rosacea (ETR): severity of rosacea assessed using the National Rosacea Society clinical grading system ranged from mild to moderate,19,19,"4 weeks for topical antibiotics, corticosteroids, and other anti-inflammatory medications, within 8 weeks for systemic antibiotics, corticosteroids, and other immunosuppressive agents",16S,34,Illumina,Metastats,0.05,TRUE,NA,"age,race,sex",NA,NA,NA,NA,NA,NA,unchanged,Signature 1,Table 1,3 June 2021,Madhubani Dey,Madhubani Dey,Significantly depleted species in erythematotelangiectatic rosacea (ETR) compared to healthy controls,decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Azorhizobium|s__Azorhizobium doebereinerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia|s__Providencia stuartii,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Roseomonas|s__Roseomonas mucosa,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Shewanellaceae|g__Shewanella|s__Shewanella algae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus",2|1224|28211|356|335928|6|281091;2|976|200643|171549|171551|836|28124;2|1224|1236|91347|1903414|586|588;2|1224|28211|204441|433|125216|207340;2|1224|1236|135622|267890|22|38313;2|1239|186801|186802|186803|2316020|33038,Complete,NA
Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,30,30,4 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3a,3 June 2021,Claregrieve1,Claregrieve1,Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1239|909932|1843489|31977|29465;2|1239|526524|526525|128827|1505663;2|201174|1760|2037|2049|1654,Complete,Fatima
Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,30,30,4 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Figure 3a,3 June 2021,Claregrieve1,"Claregrieve1,Fatima",Differences in microbial composition between patients with coronavirus disease 2019 and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|186802|186803|1766253;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186804|1505657;2|1224|1236|91347|543|570;2|1239|186801|186802|186804|1501226;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|186803|2316020|33039;2|1239|186801|186802|31979|1485,Complete,Fatima
Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,influenza A (H1N1),EFO:1001488,Healthy controls,H1N1 cases,H1N1 patients with viral infection confirmed by real-time reverse-transcription polymerase chain reaction hospitalized between January 2018 and March 2019 with severe disease at time of admission,30,24,4 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Supplementary Figure 2,3 June 2021,Claregrieve1,Claregrieve1,Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.",2|1239|186801|186802|186803|572511;2|1239|186801|186802|186804|1501226;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186803|2569097|39488;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|1766253;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|2316020|33039;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|1263|41978,Complete,NA
Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,influenza A (H1N1),EFO:1001488,Healthy controls,H1N1 cases,H1N1 patients with viral infection confirmed by real-time reverse-transcription polymerase chain reaction hospitalized between January 2018 and March 2019 with severe disease at time of admission,30,24,4 weeks,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Supplementary Figure 2,3 June 2021,Claregrieve1,Claregrieve1,Comparison of estimated fecal microbiome phylotypes in H1N1 patients and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1239|91061|186826|81852|1350;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289,Complete,NA
Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,H1N1 patients,COVID-19 patients,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,24,30,subjects who received antibiotics and/or probiotics within 4 weeks of enrollment were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,NA,NA,NA,increased,increased,NA,NA,NA,Signature 1,Figure 4a,3 June 2021,Claregrieve1,"Claregrieve1,Fatima",Differences in microbiota composition between COVID-19 patients and H1N1 patients,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|186802|186803|1766253;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|207244;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|572511;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803;2|201174|1760|85006|1268|32207;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186803|2316020|33039;2|1239|186801|186802|31979|1485,Complete,Fatima
Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,H1N1 patients,COVID-19 patients,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,24,30,subjects who received antibiotics and/or probiotics within 4 weeks of enrollment were excluded,16S,34,Illumina,LEfSe,0.05,TRUE,3.5,NA,NA,NA,increased,increased,NA,NA,NA,Signature 2,Figure 4a,3 June 2021,Claregrieve1,Claregrieve1,Differences in microbiota composition between COVID-19 patients and H1N1 patients,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976|200643|171549|171552|838;2|1239|1737404|1582879;2|74201|203494|48461|1647988|239934;2|1239|1737404|1737405|1570339|1161127;2|976|200643|171549|171551|836,Complete,Fatima
Study 441,"cross-sectional observational, not case-control",32497191,https://doi.org/10.1093/cid/ciaa709,NA,"Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L , Li L",Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2020,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,viral COVID-19 infections confirmed by real-time reverse-transcription polymerase chain reaction,30,30,4 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,NA,Signature 1,"Figure 2A, 2B, 2C, 2D",30 June 2021,Fatima,Fatima,Taxonomic differences in fecal microbiota between patients with covid-19 and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli",2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|91061,Complete,NA
Study 442,"cross-sectional observational, not case-control",31834952,10.1111/myc.13046,https://pubmed.ncbi.nlm.nih.gov/31834952/,"Han SH, Lee JS, Song KH, Choe YB, Ahn KJ , Lee YW",Differences in foot skin microbiomes between patients with type 2 diabetes and healthy individuals,Mycoses,2020,Experiment 1,South Korea,Homo sapiens,"skin of sole of pes,interdigital space","UBERON:0013778,UBERON:0036252",type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Type 2 Diabetes Mellitus patients diagnosed by an endocrinologist at Konkuk University Medical Center, Seoul, Korea",18,17,concomitant systemic (within four weeks of enrolment) or topical (within two weeks of enrolment) treatments,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,unchanged,NA,decreased,Signature 1,Table 2,7 June 2021,Madhubani Dey,Madhubani Dey,Decrease in the abundance of fungal species in Diabetes Mellitus patients,decreased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Pleosporaceae|g__Alternaria|s__Alternaria alternata,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Didymellaceae|g__Ascochyta|s__Ascochyta herbicola,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium flabelliforme,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium herbarum",2759|4751|4890|147541|92860|28556|5598|5599;2759|4751|4890|147541|92860|683158|5453|749840;2759|4751|4890|4891|4892|766764|1535326|5480;2759|4751|4890|147541|2726946|452563|5498|887091;2759|4751|4890|147541|2726946|452563|5498|29918,Complete,NA
Study 442,"cross-sectional observational, not case-control",31834952,10.1111/myc.13046,https://pubmed.ncbi.nlm.nih.gov/31834952/,"Han SH, Lee JS, Song KH, Choe YB, Ahn KJ , Lee YW",Differences in foot skin microbiomes between patients with type 2 diabetes and healthy individuals,Mycoses,2020,Experiment 1,South Korea,Homo sapiens,"skin of sole of pes,interdigital space","UBERON:0013778,UBERON:0036252",type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Type 2 Diabetes Mellitus patients diagnosed by an endocrinologist at Konkuk University Medical Center, Seoul, Korea",18,17,concomitant systemic (within four weeks of enrolment) or topical (within two weeks of enrolment) treatments,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,unchanged,NA,decreased,Signature 2,Table 2,7 June 2021,Madhubani Dey,Madhubani Dey,Increase in the abundance of fungal species in Diabetes Mellitus patients,increased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Onygenales|f__Arthrodermataceae|g__Trichophyton|s__Trichophyton rubrum",2759|4751|5204|1538075|162474|742845|55193|76775;2759|4751|4890|147545|33183|34384|5550|5551,Complete,NA
Study 442,"cross-sectional observational, not case-control",31834952,10.1111/myc.13046,https://pubmed.ncbi.nlm.nih.gov/31834952/,"Han SH, Lee JS, Song KH, Choe YB, Ahn KJ , Lee YW",Differences in foot skin microbiomes between patients with type 2 diabetes and healthy individuals,Mycoses,2020,Experiment 2,South Korea,Homo sapiens,"skin of sole of pes,interdigital space","UBERON:0013778,UBERON:0036252",type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Type 2 Diabetes Mellitus patients diagnosed by an endocrinologist at Konkuk University Medical Center, Seoul, Korea",18,17,concomitant systemic (within four weeks of enrolment) or topical (within two weeks of enrolment) treatments,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,Experiment 1,India,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Health Control,IBS,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C), diarrhea predominant (IBS-D), and un-subtyped (IBS-U). All participants.",30,47,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3.,28 June 2021,Kwekuamoo,Kwekuamoo,Relative difference in 16S rRNA copy number of fecal bacteria between patients with IBS and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|572511|1532;2|1239|909932|1843489|31977|29465;2|976|200643|171549|815|816;2|1224|1236|72274|135621|286|287,Complete,NA
Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,Experiment 1,India,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Health Control,IBS,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C), diarrhea predominant (IBS-D), and un-subtyped (IBS-U). All participants.",30,47,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 3.,18 July 2021,Kwekuamoo,Kwekuamoo,Relative difference in 16S rRNA copy number of fecal bacteria between patients with IBS and healthy controls,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,Experiment 2,India,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Health Control,IBS-C,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C).",30,20,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4.,18 July 2021,Kwekuamoo,Kwekuamoo,Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|815|816;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|572511|1532;2|1239|91061|186826|33958|1578;2|1224|1236|72274|135621|286|287;2|1239|909932|1843489|31977|29465,Complete,NA
Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,Experiment 2,India,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Health Control,IBS-C,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: constipation predominant IBS (IBS-C).",30,20,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4.,18 July 2021,Kwekuamoo,Kwekuamoo,Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,2|201174|1760|85004|31953|1678|1686,Complete,NA
Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,Experiment 3,India,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Health Control,IBS-D,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: diarrhea predominant IBS (IBS-D).",30,20,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4.,18 July 2021,Kwekuamoo,Kwekuamoo,Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|572511|1532;2|1239|909932|1843489|31977|29465;2|976|200643|171549|815|816;2|1224|1236|72274|135621|286|287,Complete,NA
Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,Experiment 3,India,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Health Control,IBS-D,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: diarrhea predominant IBS (IBS-D).",30,20,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4.,18 July 2021,Kwekuamoo,Kwekuamoo,Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum",2|1239|91061|186826|33958|1578;2|201174|1760|85004|31953|1678|1686,Complete,NA
Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,Experiment 4,India,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Health Control,IBS-U,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: un-subtyped (IBS-U).",30,7,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 4.,18 July 2021,Kwekuamoo,Kwekuamoo,Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|201174|1760|85004|31953|1678|1686;2|976|200643|171549|815|816;2|1224|1236|72274|135621|286|287,Complete,NA
Study 443,case-control,25784074,10.1007/s10620-015-3607-y,NA,"Shukla R, Ghoshal U, Dhole TN , Ghoshal UC",Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis,Digestive diseases and sciences,2015,Experiment 4,India,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Health Control,IBS-U,"Patients with IBS diagnosed using Rome III. Patients were classified into three sub-types
using Rome III criteria: un-subtyped (IBS-U).",30,7,"Patients who had prior history of gastrointestinal surgery, inflammatory bowel disease, and celiac disease were excluded. Patients with IBS who used antibiotics, probiotics, or prokinetics within last 4 weeks of inclusion into the study were also excluded.",16S,NA,RT-qPCR,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 4.,18 July 2021,Kwekuamoo,Kwekuamoo,Relative difference in 16S rRNA copy number of fecal bacteria in subgroups of patients with IBS and healthy controls.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia coccoides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|572511|1532;2|1239|909932|1843489|31977|29465,Complete,NA
Study 445,"cross-sectional observational, not case-control",32728349,10.1186/s12575-020-00131-7,NA,"De Maio F, Posteraro B, Ponziani FR, Cattani P, Gasbarrini A , Sanguinetti M",Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients,Biological procedures online,2020,Experiment 1,Italy,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients,COVID-19 cases,Diagnosis with COVID-19 based on SARS-CoV-2 RNA detection using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay,22,18,NA,16S,56,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 446,"cross-sectional observational, not case-control",33219095,10.1128/mBio.01969-20,NA,"Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR , Simner PJ",Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients,mBio,2020,Experiment 1,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 cases,Positive for SaRS-CoV-2 by diagnostic RT-PCR,10,40,NA,WMS,NA,Nanopore,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 1,Figure 3,5 June 2021,Claregrieve1,Claregrieve1,Relative abundance of bacteria at species level in COVID-19-positive and COVID-19-negative samples,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,2|201174|1760|85007|1653|1716|38284,Complete,NA
Study 446,"cross-sectional observational, not case-control",33219095,10.1128/mBio.01969-20,NA,"Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR , Simner PJ",Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients,mBio,2020,Experiment 1,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 cases,Positive for SaRS-CoV-2 by diagnostic RT-PCR,10,40,NA,WMS,NA,Nanopore,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,decreased,NA,NA,Signature 2,Figure 3,5 June 2021,Claregrieve1,Claregrieve1,Relative abundance of bacteria at species level in COVID-19-positive and COVID-19-negative samples,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,2|201174|1760|85009|31957,Complete,NA
Study 447,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y, Zhang M, Zhang J, Sun Z, Ran L, Ban Y, Wang B, Hou X, Zhai S, Ren L, Wang M , Hu J",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy;,31,30,2 weeks,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 1 D,27 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals diagnosed with gestational diabetes,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales",2|1224|1236;2|1224|1236|135625|712|724;2|1224|1236|135625|712;2|1224|1236|135625,Complete,NA
Study 447,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y, Zhang M, Zhang J, Sun Z, Ran L, Ban Y, Wang B, Hou X, Zhai S, Ren L, Wang M , Hu J",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy;,31,30,2 weeks,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 1 D,27 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals diagnosed with gestational diabetes,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|976|200643|171549|171550|239759;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171550,Complete,NA
Study 447,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y, Zhang M, Zhang J, Sun Z, Ran L, Ban Y, Wang B, Hou X, Zhai S, Ren L, Wang M , Hu J",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Figure 2D,9 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of oral microbial species in GDM individuals,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|201174|1760|85004|31953;2|201174|1760|85004;2|201174|1760|85004|31953|1678;2|1239|909932|909929|1843491|970,Complete,NA
Study 447,case-control,31891538,10.1152/ajpendo.00266.2019,https://pubmed.ncbi.nlm.nih.gov/31891538/,"Xu Y, Zhang M, Zhang J, Sun Z, Ran L, Ban Y, Wang B, Hou X, Zhai S, Ren L, Wang M , Hu J",Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation,American journal of physiology. Endocrinology and metabolism,2020,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,gestational diabetes,EFO:0004593,Healthy controls,Individuals with gestational diabetes,Individuals with gestational diabetes at third trimester during pregnancy,31,30,2 weeks,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,FALSE,2,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Figure 2D,27 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals diagnosed with gestational diabetes,decreased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc",2|32066;2|32066|203490|203491|203492;2|32066|203490;2|1239|186801|186802|186803|1164882;2|1239|91061|186826|33958;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771;2|1239|91061|186826|33958|1243,Complete,NA
Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1a-c,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients,increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus",2|1239;2|1224;2|1239|91061|1385|186817;2|1224|1236|2887326|468;2|1224|1236|72274|135621;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|286;2|1239|91061|1385|186817|1386,Complete,Fatima
Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1a-c,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976;2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|1224|28216|206351|481;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465,Complete,Fatima
Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 1b,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the family level,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1239|91061|1385|186817;2|1224|1236|2887326|468;2|1224|1236|72274|135621,Complete,Fatima
Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 4,Figure 1b,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the family level,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|1224|28216|206351|481;2|976|200643|171549|171552;2|1239|909932|1843489|31977,Complete,Fatima
Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 5,Figure 1c,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the genus level,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|1224|1236|2887326|468|469;2|1239|91061|1385|186817|1386;2|1224|1236|72274|135621|286,Complete,Fatima
Study 448,case-control,23167452,https://doi.org/10.1111/1469-0691.12054,NA,"Leung RK, Zhou JW, Guan W, Li SK, Yang ZF , Tsui SK",Modulation of potential respiratory pathogens by pH1N1 viral infection,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2013,Experiment 1,China,Homo sapiens,throat,UBERON:0000341,influenza A (H1N1),EFO:1001488,Pneumonia patients without any influenza A infection,Pneumonia patients with pH1N1 infection,"Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection",11,11,NA,WMS,NA,Illumina,DESeq2,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 6,Figure 1c,9 June 2021,Claregrieve1,Claregrieve1,Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the genus level,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465,Complete,Fatima
Study 449,"cross-sectional observational, not case-control",NA,https://doi.org/10.1101/2020.08.20.20144014,NA,NA,NA,NA,NA,Experiment 1,"China,Switzerland",Homo sapiens,lung,UBERON:0002048,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,COVID-19 infected patients,23,19,NA,WMS,NA,NA,DESeq2,1e-11,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Supplementary Table 2,12 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter braakii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas terrigena,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter kobei,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. T2,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Filimonas|s__Filimonas lacunae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora saccharolytica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia adecarboxylata,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus sphaericus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium|s__Phyllobacterium myrsinacearum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. JY-Q,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. G1-14,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas sp. FARSPH,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax paradoxus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. PMC12,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces pacaensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerocolumna|s__Anaerocolumna sedimenticola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerotignum|s__Anaerotignum propionicum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__[Brevibacterium] frigoritolerans,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium cucumeris,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii complex sp. CFNIH3,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium CCNA10,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium beijerinckii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium carboxidivorans,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas testosteroni,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter asburiae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter bugandensis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cancerogenus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae complex sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter oligotrophicus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter roggenkampii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter soli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. 638,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. E76,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. ODB01,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella michiganensis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus|s__Latilactobacillus curvatus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus delbrueckii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus|s__Lactiplantibacillus plantarum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. 29361,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. J807,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. LSNIH1,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia|s__Leclercia sp. W17,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia amnigena,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia jeotgali,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Lelliottia|s__Lelliottia sp. WB101,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus|s__Lysinibacillus sp. B2A1,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium|s__Methylobacterium sp. DM1,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mesomycoplasma|s__Mesomycoplasma hyorhinis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus graminis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus|s__Paenibacillus guangzhouensis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea sp. SO10,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter|s__Pluralibacter gergoviae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas alkylphenolica,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas oryzihabitans,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas rhodesiae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. MRSN12121,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. PONIH3,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp. XWY-1,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella aquatilis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Ruminobacter|s__Ruminobacter amylophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium sp. B29,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas|s__Stenotrophomonas sp. LM091,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 064,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio|s__Succinivibrio dextrinosolvens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Suicoccus|s__Suicoccus acidiformans,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__uncultured Variovorax sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax boronicumulans,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax|s__Variovorax sp. PBL-H6,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio anguillarum",2|1224|1236|91347|543|544|57706;2|1224|28216|80840|80864|283|32013;2|1224|1236|91347|543|547|550;2|1224|1236|91347|543|547|158836;2|1224|1236|91347|543|547|208224;2|1224|1236|91347|543|547|2707174;2|976|1853228|1853229|563835|649460|477680;2|1239|186801|186802|186803|2719231|84030;2|1239|186801|186802|186803|2719231|29370;2|1224|1236|91347|543|83654|83655;2|1239|91061|1385|186817|400634|1421;2|1224|28211|356|69277|28100|28101;2|1224|1236|72274|135621|286|306;2|1224|1236|72274|135621|286|1338689;2|201174|1760|85006|1268|32207|43675;2|976|117747|200666|84566|28453|2003121;2|1224|28211|204457|41297|13687|2219696;2|1224|28216|80840|80864|34072|34073;2|1224|28216|80840|80864|34072|2126319;2|201174|1760|2037|2049|1654|1852377;2|1239|186801|186802|186803|1843210|2696063;2|1239|186801|186802|186803|2039240|28446;2|1239|91061|1385|186817|1386|1396;2|1239|91061|1385|186817|1386|450367;2|976|117743|200644|2762318|59732|1813611;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|2077147;2|1239|186801|186802|1898207;2|1239|186801|186802|2109688;2|1239|186801|186802|31979|1485|1520;2|1239|186801|186802|31979|1485|217159;2|1224|28216|80840|80864|283|285;2|1224|1236|91347|543|547|61645;2|1224|1236|91347|543|547|881260;2|1224|1236|91347|543|547|69218;2|1224|1236|91347|543|547|2027919;2|1224|1236|91347|543|547|2478464;2|1224|1236|91347|543|547|1812935;2|1224|1236|91347|543|547|885040;2|1224|1236|91347|543|547|399742;2|1224|1236|91347|543|547|2596949;2|1224|1236|91347|543|547|1827481;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|946234|292800;2|1224|1236|91347|543|570|1134687;2|1224|1236|91347|543|570|571;2|1239|186801|186802|186803|1506553|66219;2|1239|91061|186826|33958|2767885|28038;2|1239|91061|186826|33958|1578|1584;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|1578|33959;2|1239|91061|186826|33958|2767842|1590;2|1239|91061|186826|33958|2742598|1598;2|1239|91061|186826|33958|2767887|1624;2|1224|1236|91347|543|83654|2714951;2|1224|1236|91347|543|83654|2681307;2|1224|1236|91347|543|83654|1920114;2|1224|1236|91347|543|83654|2282309;2|1224|1236|91347|543|1330545|61646;2|1224|1236|91347|543|1330545|1907578;2|1224|1236|91347|543|1330545|2153385;2|1239|91061|1385|186817|400634|2081964;2|1224|28211|356|119045|407|2067957;2|544448|31969|2085|2092|2923352|2100;2|1239|91061|1385|186822|44249|189425;2|1239|91061|1385|186822|44249|1473112;2|1224|1236|91347|1903409|53335|2575375;2|1224|1236|91347|543|1330546|61647;2|1224|1236|72274|135621|286|237609;2|1224|1236|72274|135621|286|47885;2|1224|1236|72274|135621|286|76760;2|1224|1236|72274|135621|286|1611770;2|1224|1236|72274|135621|286|1636610;2|1224|1236|72274|135621|286|2069256;2|1224|1236|91347|1903411|34037|34038;2|1224|28216|80840|119060|48736|329;2|201174|1760|85006|1268|32207|172042;2|1224|1236|135624|83763|866|867;2|1239|186801|186802|186803|2316020|33038;2|201174|1760|2037|2049|2529408|52773;2|976|117747|200666|84566|28453|1933220;2|1224|1236|135614|32033|40323|1904944;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1305;2|1239|91061|186826|1300|1301|712624;2|1224|1236|135624|83763|83770|83771;2|1239|91061|186826|186827|2689587|2036206;2|1224|28216|80840|80864|34072|114708;2|1224|28216|80840|80864|34072|436515;2|1224|28216|80840|80864|34072|434009;2|1224|1236|135623|641|662|55601,Complete,NA
Study 449,"cross-sectional observational, not case-control",NA,https://doi.org/10.1101/2020.08.20.20144014,NA,NA,NA,NA,NA,Experiment 1,"China,Switzerland",Homo sapiens,lung,UBERON:0002048,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,COVID-19 infected patients,23,19,NA,WMS,NA,NA,DESeq2,1e-11,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table 2,12 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls,decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema putidum",2|1224|29547|213849|72294|194|824;2|1224|29547|213849|72294|194|203;2|1224|29547|213849|72294|194|204;2|203691|203692|136|2845253|157|221027,Complete,NA
Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,Experiment 1,United Kingdom,Mus musculus,feces,UBERON:0001988,viral pneumonia,EFO:0007541,Day 0,Day 7,Mice assessed 7 days after infection,NA,NA,NA,16S,4,Illumina,"ANOVA,DESeq2",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Figure 2a,13 June 2021,Claregrieve1,Claregrieve1,Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,Experiment 1,United Kingdom,Mus musculus,feces,UBERON:0001988,viral pneumonia,EFO:0007541,Day 0,Day 7,Mice assessed 7 days after infection,NA,NA,NA,16S,4,Illumina,"ANOVA,DESeq2",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,Figure 2a,13 June 2021,Claregrieve1,Claregrieve1,Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection,increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,NA
Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,Experiment 2,United Kingdom,Mus musculus,feces,UBERON:0001988,viral pneumonia,EFO:0007541,Day 0,Day 7,Day 7 of infection for mice infected with influenza virus (H1N1),NA,NA,NA,16S,4,Illumina,"ANOVA,DESeq2",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Figure 4c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,NA
Study 450,laboratory experiment,29483910,10.3389/fimmu.2018.00182,NA,"Groves HT, Cuthbertson L, James P, Moffatt MF, Cox MJ , Tregoning JS",Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota,Frontiers in immunology,2018,Experiment 2,United Kingdom,Mus musculus,feces,UBERON:0001988,viral pneumonia,EFO:0007541,Day 0,Day 7,Day 7 of infection for mice infected with influenza virus (H1N1),NA,NA,NA,16S,4,Illumina,"ANOVA,DESeq2",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,Figure 4c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of gut microbiota of respiratory syncytial virus (RSV) infected mice between Day 0 and Day 7 of infection,increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,NA
Study 451,case-control,33613481,10.3389/fmicb.2021.610370,https://pubmed.ncbi.nlm.nih.gov/33613481/,"Almeida-Santos A, Martins-Mendes D, Gayà-Vidal M, Pérez-Pardal L , Beja-Pereira A",Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients,Frontiers in microbiology,2021,Experiment 1,Portugal,Homo sapiens,saliva,UBERON:0001836,type II diabetes mellitus,MONDO:0005148,Healthy controls,Medicated Type II Diabetes individuals,Medicated Type II Diabetes individuals,24,22,2 months,16S,34,Illumina,"ANCOM,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 6,17 June 2021,Madhubani Dey,"Madhubani Dey,Chloe",Decreased abundance of microbes in individuals with medicated Type 2 Diabetes (Mann-Whitney's U results),decreased,k__Bacteria|p__Synergistetes|c__Synergistia,2|508458|649775,Complete,Chloe
Study 451,case-control,33613481,10.3389/fmicb.2021.610370,https://pubmed.ncbi.nlm.nih.gov/33613481/,"Almeida-Santos A, Martins-Mendes D, Gayà-Vidal M, Pérez-Pardal L , Beja-Pereira A",Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients,Frontiers in microbiology,2021,Experiment 1,Portugal,Homo sapiens,saliva,UBERON:0001836,type II diabetes mellitus,MONDO:0005148,Healthy controls,Medicated Type II Diabetes individuals,Medicated Type II Diabetes individuals,24,22,2 months,16S,34,Illumina,"ANCOM,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table S6,14 March 2022,Chloe,Chloe,Decreased abundance of microbes in individuals with medicated Type 2 Diabetes (ANCOM results),decreased,NA,NA,Complete,Chloe
Study 452,"cross-sectional observational, not case-control",33193081,10.3389/fendo.2020.550319,https://pubmed.ncbi.nlm.nih.gov/33193081/,"Tang N, Luo ZC, Zhang L, Zheng T, Fan P, Tao Y , Ouyang F",The Association Between Gestational Diabetes and Microbiota in Placenta and Cord Blood,Frontiers in endocrinology,2020,Experiment 1,China,Homo sapiens,placenta,UBERON:0001987,gestational diabetes,EFO:0004593,euglycemic (control) singleton pregnant women,Pregnant women with Gestational Diabetes Mellitus,"Pregnant women with Gestational Diabetes Mellitus (GDM) who had prenatal care at Xinhua Hospital, a tertiary hospital in Shanghai, and were admitted to the hospital for cesarean deliveries",7,8,Women who were treated with any antibiotics during pregnancy,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 1,Table 3,14 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of microbes in GDM individuals,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Defluviitaleaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|186802|216572|244127;2|1239|186801|186802|186803|33042;2|1239|186801|186802|1185407;2|1239|186801|186802|186803|189330;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|1263,Complete,NA
Study 452,"cross-sectional observational, not case-control",33193081,10.3389/fendo.2020.550319,https://pubmed.ncbi.nlm.nih.gov/33193081/,"Tang N, Luo ZC, Zhang L, Zheng T, Fan P, Tao Y , Ouyang F",The Association Between Gestational Diabetes and Microbiota in Placenta and Cord Blood,Frontiers in endocrinology,2020,Experiment 1,China,Homo sapiens,placenta,UBERON:0001987,gestational diabetes,EFO:0004593,euglycemic (control) singleton pregnant women,Pregnant women with Gestational Diabetes Mellitus,"Pregnant women with Gestational Diabetes Mellitus (GDM) who had prenatal care at Xinhua Hospital, a tertiary hospital in Shanghai, and were admitted to the hospital for cesarean deliveries",7,8,Women who were treated with any antibiotics during pregnancy,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,increased,NA,NA,increased,Signature 2,Table 3,14 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of microbes in GDM individuals,decreased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,NA
Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,SARS-CoV-2 infected patients,">age 18, positive nasopharyngeal swab for SARS-CoV-2 by PCR, COVID-19 related symptoms present, weight > 110 pounds",34,50,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 2c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial genera in COVID-19 infected cases and controls,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas",2|201174|1760|85007|1653|1716;2|1224|29547|213849|72294|194;2|1239|1737404|1737405|1570339|150022;2|201174|1760|2037|2049|2050;2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1582879;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|1737404|1737405|1570339|1161127;2|1239|186801|186802|216572|236752;2|1239|91061|186826|186827|66831;2|1239|1737404|1737405|1570339|162290;2|1239|91061|1385|90964|1279;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|990719|990721;2|1239|909932|1843489|31977|39948;2|1224|28216|80840|995019|577310;2|1239|186801|186802|31979|1649459;2|1239|186801|186802|1392389,Complete,Lwaldron
Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,SARS-CoV-2 infected patients,">age 18, positive nasopharyngeal swab for SARS-CoV-2 by PCR, COVID-19 related symptoms present, weight > 110 pounds",34,50,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial genera in COVID-19 infected cases and controls,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Monoglobus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",2|1239|91061|186826|33958|1578;2|1239|186801|186802|186804|1505657;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|572511;2|201174|1760|85006|1268|32207;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803;2|1224|1236|91347|543|561;2|1239|186801|186802|216572|2039302;2|1239|186801|186802|216572|292632;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|1766253;2|1224|1236|91347|543|570,Complete,Lwaldron
Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,SARS-CoV-2 infected patients,SARS-CoV-2 recovered individuals,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",50,9,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between COVID-19 infected and COVID-19 recovered samples,decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Fastidiosipila,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Gallicola,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio",2|1224|29547|213849|72294|194;2|201174|1760|85007|1653|1716;2|201174|1760|2037|2049|2050;2|1239|186801|186802|1686313;2|1239|1737404|1582879;2|1239|1737404|1737405|1570339|1161127;2|1239|186801|186802|216572|236752;2|1239|91061|186826|186827|66831;2|1239|91061|1385|90964|1279;2|1239|1737404|1737405|1570339|162290;2|201174|1760|85007|2805586|1847725;2|1239|1737404|1737405|1570339|150022;2|1224|28216|80840|995019|40544;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|201174|84998|84999|1643824|1380;2|201174|1760|85006|85023|255204;2|508458|649775|649776|649777|508459;2|1239|186801|186802|186803|1769710;2|1239|526524|526525|2810281|191303;2|1239|1737404|1737405|1570339|31983;2|1239|1737404|1737405|1570339|165779;2|201174|1760|85006|85020|36739;2|1224|28221|213115|194924|872,Complete,Lwaldron
Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,SARS-CoV-2 infected patients,SARS-CoV-2 recovered individuals,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",50,9,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between COVID-19 infected and COVID-19 recovered samples,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Phocea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter",2|1239|91061|186826|1300|1357;2|1239|186801|186802|186803|207244;2|1239|186801|186802|216572|1926663;2|1239|186801|186802|216572|216851;2|1224|1236|91347|543|561;2|1239|186801|186802|186804|1505657;2|1239|526524|526525|2810280|135858;2|1224|1236|91347|543|570;2|1239|186801|186802|216572|292632;2|1239|91061|186826|186828|117563;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|1766253,Complete,Lwaldron
Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,Recovered COVID-19 patients,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",38,9,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 4c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between recovered COVID-19 patients and non-infected controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Phocea,k__Bacteria|s__rumen bacterium NK4A214",2|1239|186801|186802|186803|207244;2|1239|186801|186802|216572|1926663;2|877428,Complete,Lwaldron
Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,Experiment 3,United States of America,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Non-infected patients with unrelated respiratory medical conditions,Recovered COVID-19 patients,">age 18, more than 2 weeks post-COVID-19 infection that was confirmed by positive PCR for SARS-CoV-2",38,9,NA,16S,123,Illumina,edgeR,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 4c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial genera between recovered COVID-19 patients and non-infected controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|186802|186803|248744;2|1239|186801|186802|186803;2|1239|526524|526525|128827|1470349;2|1224|28221|213115|194924|35832;2|976|200643|171549|171552|577309;2|1239|909932|1843489|31977|39948;2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572|1263,Complete,Lwaldron
Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Negative for COVID-19 viral RNA in feces,Positive for COVID-19 viral RNA in feces,COVID-19 viral RNA present in feces sample,26,24,NA,16S,123,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 5c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial genera in COVID-19 qPCR positive and qPCR negative fecal samples,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Sphaerochaetaceae|g__Sphaerochaeta,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Synergistes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Defluviitaleaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Dolosicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter",2|1224|28216|80840|80864|283;2|203691|203692|136|2791015|399320;2|508458|649775|649776|649777|2753;2|1239|909932|909929|1843491|158846;2|1239|186801|186802|186803|588605;2|1239|186801|186802|1185407;2|1239|186801|186802|186804|1505657;2|1224|1236|91347|543|570;2|1239|186801|186802|31979|1485|1506;2|976|200643|171549|171552|577309;2|1239|91061|186826|186827|171413;2|1239|186801|186802|186804|1870884;2|1224|1236|91347|1903414|583;2|32066|203490|203491|203492|848;2|1239|526524|526525|128827|1505663;2|1239|526524|526525|128827|1573535;2|1239|186801|186802|186803|1769710;2|544448|31969|2085|2092|2129;2|1239|186801|186802|186803|1766253,Complete,Lwaldron
Study 453,case-control,34100340,10.1080/19490976.2021.1926840,NA,"Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ , Jobin C",The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort,Gut microbes,2021,Experiment 4,United States of America,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Negative for COVID-19 viral RNA in feces,Positive for COVID-19 viral RNA in feces,COVID-19 viral RNA present in feces sample,26,24,NA,16S,123,Illumina,PERMANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 5c,16 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial genera in COVID-19 qPCR positive and qPCR negative fecal samples,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniferax,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Tessaracoccus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Soonwooa,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Phocea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerosphaera,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Pseudoclavibacter",2|1239|91061|186826|186827|171412;2|201174|1760|85009|31957|53456;2|201174|84998|1643822|1643826|447020;2|201174|1760|85009|31957|72763;2|201174|1760|85006|1268|1269;2|1239|91061|186826|1300|1357;2|976|117743|200644|2762318|944321;2|1239|186801|186802|216572|1926663;2|976|200643|171549|2005520|156973;2|32066|203490|203491|1129771|168808;2|201174|1760|85006|85020|36739;2|1239|186801|186802|186804|1501226;2|1224|1236|91347|543|547;2|1239|186801|186802|186804|1505652;2|1239|186801|186802|186803|1213720;2|1239|1737404|1737405|1570339|1273095;2|201174|1760|85006|85019|1696;2|201174|1760|85009|31957|1912216;2|201174|1760|85006|85023|255204,Complete,Lwaldron
Study 454,"case-control,meta-analysis",26992426,10.1136/gutjnl-2015-309595,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529966/,"Flemer B, Lynch DB, Brown JM, Jeffery IB, Ryan FJ, Claesson MJ, O'Riordain M, Shanahan F , O'Toole PW",Tumour-associated and non-tumour-associated microbiota in colorectal cancer,Gut,2017,Experiment 1,Ireland,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy controls,CRC patients,patients undergoing surgery for CRC,56,59,1 month,16S,34,Illumina,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,Experiment 1,Singapore,Homo sapiens,subgingival dental plaque,UBERON:0016484,pregnancy,EFO:0002950,non pregnant women without gingivitis,pregnant women without gingivitis,Pregnant women sampled between 21 to 24 wk of gestation without gingivitis,10,10,6 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,decreased,increased,Signature 1,"Appendix Figure 1, 2, text",16 June 2021,Tislam,"Tislam,Fatima",Phylum and Genera showing significant differential abundance in subgingival samples.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Candidatus Saccharibacteria",2|976|200643|171549|815|816;2|32066|203490;2|32066|203490|203491|203492|848;2|203691;2|203691|203692|136|2845253|157;2|95818,Complete,Fatima
Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,Experiment 1,Singapore,Homo sapiens,subgingival dental plaque,UBERON:0016484,pregnancy,EFO:0002950,non pregnant women without gingivitis,pregnant women without gingivitis,Pregnant women sampled between 21 to 24 wk of gestation without gingivitis,10,10,6 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,increased,NA,decreased,increased,Signature 2,"Appendix Figure 2, text",16 June 2021,Tislam,"Tislam,Fatima",Phylum and Genera showing significant differential abundance in subgingival samples.,decreased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Terrahaemophilus",2|976|117743|200644|2762318|59735;2|1239|91061|1385|1378;2|1224|1236|135625|712|724;2|1239|91061|186826|1300|1301;2|1224|1236|135625|712|217201,Complete,Fatima
Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,Experiment 2,Singapore,Homo sapiens,subgingival dental plaque,UBERON:0016484,gingivitis,MONDO:0002508,pregnant women without gingivitis,pregnant women with gingivitis,NA,10,10,6 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Appendix Figure 1, 2, text",24 June 2021,Tislam,"Tislam,Fatima",Genera showing significant differential abundance in subgingival samples.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Fretibacterium,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|976|200643|171549|815|816;2|1224|29547|213849|72294|194;2|95818;2|1239|186801|186802|186804|44259;2|508458|649775|649776|649777|1434006;2|203691;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,Fatima
Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,Experiment 3,Singapore,Homo sapiens,subgingival dental plaque,UBERON:0016484,gingivitis,MONDO:0002508,pregnant women without gingivitis,pregnant women with gingivitis,NA,10,10,6 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,"Figure 3, text",24 June 2021,Tislam,Tislam,Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 349,k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium oral taxon 500,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 346,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 258,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] saphenum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella|s__Catonella morbi,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema maltophilum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor|s__Filifactor alocis,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema lecithinolyticum,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 238,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 304,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter actinomycetemcomitans,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp. oral taxon 270,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Fretibacterium|s__Fretibacterium sp.",2|1239|909932|1843489|31977;2|32066|203490|203491|1129771|32067;2|95818|713051;2|544448|2790996|2895623|2895509|56142;2|1239|186801|186802|186803|712991;2|95818|713049;2|203691|203692|136|2845253|157|712739;2|1239|186801|186802|543314|51123;2|1239|186801|186802|186803|43996|43997;2|203691|203692|136|2845253|157|51160;2|1239|186801|186802|186804|44259|143361;2|508458|649775|649776|649777|1434006|651822;2|976|200643|171549|2005525|195950|28112;2|203691|203692|136|2845253|157|53418;2|203691|203692|136|2845253|157|712725;2|976|200643|171549|171552|838|712459;2|1224|1236|135625|712|416916|714;2|203691|203692|136|2845253|157|671227;2|203691|203692|136|2845253|157|158;2|508458|649775|649776|649777|1434006|2699746,Complete,NA
Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,Experiment 3,Singapore,Homo sapiens,subgingival dental plaque,UBERON:0016484,gingivitis,MONDO:0002508,pregnant women without gingivitis,pregnant women with gingivitis,NA,10,10,6 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,"Figure 3, text",24 June 2021,Tislam,Tislam,Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 875,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 448,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 172,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 221,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral taxon 478,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium sp. oral taxon 194,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula",2|1239|909932|1843489|31977|29465|29466;2|201174|1760|2037|2049|1654|1655;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|186828|117563|46124;2|201174|1760|85006|1268|32207|2047;2|221235|1226342;2|201174|1760|2037|2049|1654|712124;2|201174|1760|2037|2049|1654|712118;2|1224|28216|206351|481|32257|505;2|1239|186801|186802|186803|265975|712414;2|32066|203490|203491|1129771|32067|712362;2|1239|909932|909929|1843491|970|712538;2|201174|1760|85009|31957|1743|712503;2|201174|1760|2037|2049|1654|55565;2|201174|84998|84999|1643824|2767353|1382,Complete,NA
Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,Experiment 4,Singapore,Homo sapiens,subgingival dental plaque,UBERON:0016484,pregnancy,EFO:0002950,non pregnant women,pregnant women,pregnant women,10,10,6 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,decreased,NA,Signature 1,"Figure 3, text",7 July 2021,Tislam,Tislam,Linear discriminant analysis effect size. pregnant women without gingivitis versus nonpregnant women without gingivitis,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Fretibacterium|s__Fretibacterium fastidiosum,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Fretibacterium|s__Fretibacterium sp.,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Tenericutes|o__Mycoplasmoidales|f__Metamycoplasmataceae|g__Metamycoplasma|s__Metamycoplasma faucium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella baroniae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella micans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema denticola,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] saphenum",2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171552|1283313|1872471;2|976|200643|171549|171552|1283313|76122;2|976|117743|200644|2762318|59735;2|1224|29547|213849|72294|194;2|976|117743|200644|49546|1016|45243;2|508458|649775|649776|649777|1434006|651822;2|508458|649775|649776|649777|1434006|2699746;2|32066|203490|203491|203492|848|860;2|32066|203490|203491|1129771|2755140|157692;2|32066|203490|203491|1129771|32067|157691;2|32066|203490|203491|1129771|32067|104608;2|1239|909932|1843489|31977|906|187326;2|544448|2790996|2895623|2895509|56142;2|1239|186801|186802|186803|265975;2|1239|186801|186802|186804|1257;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838|305719;2|976|200643|171549|171552|838|52227;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|189723;2|976|200643|171549|171552|838|59823;2|201174|1760|85004|31953|196081|230143;2|1239|909932|909929|1843491|970|2053611;2|1239|909932|909929|1843491|970|69823;2|976|200643|171549|2005525|195950|28112;2|203691|203692|136|2845253|157|158;2|203691|203692|136|2845253|157|166;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|1926307;2|1239|186801|186802|543314|51123,Complete,NA
Study 455,"cross-sectional observational, not case-control",32777190,10.1177/2380084420948779,NA,"Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG , Seneviratne CJ",Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis,JDR clinical and translational research,2021,Experiment 4,Singapore,Homo sapiens,subgingival dental plaque,UBERON:0016484,pregnancy,EFO:0002950,non pregnant women,pregnant women,pregnant women,10,10,6 months,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,increased,NA,decreased,NA,Signature 2,"Figure 3, text",7 July 2021,Tislam,Tislam,pregnant women without gingivitis versus nonpregnant women without gingivitis,decreased,"k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria bacilliformis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Terrahaemophilus|s__Terrahaemophilus aromaticivorans",2|976|117743|200644|2762318|59735|712187;2|1239|91061|1385|1378|29391;2|1224|1236|135625|712|724|740;2|1224|28216|206351|481|482|267212;2|201174|1760|85006|1268|32207|172042;2|1239|91061|186826|1300|1301|1306;2|1224|1236|135625|712|217201|217202,Complete,NA
Study 456,"cross-sectional observational, not case-control",33224990,10.1155/2020/8842651,https://pubmed.ncbi.nlm.nih.gov/33224990/,"Zhao X, Zhang Y, Guo R, Yu W, Zhang F, Wu F , Shang J",The Alteration in Composition and Function of Gut Microbiome in Patients with Type 2 Diabetes,Journal of diabetes research,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Patients with Type 2 Diabetes who were admitted to the First Affiliated Hospital of Zhengzhou University from October 2018 to October 2019;  The diagnostic criteria of diabetes mellitus were as follows: (1) twice fasting plasma glucose ðFPGÞ ≥ 7:0 mmol/L, (2) twice oral glucose tolerance test (OGTT ≥ 11:1 mmol/L), and (3) diabetic symptoms (polyuria, thirst, drinking more water, and unexplained weight loss) accompanied with twice random blood glucose ≥ 11:1 mmol/L.",179,137,long-term antibiotic application,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,NA,2,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 2,27 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals with Type 2 Diabetes,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1239|186801|186802|186803|207244;2|976|200643|171549|815|816;2|976;2|1224|28221|213115|194924|35832;2|1239|186801|186802|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803|33042;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|248744;2|976|200643|171549|1853231|283168;2|1224|28216|80840|995019|577310;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|186803|46205;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263;2|1224|28211|204457|41297|13687;2|1224|28216|80840|995019|40544,Complete,NA
Study 456,"cross-sectional observational, not case-control",33224990,10.1155/2020/8842651,https://pubmed.ncbi.nlm.nih.gov/33224990/,"Zhao X, Zhang Y, Guo R, Yu W, Zhang F, Wu F , Shang J",The Alteration in Composition and Function of Gut Microbiome in Patients with Type 2 Diabetes,Journal of diabetes research,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Patients with Type 2 Diabetes who were admitted to the First Affiliated Hospital of Zhengzhou University from October 2018 to October 2019;  The diagnostic criteria of diabetes mellitus were as follows: (1) twice fasting plasma glucose ðFPGÞ ≥ 7:0 mmol/L, (2) twice oral glucose tolerance test (OGTT ≥ 11:1 mmol/L), and (3) diabetic symptoms (polyuria, thirst, drinking more water, and unexplained weight loss) accompanied with twice random blood glucose ≥ 11:1 mmol/L.",179,137,long-term antibiotic application,16S,34,Illumina,"LEfSe,Mann-Whitney (Wilcoxon)",0.05,NA,2,"age,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 2,27 June 2021,Madhubani Dey,"Madhubani Dey,Lwaldron",Increased abundance of bacterial communities in individuals with Type 2 Diabetes,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Raoultella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|201174;2|201174|1760|2037|2049|1654;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|216572|244127;2|201174|1760|85004|31953|1678;2|95818;2|1224|1236|91347|543|544;2|201174|84998|84999|84107|102106;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|1224|1236|91347|543|570;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|976|200643|171549|2005525|375288;2|1224;2|1224|1236|91347|543|160674;2|1239|91061|186826|1300|1301;2|1239|186801|186802|216572|292632;2|74201;2|1239|91061|186826|33958|46255,Complete,NA
Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,periodontitis,EFO:0000649,Healthy controls,Individuals diagnosed with Periodontitis,"Individuals with Peridontitis; Periodontal disease was assessed by determining the PD, CAL, BI, GI, and PLI, which were measured at six sites (i.e., mesiobuccal, buccal, distobuccal, distolingual, lingual, and mesiolingual) according to the Community Periodontal Index by an experienced dentist. Periodontitis patients had a PD of ≥ 5 mm and a CAL of ≥ 3 mm.",27,31,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Figure 3,22 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial species in individuals with Periodontitis as compared to healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella forsythia,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",2|976|200643|171549|171551|836|28124;2|976|200643|171549|171551|836|837;2|976|200643|171549|171552|838|165179;2|976|200643|171549|171552|838|28133;2|976|200643|171549|2005525|195950|28112;2|203691|203692|136|2845253|157|58231,Complete,NA
Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,periodontitis,EFO:0000649,Healthy controls,Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP),Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP); Patients were classified into the DAP group when both periodontitis and T2DM were present.,27,46,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,increased,NA,NA,Signature 1,Supplementary Fig 3a,27 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals in DAP group compared to healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella stercoricanis",2|976|200643|171549|171552|1283313|671218;2|976|200643|171549|171552|838|165179;2|1224|28216|80840|119060|48736|329;2|1224|28216|80840|995019|40544|234908,Complete,NA
Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,Experiment 3,China,Homo sapiens,saliva,UBERON:0001836,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals with Type 2 Diabetes; Type 2 Diabetes determined by a fasting blood sugar of > 7.0 mmol/L and an HbA1c concentration of > 7%, as stated by the American Diabetes Association in 201834",27,9,3 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,Experiment 4,China,Homo sapiens,saliva,UBERON:0001836,periodontitis,EFO:0000649,Healthy controls,Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group),"Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group",27,20,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Supplementary Fig 3b,27 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of microbial communities in individuals in Met group compared to the contriols,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella salivae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema medium",2|1239|1737404|1737405|1570339|543311|33033;2|1239|186801|186802|186804|1257|341694;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|1177574;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552|838|228604;2|1239|526524|526525|128827|123375|102148;2|203691|203692|136|2845253|157|59892;2|203691|203692|136|2845253|157|58231,Complete,NA
Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,Experiment 5,China,Homo sapiens,saliva,UBERON:0001836,periodontitis,EFO:0000649,Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP),Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group),"Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group",46,20,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 5c, 5d",27 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in Met group compared to DAP group,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium|s__Phyllobacterium myrsinacearum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia|s__Ralstonia pickettii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella stercoricanis",2|976|200643|171549|171552|1283313|671218;2|1224|28211|356|69277|28100|28101;2|976|200643|171549|171552|838|165179;2|1224|28216|80840|119060|48736|329;2|1224|28216|80840|995019|40544|234908,Complete,NA
Study 457,"cross-sectional observational, not case-control",32958790,10.1038/s41598-020-72035-1,https://pubmed.ncbi.nlm.nih.gov/32958790/,"Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q , Yang P",Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment,Scientific reports,2020,Experiment 5,China,Homo sapiens,saliva,UBERON:0001836,periodontitis,EFO:0000649,Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP),Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group),"Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group",46,20,patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 5c, 5d",27 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals of Met group compared to DAP group,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus|s__Streptobacillus moniliformis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans",2|976|200643|171549|171552|838|1177574;2|32066|203490|203491|1129771|34104|34105;2|1239|91061|186826|1300|1301|1309,Complete,NA
Study 458,"cross-sectional observational, not case-control",34103263,10.1016/j.jmii.2021.03.015,NA,"Miao Q, Ma Y, Ling Y, Jin W, Su Y, Wang Q, Pan J, Zhang Y, Chen H, Yuan J, Wu H , Hu B","Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai","Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2021,Experiment 1,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Non-intubated patients with non-incubation viral pneumonia or non-incubation non-infectious diseases,COVID-19 patients,Intubated patients with critically severe COVID-19 infection,54,50,NA,WMS,NA,BGISEQ-500 Sequencing,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Text,17 June 2021,Claregrieve1,Claregrieve1,Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pelomonas|s__Pelomonas sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas",2|1224|1236|2887326|468|469;2|1224|1236|91347|543|570;2|1224|28216|80840|80864|335058|1909303;2|1224|28216|80840|119060|48736;2|1224|28211|204457|41297|13687,Complete,NA
Study 458,"cross-sectional observational, not case-control",34103263,10.1016/j.jmii.2021.03.015,NA,"Miao Q, Ma Y, Ling Y, Jin W, Su Y, Wang Q, Pan J, Zhang Y, Chen H, Yuan J, Wu H , Hu B","Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai","Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2021,Experiment 1,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Non-intubated patients with non-incubation viral pneumonia or non-incubation non-infectious diseases,COVID-19 patients,Intubated patients with critically severe COVID-19 infection,54,50,NA,WMS,NA,BGISEQ-500 Sequencing,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Text,17 June 2021,Claregrieve1,Claregrieve1,Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|724;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 458,"cross-sectional observational, not case-control",34103263,10.1016/j.jmii.2021.03.015,NA,"Miao Q, Ma Y, Ling Y, Jin W, Su Y, Wang Q, Pan J, Zhang Y, Chen H, Yuan J, Wu H , Hu B","Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai","Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi",2021,Experiment 2,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Intubated control patients with viral pneumonia or non-infectious diseases,Intubated COVID-19 patients,Intubated patients with critically severe COVID-19 infection,20,50,NA,WMS,NA,BGISEQ-500 Sequencing,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 459,"cross-sectional observational, not case-control",34058978,10.1186/s12575-021-00148-6,NA,"Engen PA, Naqib A, Jennings C, Green SJ, Landay A, Keshavarzian A , Voigt RM",Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients,Biological procedures online,2021,Experiment 1,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients who are COVID-19 positive by RT-PCR,10,9,NA,16S,4,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 1,Supplementary Tables 5 & 6,17 June 2021,Claregrieve1,"Claregrieve1,Chloe,WikiWorks743",Differential abundance of nasopharyngeal bacteria between COVID-19-positive and COVID-19-negative samples,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Firmicutes|c__Bacilli",2|976|200643|171549|171552|1283313;2|1239|1737404|1737405|1570339|165779;2|976;2|201174|1760|1643682|85030|38501;2|1239|186801|186802|31979|580596;2|1224|29547|213849|72294|194;2|976|117743|200644|49546|1016;2|976|117743|200644|2762318|59732;2|1239|1737404|1737405|1570339|150022;2|976|117743|200644|49546|237;2|1239|91061|1385|1378;2|201174|1760|85006|1268|57493;2|201174|1760|85006|1268|1269;2|1224|1236|2887326|468|475;2|1239|1737404|1737405|1570339|162289;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|201174|1760|85006|1268|32207;2|1239|909932|909929|1843491|970;2|1239|909932|1843489|31977|29465;2|1224|1236|135623|641|662;2|1239|91061,Complete,Chloe
Study 459,"cross-sectional observational, not case-control",34058978,10.1186/s12575-021-00148-6,NA,"Engen PA, Naqib A, Jennings C, Green SJ, Landay A, Keshavarzian A , Voigt RM",Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients,Biological procedures online,2021,Experiment 1,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients who are COVID-19 positive by RT-PCR,10,9,NA,16S,4,Illumina,DESeq2,0.05,FALSE,NA,NA,NA,unchanged,unchanged,NA,unchanged,NA,unchanged,Signature 2,Supplementary Tables 5 & 6,17 June 2021,Claregrieve1,Claregrieve1,Differential abundance of nasopharyngeal bacteria between COVID-19-positive and COVID-19-negative samples,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae|g__Tumebacillus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania",2|1239|91061|1385|186823|432330;2|1224|28216|206351|1499392|397456,Complete,Chloe
Study 460,"cross-sectional observational, not case-control",33903709,10.1038/s41598-021-88536-6,NA,"Braun T, Halevi S, Hadar R, Efroni G, Glick Saar E, Keller N, Amir A, Amit S , Haberman Y",SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition,Scientific reports,2021,Experiment 1,Israel,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients,COVID-19 positive patients,SARS-CoV-2 presence by RT-PCR,29,26,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,Experiment 1,Poland,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,Healthy controls,Individuals diagnosed with Type 1 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,30 days,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,20 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of the fungal genus in individuals diagnosed with Type 1 Diabetes compared to healthy controls,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Dioszegia,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces",2759|4751|5204|155616|5234|1884640|165440;2759|4751|4890|4891|4892|4893|4930,Complete,NA
Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,Experiment 1,Poland,Homo sapiens,feces,UBERON:0001988,type I diabetes mellitus,MONDO:0005147,Healthy controls,Individuals diagnosed with Type 1 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,30 days,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,20 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of the fungal genus in individuals diagnosed with Type 1 Diabetes compared to healthy controls,increased,"k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mortierellomycetes|o__Mortierellales|f__Mortierellaceae|g__Mortierella,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Hymenochaetales|f__Schizoporaceae|g__Xylodon",2759|4751|1913637|2212732|214503|4854|4855;2759|4751|5204|155616|90883|1851551|42658;2759|4751|5204|155619|139380|574935|1124675,Complete,NA
Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,Experiment 2,Poland,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,26,30 days,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,20 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of the fungal genus in individuals diagnosed with Type 2 Diabetes compared to the healthy controls,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae|g__Bullera,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Ganoderma,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|g__Naganishia,k__Eukaryota|k__Fungi|p__Ascomycota|g__Saitoella,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Wallemiomycetes|o__Wallemiales|f__Wallemiaceae|g__Wallemia",2759|4751|5204|155616|5234|1905116|4970;2759|4751|5204|155619|5303|5317|5314;2759|4751|5204|155616|90886|5408|1851509;2759|4751|4890|5605;2759|4751|5204|431957|431958|431959|148959,Complete,NA
Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,Experiment 2,Poland,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 1 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,26,30 days,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,20 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of the fungal genus in individuals diagnosed with Type 2 Diabetes compared to healthy controls,increased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Exobasidiomycetes|o__Entylomatales|g__Tilletiopsis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleribasidiaceae|g__Vishniacozyma",2759|4751|5204|452283|62914|1500560;2759|4751|5204|155616|90883|1851551|42658;2759|4751|5204|155616|5234|1884640|1891946,Complete,NA
Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,Experiment 3,Poland,Homo sapiens,feces,UBERON:0001988,diabetes mellitus,EFO:0000400,Individuals diagnosed with Type 1 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,30 days,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,20 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance in the fungal communities in Type 2 Diabetes patients compared to Type 1 Diabetes patients,decreased,"k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Bulleraceae|g__Bullera,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Polyporales|f__Polyporaceae|g__Ganoderma,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|g__Naganishia,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces",2759|4751|5204|155616|5234|1905116|4970;2759|4751|5204|155619|5303|5317|5314;2759|4751|5204|155616|90886|5408|1851509;2759|4751|5204|155616|90883|1851551|42658,Complete,NA
Study 462,"cross-sectional observational, not case-control",33806027,10.3390/nu13041066,https://pubmed.ncbi.nlm.nih.gov/33806027/,"Salamon D, Sroka-Oleksiak A, Gurgul A, Arent Z, Szopa M, Bulanda M, Małecki MT , Gosiewski T",Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity-Pilot Study,Nutrients,2021,Experiment 3,Poland,Homo sapiens,feces,UBERON:0001988,diabetes mellitus,EFO:0000400,Individuals diagnosed with Type 1 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus,"Individuals diagnosed with Type 2 Diabetes Mellitus in 2012–2015 at the Department of Metabolic Diseases, University Hospital, Krakow, Poland",26,24,30 days,16S,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4 and Figure 6,20 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance in the fungal communities in Type 2 Diabetes patients compared to Type 1 Diabetes patients,increased,"k__Eukaryota|k__Fungi|p__Ascomycota,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Exobasidiomycetes|o__Entylomatales|g__Tilletiopsis",2759|4751|4890;2759|4751|4890|4891|4892|4893|4930;2759|4751|5204|452283|62914|1500560,Complete,NA
Study 463,time series / longitudinal observational,33833065,10.1136/gutjnl-2021-324090,NA,"Chen Y, Gu S, Chen Y, Lu H, Shi D, Guo J, Wu WR, Yang Y, Li Y, Xu KJ, Ding C, Luo R, Huang C, Yu L, Xu M, Yi P, Liu J, Tao JJ, Zhang H, Lv L, Wang B, Sheng J , Li L",Six-month follow-up of gut microbiota richness in patients with COVID-19,Gut,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients 6 months post-COVID-19 infection,30,30,Any antibiotic or prebiotic use in previous months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 463,time series / longitudinal observational,33833065,10.1136/gutjnl-2021-324090,NA,"Chen Y, Gu S, Chen Y, Lu H, Shi D, Guo J, Wu WR, Yang Y, Li Y, Xu KJ, Ding C, Luo R, Huang C, Yu L, Xu M, Yi P, Liu J, Tao JJ, Zhang H, Lv L, Wang B, Sheng J , Li L",Six-month follow-up of gut microbiota richness in patients with COVID-19,Gut,2021,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients in convalescence,Sample from COVID-19 convalescence period (from viral clearance to 2 weeks after hospital discharge),30,30,Any antibiotic or prebiotic use in previous months,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,"age,body mass index,sex",NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,Experiment 1,China,Homo sapiens,tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Confirmed COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",100,48,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 1,Supplementary Figures 1E and 1G,21 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Candidatus Gracilibacteria,k__Bacteria|p__Candidatus Saccharibacteria|s__Candidatus Saccharibacteria genomosp. TM7-H1,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Tenericutes,k__Bacteria|p__Candidatus Absconditabacteria|s__candidate division SR1 bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Candidatus Saccharibacteria|s__candidate division TM7 genomosp. GTL1,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Candidatus Saccharibacteria|g__Candidatus Saccharimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|976;2|363464;2|95818|2080739;2|1224;2|544448;2|221235|2044938;2|1239|186801|186802|186803|43996;2|1239|186801|186802|543314|86331;2|1239|186801|186802|186804;2|1239|186801|186802|186804|44259;2|1239|186801|186802|543314;2|1224|1236|135615|868|2717;2|1239|1737404|1737405|1570339|543311;2|1239|91061|1385|1378;2|201174|1760|85007|1653|1716;2|1239|526524|526525|128827|123375;2|95818|443342;2|1239|186801|186802|186803|265975;2|95818|1331051;2|1239|186801|186802|186804|1257;2|1239|91061|186826|1300|1301;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724;2|976|200643|171549|171551|836,Complete,NA
Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,Experiment 1,China,Homo sapiens,tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Confirmed COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",100,48,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,NA,Signature 2,Supplementary Figures 1E and 1G,21 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance in tongue-coating samples from healthy controls compared with confirmed COVID-19 patients,increased,"k__Bacteria|p__Cyanobacteria,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Spirochaeta,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|1117;2|203691|203692|136|137|146;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|186828|117563;2|1239|909932|1843489|31977|906;2|1224|29547|213849|72294|194;2|1239|909932|909929|1843491|970;2|1239|186801|186802|216572|1263|41978;2|976|200643|171549|2005525|195950,Complete,NA
Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,Experiment 2,China,Homo sapiens,tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Confirmed COVID-19 patients who recovered,150,22,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4c,25 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls,decreased,"k__Bacteria|p__Candidatus Saccharibacteria|g__Candidatus Saccharimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas",2|95818|1331051;2|1239|186801|186802|543314;2|1224|1236|135625|712|724;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171551|836,Complete,NA
Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,Experiment 2,China,Homo sapiens,tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Confirmed COVID-19 patients who recovered,150,22,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,2,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4c,25 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance in oral microbiome samples between recovered COVID-19 cases and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas",2|1239|909932|909929|1843491|82202;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|970,Complete,NA
Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",48,24,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 1,"Figure 5c, S3E, S3G -Supp 05",25 June 2021,Claregrieve1,"Claregrieve1,Lwaldron",Differential microbial abundance between samples from healthy controls and samples from COVID-19 patients,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Pseudobutyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|s__bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|1224|28221|213115|194924|35832;2|1239|186801|186802|186803|572511;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1239|186801|186802|186803|33042;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|216851;2|1224|1236|135625|712|724;2|1239|526524|526525|128827|61170;2|1239|186801|186802|1392389;2|1224|1236|91347|543|570;2|1239|186801|186802|186803|28050;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|186801|186802|186803|46205;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263;2|1224|28211|204457|41297|13687;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303;2|1869227;2|1239|186801|186802|216572|707003,Complete,NA
Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,"Suspected COVID-19 cases with one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",48,24,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,decreased,NA,decreased,Signature 2,Figure 5c,25 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between samples from healthy controls and samples from COVID-19 patients,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Devosiaceae|g__Pelagibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953|1678;2|1239|91061|186826|81852|1350;2|1239|186801|186802|186803;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1224|1236|135619|28256|2745;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|265975;2|1239|909932|1843489|31977|29465;2|1239|526524|526525|128827|123375;2|201174|84998|84999|1643824|1380;2|1239|186801|186802|216572|946234;2|1224|28211|356|2831106|1082930;2|1239|91061|1385|1378;2|1239|91061|186826|186828|117563,Complete,NA
Study 464,"cross-sectional observational, not case-control",33789966,10.1136/gutjnl-2020-323826,NA,"Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, Liu X, Liu C, Li A, Wang X, Rao B, Yuan C, Zhang H, Sun J, Chen X, Li B, Hu C, Wu Z, Yu Z, Kan Q , Li L",Alterations in the human oral and gut microbiomes and lipidomics in COVID-19,Gut,2021,Experiment 4,China,Homo sapiens,tongue,UBERON:0001723,COVID-19,MONDO:0100096,Healthy controls,Suspected COVID-19 patients,"Suspected COVID-19 cases without one of the following etiological or serological evidence:
(1) Fluorescence RT-PCR detects the positive of the COVID-19 virus nucleic acid.
(2) Viral gene sequencing finds highly homologous to COVID-19 virus",150,37,Receipt of antibiotics and/or probiotics within 8 weeks prior to enrollment,16S,345,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,decreased,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 465,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y, Ye X, Ding D , Lu Y",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,diabetic neuropathy,EFO:1000783,Healthy controls,Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes,"Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes; The criteria for DPN were as follows: spontaneous limb pain, symmetrical or unilateral limb numbness, sensation of dullness and body tension, muscle weakness, weakened or absent tendon reflexes, and significant decreases in sensory and motor nerve conduction velocities as revealed via electromyography indicating the positive involvement of two or more nerves and normal arterial pulses in the foot and back.",14,45,3 months,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 5a, 5b",24 June 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals with diabetic peripheral neuropathy,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|201174;2|1239|186801|186802|186803|572511;2|1224|1236|91347|543|561;2|1239;2|1239|186801|186802|186803|1506553;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803|2316020|33039;2|1224|1236|91347|543|1940338,Complete,NA
Study 465,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y, Ye X, Ding D , Lu Y",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,diabetic neuropathy,EFO:1000783,Healthy controls,Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes,"Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes; The criteria for DPN were as follows: spontaneous limb pain, symmetrical or unilateral limb numbness, sensation of dullness and body tension, muscle weakness, weakened or absent tendon reflexes, and significant decreases in sensory and motor nerve conduction velocities as revealed via electromyography indicating the positive involvement of two or more nerves and normal arterial pulses in the foot and back.",14,45,3 months,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 5a, 5b",24 June 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals with diabetic peripheral neuropathy,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976|200643|171549|815|816;2|976;2|1239|186801|186802|216572|216851,Complete,NA
Study 465,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y, Ye X, Ding D , Lu Y",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,diabetic neuropathy,EFO:1000783,Individuals diagnosed with type 2 diabetes Mellitus,Individuals diagnosed with peripheral neuropathy associated with type 2 diabetes,"Patients with peripheral neuropathy associated with type 2 diabetes; the criteria for DPN were as follows: spontaneous limb pain, symmetrical or unilateral limb numbness, sensation of dullness and body tension, muscle weakness, weakened or absent tendon reflexes, and significant decreases in sensory and motor nerve conduction velocities as revealed via electromyography indicating the positive involvement of two or more nerves and normal arterial pulses in the foot and back.",21,45,3 months,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 465,case-control,32938282,10.1177/0300060520936806,https://pubmed.ncbi.nlm.nih.gov/32938282/,"Wang Y, Ye X, Ding D , Lu Y",Characteristics of the intestinal flora in patients with peripheral neuropathy associated with type 2 diabetes,The Journal of international medical research,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; The diagnoses of type 2 diabetes mellitus were established according to the diagnostic criteria of the American Diabetes Association,14,21,3 months,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 1,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",HER2 Positive Breast Carcinoma,EFO:1000294,Her2 negative tumor,Her2 positive tumor,Breast cancer patients with Her2 positive tumors (human epidermal growth factor receptive 2 positive),25,12,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,29 June 2021,Itslanapark,Itslanapark,Mean ratio estimates found using zero-inflated negative binomial model of taxa abundance by HER2 status,increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,2|1239|909932|1843488|909930|904,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 1,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",HER2 Positive Breast Carcinoma,EFO:1000294,Her2 negative tumor,Her2 positive tumor,Breast cancer patients with Her2 positive tumors (human epidermal growth factor receptive 2 positive),25,12,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,age,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 3,30 June 2021,Itslanapark,Itslanapark,"Mean ratio estimates found using zero-inflated negative binomial model of taxa abundance by ER, PR, and HER2 status",decreased,"k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1224|28221|213115|194924|872;2|1239|186801|186802|216572|1263,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 2,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",age at menarche,EFO:0004703,early age at menarche (≤11),later age at menarche (≥12),breast cancer patients with age at menarche being over 12 years old,11,26,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,increased,NA,NA,NA,Signature 1,Table 5,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios gound using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",increased,NA,NA,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 2,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",age at menarche,EFO:0004703,early age at menarche (≤11),later age at menarche (≥12),breast cancer patients with age at menarche being over 12 years old,11,26,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,increased,NA,NA,NA,Signature 2,Table 5,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",decreased,"k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2157|28890|183925|2158|2159|2172;2|1239|186801|186802|216572|1263,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 3,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",estrogen receptor status,EFO:0005512,ER+,ER-,breast cancer patients with negative Estrogen Receptor status,9,28,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 3,5 July 2021,Itslanapark,Itslanapark,"Mean ratio estimates obtained by zero-inflated negative binomial model of taxa abundances by estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 status.",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|29465,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 4,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",progesterone receptor status,EFO:0005513,PR+,PR-,breast cancer patients with negative progesterone receptor status,23,14,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 5,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",breast cancer,MONDO:0007254,Grade Low (I/II),Grade High (III),breast cancer patients with grade high level tumors (Grade III),14,23,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,7 July 2021,Itslanapark,Itslanapark,Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,increased,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,2|201174|84998|1643822|1643826|84111,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 5,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",breast cancer,MONDO:0007254,Grade Low (I/II),Grade High (III),breast cancer patients with grade high level tumors (Grade III),14,23,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,7 July 2021,Itslanapark,Itslanapark,Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes",2|1239|186801|186802|186803;2|1239|186801|186802|186803|207244,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 6,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",breast cancer stage,EFO:0005607,Stage Low (I/II),Stage High (III),Breast cancer patients with high stage progression of breast cancer (Stage III).,22,15,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 4,7 July 2021,Itslanapark,Itslanapark,Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1239|186801|186802|31979|1485;2|1239|909932|1843489|31977|29465;2|1224|1236|135625|712|724,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 6,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",breast cancer stage,EFO:0005607,Stage Low (I/II),Stage High (III),Breast cancer patients with high stage progression of breast cancer (Stage III).,22,15,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table 4,7 July 2021,Itslanapark,Itslanapark,Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium",2|1239|909932|1843488|909930|904;2|1239|526524|526525|2810280|135858,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 7,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",age,EFO:0000246,Age 50+,Age ≤50,Breast cancer patients who's age is ≤50 years old.,17,20,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Kruskall-Wallis,0.001,FALSE,NA,NA,"ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 5,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus",2|1239|186801|186802|31979;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543;2|1239|91061|186826|1300|1357,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 8,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",parous,EFO:0002947,Parous,Nulliparous,Breast cancer patients who are nulliparous (have had no live births.),29,8,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Kruskall-Wallis,0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 5,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.",decreased,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,2|1239|526524|526525|2810280|135858,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 9,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",body mass index,EFO:0004340,BMI<25,BMI≥25,Breast cancer patients with a high body mass index (BMI≥25),9,28,Antibiotic use one week or more during the month prior to fecal sample collection.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,ethnic group,race",NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table 6,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.",increased,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,2|74201|203494|48461|1647988|239934,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 10,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",body fat percentage,EFO:0007800,TBF≤46%,TBF>46%,Breast cancer patients with a total body fat percentage ≥46%.,25,12,NA,NA,NA,NA,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table 6,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.",increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 10,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",body fat percentage,EFO:0007800,TBF≤46%,TBF>46%,Breast cancer patients with a total body fat percentage ≥46%.,25,12,NA,NA,NA,NA,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table 6,7 July 2021,Itslanapark,Itslanapark,"Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.",decreased,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,2|201174|84998|84999|84107,Complete,NA
Study 467,"cross-sectional observational, not case-control",32468338,10.1007/s10549-020-05702-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297869/,"Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA , Spicer D",Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study,Breast cancer research and treatment,2020,Experiment 11,United States of America,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",physical activity,EFO:0003940,Yes Physical Activity,No Physical Activity,Breast cancer patients who do not have regular physical activity.,24,13,Antibiotic use one week or more during the month prior to fecal sample collection.,NA,NA,NA,Mann-Whitney (Wilcoxon),0.001,FALSE,NA,NA,"age,race",NA,unchanged,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 468,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A , Urman B","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,Experiment 1,Turkey,Homo sapiens,vagina,UBERON:0000996,endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,"All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification. 

Diagnosis of endometriosis was verified through histology.",14,14,Participants were excluded if they had taken antibiotics within the past 8 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3 and Table 1,24 June 2021,Samara.Khan,Samara.Khan,Gemella and Atopobium were completely absent in the vagina of endometriosis stage 3/4 patients when compared to healthy controls.,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella",2|201174|84998|84999|1643824|1380;2|1239|91061|1385|1378,Complete,NA
Study 468,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A , Urman B","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,Experiment 2,Turkey,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification. Diagnosis of endometriosis was verified through histology.,14,14,Participants were excluded if they had taken antibiotics within the past 8 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3 and Table 1,24 June 2021,Samara.Khan,Samara.Khan,Atopobium and Sneathia bacteria were decreased in endometriosis stage 3/4 patients compared to healthy controls. Atopobium bacteria were completely absent in endometriosis patients.,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia",2|201174|84998|84999|1643824|1380;2|32066|203490|203491|1129771|168808,Complete,NA
Study 468,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A , Urman B","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,Experiment 2,Turkey,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification. Diagnosis of endometriosis was verified through histology.,14,14,Participants were excluded if they had taken antibiotics within the past 8 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1,24 June 2021,Samara.Khan,Samara.Khan,Alloprevotella bacteria were significantly increased in endometriosis stage 3/4 patients when compared to healthy controls,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,2|976|200643|171549|171552|1283313,Complete,NA
Study 468,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A , Urman B","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,Experiment 3,Turkey,Homo sapiens,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,"All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to
American Fertility Society Revised Classification. Diagnosis of endometriosis was verified through histology.",14,14,Participants were excluded if they had taken antibiotics within the past 8 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1 and Figure 3,24 June 2021,Samara.Khan,Samara.Khan,"Gardnerella, Sneathia, and Barnesiella bacteria were significantly decreased in endometriosis stage 3/4 patients when compared to healthy controls",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",2|201174|1760|85004|31953|2701;2|32066|203490|203491|1129771|168808;2|976|200643|171549|2005519|397864,Complete,NA
Study 468,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A , Urman B","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,Experiment 4,Turkey,Homo sapiens,vagina,UBERON:0000996,endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,"All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification. 

Diagnosis of endometriosis was verified through histology.",14,14,Participants were excluded if they had taken antibiotics within the past 8 weeks.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1,4 August 2021,Samara.Khan,Samara.Khan,Gardnerella and Escherichia/Shigella bacteria were significantly increased in endometriosis stage 3/4 patients when compared to healthy controls. This was part of a sensitivity analysis excluding all Lactobacillus species since Lactobacillus is the predominant species in the lower female reproductive tract.,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|201174|1760|85004|31953|2701;2|1224|1236|91347|543|1940338,Complete,NA
Study 468,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A , Urman B","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,Experiment 5,Turkey,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification. Diagnosis of endometriosis was verified through histology.,14,14,Participants were excluded if they had taken antibiotics within the past 8 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1,4 August 2021,Samara.Khan,Samara.Khan,"Gardnerella, Escherichia/Shigella, Streptococcus, and Ureaplasma bacteria were significantly increased in endometriosis stage 3/4 patients when compared to healthy controls. This was part of a sensitivity analysis excluding all Lactobacillus species since Lactobacillus is the predominant species in the lower female reproductive tract.",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|201174|1760|85004|31953|2701;2|1239|91061|186826|1300|1301;2|544448|31969|2085|2092|2129;2|1224|1236|91347|543|1940338,Complete,NA
Study 468,prospective cohort,30778155,10.1038/s41598-019-39700-6,https://pubmed.ncbi.nlm.nih.gov/30778155/,"Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A , Urman B","The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls",Scientific reports,2019,Experiment 5,Turkey,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification. Diagnosis of endometriosis was verified through histology.,14,14,Participants were excluded if they had taken antibiotics within the past 8 weeks,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1,4 August 2021,Samara.Khan,Samara.Khan,"Prevotella, Dialister, and Megasphaera bacteria were significantly increased in endometriosis stage 3/4 patients when compared to healthy controls. This was part of a sensitivity analysis excluding all Lactobacillus species since Lactobacillus is the predominant species in the lower female reproductive tract.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|906,Complete,NA
Study 469,"cross-sectional observational, not case-control",34151035,10.1016/j.synbio.2021.06.002,NA,"Liu J, Liu S, Zhang Z, Lee X, Wu W, Huang Z, Lei Z, Xu W, Chen D, Wu X, Guo Y, Peng L, Lin B, Chong Y, Mou X, Shi M, Lan P, Chen T, Zhao W , Gao Z",Association between the nasopharyngeal microbiome and metabolome in patients with COVID-19,Synthetic and systems biotechnology,2021,Experiment 1,China,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-COVID-19 controls,COVID-19 patients,Positive for infection with SARS-CoV-2 by nucleic acid testing,3,6,NA,WMS,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figures 3c-d,25 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance in nasopharyngeal samples between COVID-19 cases and controls,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia",2|1239|91061|1385|1378|1379;2|1224|29547|213849|72294|194|824;2|32066|203490|203491|1129771|32067|157688;2|1239|91061|1385|1378|29391;2|1224|1236|135614|32033|40323|40324,Complete,NA
Study 470,"case-control,meta-analysis",30936547,10.1038/s41591-019-0406-6,NA,"Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P , Zeller G",Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer,Nature medicine,2019,Experiment 1,"Austria,China,France,Germany,Italy,Japan,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,colorectal cancer,Colorectal cancer cases from eight independent studies,392,386,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1 (species) and extended data fig. 4 (genera),26 June 2021,Lwaldron,Lwaldron,Species and genera enriched in CRC vs controls,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum|s__Fusobacterium nucleatum subsp. animalis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum|s__Fusobacterium nucleatum subsp. vincentii,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|1737404|1737405|1570339|165779;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|186801|186802|216572|244127|1872531;2|1239|186801|186802|1898207;2|1239|909932|1843489|31977|39948|1955814;2|1239|186801|186802|186803|2719313|208479;2|1239|186801|186802|186806|1730;2|32066|203490|203491|203492|848;2|32066|203490|203491|203492|848|851;2|32066|203490|203491|203492|848|851|76859;2|32066|203490|203491|203492|848|851|155615;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|1378;2|1239|91061|1385|1378|29391;2|1239|186801|186802|31979|1649459;2|1239|186801|186802|31979|1649459|154046;2|1239|186801|186802|186803|1506553;2|32066|203490|203491|1129771|32067;2|1239|1737404|1737405|1570339|543311;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|186802|186804|1904861;2|1239|186801|186802|186804|1257;2|1239|186801|186802|186804|1257|341694;2|976|200643|171549|171551|836;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|28133;2|1239|526524|526525|128827|123375;2|1239|526524|526525|128827|123375|102148;2|1239|186801|186802|216572|292632;2|1239|186801|186802|216572|292632|2053618;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|2316020|33039,Complete,NA
Study 470,"case-control,meta-analysis",30936547,10.1038/s41591-019-0406-6,NA,"Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P , Zeller G",Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer,Nature medicine,2019,Experiment 1,"Austria,China,France,Germany,Italy,Japan,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,colorectal cancer,Colorectal cancer cases from eight independent studies,392,386,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Extended Data Fig. 4,5 July 2021,Lwaldron,Lwaldron,Genera enriched in CRC vs controls,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum",2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|186806|1730;2|32066|203490|203491|203492|848;2|1239|91061|1385|1378;2|1239|186801|186802|31979|1649459;2|1239|186801|186802|186803|1506553;2|32066|203490|203491|1129771|32067;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186804|1257;2|976|200643|171549|171551|836;2|1239|526524|526525|128827|123375;2|1239|186801|186802|216572|292632,Complete,NA
Study 470,"case-control,meta-analysis",30936547,10.1038/s41591-019-0406-6,NA,"Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P , Zeller G",Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer,Nature medicine,2019,Experiment 1,"Austria,China,France,Germany,Italy,Japan,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,colorectal cancer,Colorectal cancer cases from eight independent studies,392,386,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 3,Fig. 1,5 July 2021,Lwaldron,Lwaldron,Species enriched in CRC vs controls,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum|s__Fusobacterium nucleatum subsp. animalis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum|s__Fusobacterium nucleatum subsp. vincentii,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|s__Peptostreptococcaceae bacterium",2|1239|1737404|1737405|1570339|165779|1287640;2|1239|186801|186802|216572|244127|1872531;2|1239|909932|1843489|31977|39948|1955814;2|1239|186801|186802|186803|2719313|208479;2|32066|203490|203491|203492|848|851;2|32066|203490|203491|203492|848|851|76859;2|32066|203490|203491|203492|848|851|155615;2|32066|203490|203491|203492|848|68766;2|1239|91061|1385|1378|29391;2|1239|186801|186802|31979|1649459|154046;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|186802|186804|1257|341694;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28131;2|976|200643|171549|171552|838|28133;2|1239|526524|526525|128827|123375|102148;2|1239|186801|186802|216572|292632|2053618;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|2316020|33039;2|1239|186801|186802|1898207;2|1239|186801|186802|186804|1904861,Complete,NA
Study 471,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A , Segata N",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,Experiment 1,"Austria,Canada,China,France,Italy,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Extended Data Fig. 4,26 June 2021,Lwaldron,Lwaldron,taxonomic meta-analysis of CRC cases vs controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila sp.,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium limosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium mortiferum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium necrophorum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp.,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter sp.,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus harei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia cardiffensis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus dysgalactiae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. tigurinus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171552|1283313|76122;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|1737404|1737405|1570339|165779|33037;2|1239|186801|186802|216572|244127|1872531;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|291644;2|1224|28221|213115|194924|35832|1929485;2|1224|28221|213115|194924|35832|35833;2|1224|29547|213849|72294|194|824;2|1224|29547|213849|72294|194|204;2|1224|29547|213849|72294|194|827;2|1224|28221|213115|194924|872|876;2|1224|28216|206351|481|538|539;2|1224|1236|91347|543|561|562;2|1239|186801|186802|186806|1730|1736;2|1239|186801|186802|216572|946234|292800;2|32066|203490|203491|203492|848|850;2|32066|203490|203491|203492|848|859;2|32066|203490|203491|203492|848|851;2|1239|91061|1385|1378|29391;2|1239|91061|186826|186828|117563|46124;2|1239|186801|186802|186803|658086;2|201174|84998|84999|1643824|2767353|1383;2|32066|203490|203491|1129771|32067|104608;2157|28890|183925|2158|2159|2172|2173;2157|28890|183925|2158|2159|2172|66852;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|1737404|1737405|1570339|162289|54005;2|1239|186801|186802|186804|1257|1261;2|1239|186801|186802|186804|1257|1262;2|1239|186801|186802|186804|1257|341694;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28131;2|201174|1760|2037|2049|2529408|181487;2|1239|909932|909929|1843491|970|69823;2|201174|84998|1643822|1643826|84108|84109;2|201174|84998|1643822|1643826|84108|2049041;2|1239|526524|526525|128827|123375|102148;2|1239|91061|186826|1300|1301|76860;2|1239|91061|186826|1300|1301|1334;2|1239|91061|186826|1300|1301|315405;2|1239|91061|186826|1300|1301|1303|1077464;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|543314|56774;2|1239|186801|186802|186803|2316020|33039,Complete,Lwaldron
Study 471,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A , Segata N",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,Experiment 1,"Austria,Canada,China,France,Italy,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 2,Extended Data Fig. 4,26 June 2021,Lwaldron,Lwaldron,taxonomic meta-analysis of CRC cases vs controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_1_57FAA,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 5_1_39BFAA,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum",2|1239|186801|186802|186803|658081;2|1239|186801|186802|216572|1263|457412;2|1224|1236|72274|135621|286|306;2|201174|1760|85004|31953|1678|216816|1679;2|1239|186801|186802|186803|2569097|39488;2|201174|84998|1643822|1643826|447020|446660;2|1239|91061|186826|1300|1301|1308;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186803|841|166486;2|201174|84998|1643822|1643826|644652|471189;2|201174|1760|85004|31953|1678|1686,Complete,Lwaldron
Study 471,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A , Segata N",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,Experiment 1,"Austria,Canada,China,France,Italy,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 3,Extended Data Fig. 5,26 June 2021,Lwaldron,Lwaldron,putative oral species in CRC cases vs controls,increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus constellatus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] infirmum,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis|s__Streptococcus oralis subsp. tigurinus",2|32066|203490|203491|203492|848|851;2|1239|1737404|1737405|1570339|543311|33033;2|1239|91061|1385|1378|29391;2|1239|186801|186802|186804|1257|341694;2|1239|526524|526525|128827|123375|102148;2|976|200643|171549|171552|838|28131;2|1239|91061|186826|1300|1301|76860;2|1239|91061|186826|186828|117563|46124;2|1224|28216|206351|481|538|539;2|1224|29547|213849|72294|194|204;2|976|200643|171549|171552|1283313|76122;2|1239|186801|186802|543314|56774;2|1224|29547|213849|72294|194|824;2|976|200643|171549|171552|838|28133;2|1239|91061|186826|1300|1301|1303|1077464,Complete,Lwaldron
Study 471,"case-control,meta-analysis",30936548,10.1038/s41591-019-0405-7,NA,"Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A , Segata N",Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation,Nature medicine,2019,Experiment 1,"Austria,Canada,China,France,Italy,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,colorectal cancer cases,colorectal cancer cases,308,313,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 4,Extended Data Fig. 5,26 June 2021,Lwaldron,Lwaldron,putative oral species in CRC cases vs controls,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis",2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|113107,Complete,Lwaldron
Study 472,prospective cohort,34302684,10.1007/s40618-021-01595-4,https://pubmed.ncbi.nlm.nih.gov/34302684/,"Wei J, Qing Y, Zhou H, Liu J, Qi C , Gao J",16S rRNA gene amplicon sequencing of gut microbiota in gestational diabetes mellitus and their correlation with disease risk factors,Journal of endocrinological investigation,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gestational diabetes,EFO:0004593,Pregnant individuals who are normal glucose tolerance (NGT)],Pregnant individuals with gestational diabetes,Pregnant individuals with gestational diabetes,18,15,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3b, 3c, Table S1",16 August 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in GDM individuals as compared to NGT controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica|s__Salmonella enterica subsp. enterica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum",2|1239|186801;2|1239|186801|186802|1898207;2|1239;2|1239|186801|186802|216572|1263|40518;2|1224|1236|91347|543|590|28901|59201;2|1239|186801|186802|186803|1506577|36835,Complete,NA
Study 472,prospective cohort,34302684,10.1007/s40618-021-01595-4,https://pubmed.ncbi.nlm.nih.gov/34302684/,"Wei J, Qing Y, Zhou H, Liu J, Qi C , Gao J",16S rRNA gene amplicon sequencing of gut microbiota in gestational diabetes mellitus and their correlation with disease risk factors,Journal of endocrinological investigation,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,gestational diabetes,EFO:0004593,Pregnant individuals who are normal glucose tolerance (NGT)],Pregnant individuals with gestational diabetes,Pregnant individuals with gestational diabetes,18,15,1 month,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3b, 3c, Table S1",16 August 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in GDM individuals as compared to NGT controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium",2|976|200643|171549;2|976;2|976|200643;2|1239|186801|186802|186803|140625,Complete,NA
Study 473,"cross-sectional observational, not case-control",33659220,10.3389/fcimb.2021.625581,NA,"Nardelli C, Gentile I, Setaro M, Di Domenico C, Pinchera B, Buonomo AR, Zappulo E, Scotto R, Scaglione GL, Castaldo G , Capoluongo E",Nasopharyngeal Microbiome Signature in COVID-19 Positive Patients: Can We Definitively Get a Role to <i>Fusobacterium periodonticum</i>?,Frontiers in cellular and infection microbiology,2021,Experiment 1,Italy,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Symptomatic COVID-19 positive patients,12,18,NA,16S,123,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3A-F,28 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial composition between COVID-19 patients and controls,decreased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|32066;2|1224|1236;2|32066|203490|203491;2|1224|1236|135625;2|32066|203490|203491|1129771;2|32066|203490|203491|203492;2|1224|1236|135625|712;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724,Complete,NA
Study 474,case-control,33977168,10.1016/j.genrep.2021.101200,NA,"Hoque MN, Rahman MS, Ahmed R, Hossain MS, Islam MS, Islam T, Hossain MA , Siddiki AZ",Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases,Gene reports,2021,Experiment 1,"Bangladesh,China,United Kingdom,United States of America",Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-COVID patients with URTI or COPD,COVID-19 patients,Confirmed COVID-19 diagnosis by RT-qPCR,10,11,NA,WMS,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,Text/Figure 3,28 June 2021,Claregrieve1,Claregrieve1,Differential abundance of bacteria between non-COVID-19 patients and COVID-19 patients,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Tenericutes,k__Bacteria|p__Cyanobacteria",2|1224;2|544448;2|1117,Complete,NA
Study 474,case-control,33977168,10.1016/j.genrep.2021.101200,NA,"Hoque MN, Rahman MS, Ahmed R, Hossain MS, Islam MS, Islam T, Hossain MA , Siddiki AZ",Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases,Gene reports,2021,Experiment 1,"Bangladesh,China,United Kingdom,United States of America",Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-COVID patients with URTI or COPD,COVID-19 patients,Confirmed COVID-19 diagnosis by RT-qPCR,10,11,NA,WMS,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,Text/Figure 3,28 June 2021,Claregrieve1,Claregrieve1,Differential bacterial abundance between non-COVID-19 patients and COVID-19 patients,decreased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Actinobacteria",2|32066;2|1239;2|976;2|201174,Complete,NA
Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,Experiment 1,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Non-COVID-19 patients (Group NP),"6 COVID-19 patients, 10 non-COVID-19 patients, 2 healthy controls",13,18,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,Experiment 2,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type I Patients,"16 COVID-19 patients, 2 healthy controls",13,18,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,increased,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,Experiment 3,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type II patients,"47 COVID-19 patients, 1 healthy control",13,48,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,increased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,Experiment 4,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type III patients,"10 COVID-19 patients, 1 healthy control",13,11,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,decreased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,Experiment 5,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls (Group H),Community Type IV patients,4 COVID-19 patients,13,4,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,decreased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,Experiment 6,China,Homo sapiens,rectum,UBERON:0001052,COVID-19,MONDO:0100096,Group I - High Diversity COVID-19 patients,Group II - Medium Diversity COVID-19 patients,Patients with medium microbial diversity in rectal samples,15,24,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,unchanged,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 475,time series / longitudinal observational,33603076,10.1038/s42003-021-01796-w,NA,"Xu R, Lu R, Zhang T, Wu Q, Cai W, Han X, Wan Z, Jin X, Zhang Z , Zhang C",Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults,Communications biology,2021,Experiment 7,China,Homo sapiens,rectum,UBERON:0001052,COVID-19,MONDO:0100096,Group I - High Diversity COVID-19 patients,Group III - Low Diversity COVID-19 patients,Patients with low microbial diversity in rectal swab samples,15,24,NA,16S,4,Illumina,ANOSIM,0.05,TRUE,NA,NA,NA,decreased,NA,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 476,case-control,34055851,10.3389/fnut.2021.638825,NA,"Tian Y, Sun KY, Meng TQ, Ye Z, Guo SM, Li ZM, Xiong CL, Yin Y, Li HG , Zhou LQ",Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery,Frontiers in nutrition,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,"Patients between 25-45 years of age with documented recovery from COVID-19, detailed medical records during hospitalization and discharge certificate",7,7,Participants instructed to avoid any drugs affecting gastrointestinal function before sampling,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,decreased,decreased,NA,NA,Signature 1,Figure 4b,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between controls and recovered COVID-19 patients,increased,"k__Bacteria|p__Actinobacteria|c__Acidimicrobiia,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Coleoptera|f__Lycidae|s__Metriorrhynchinae|g__Microtrichalus,k__Bacteria|p__Actinobacteria|c__Acidimicrobiia|o__Acidimicrobiales|f__Microthrixaceae|g__Candidatus Microthrix,k__Bacteria|p__Actinobacteria|c__Acidimicrobiia|o__Acidimicrobiales|f__Microthrixaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae",2|201174|84992;2759|33208|6656|50557|7041|71195|2043424|343821;2|201174|84992|84993|1798913|41949;2|201174|84992|84993|1798913;2|201174|1760|85006|1268|32207;2|201174|1760|85006;2|1239|526524|526525|128827|1505663;2|201174|1760|85006|1268,Complete,NA
Study 476,case-control,34055851,10.3389/fnut.2021.638825,NA,"Tian Y, Sun KY, Meng TQ, Ye Z, Guo SM, Li ZM, Xiong CL, Yin Y, Li HG , Zhou LQ",Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery,Frontiers in nutrition,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,"Patients between 25-45 years of age with documented recovery from COVID-19, detailed medical records during hospitalization and discharge certificate",7,7,Participants instructed to avoid any drugs affecting gastrointestinal function before sampling,16S,34,Illumina,LEfSe,0.05,FALSE,3.5,NA,NA,NA,unchanged,decreased,decreased,NA,NA,Signature 2,Figure 4b,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between controls and recovered COVID-19 patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella",2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263|41978;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|2569097|39488;2|201174|84998|84999|84107;2|201174|84998|84999|84107|102106,Complete,NA
Study 477,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero MP, Cuadrat RRC, Vidal I, Andrade BGN, Molina-Pardines C, Haro-Moreno JM, Coutinho FH, Merino E, Regitano LCA, Silveira CB, Afli H, López-Pérez M , Rodríguez JC",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,Experiment 1,Spain,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,Severe COVID-19 patients,Patients with confirmed COVID-19 infection and severe symptoms; required hospital admission,18,18,NA,16S,34,Illumina,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S5,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|976|200643|171549|171552|1283313;2|976|200643|171549|171552|838;2|1239|186801|186802|186803|43996;2|1239|186801|186802|186803|1164882;2|1239|186801|186802|186803|265975;2|1239|526524|526525|128827,Complete,NA
Study 477,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero MP, Cuadrat RRC, Vidal I, Andrade BGN, Molina-Pardines C, Haro-Moreno JM, Coutinho FH, Merino E, Regitano LCA, Silveira CB, Afli H, López-Pérez M , Rodríguez JC",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,Experiment 2,Spain,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,Severe COVID-19 patients requiring ICU,Patients with confirmed COVID-19 infection and severe symptoms who were admitted into the intensive care unit,18,19,NA,16S,34,Illumina,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S5,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care,increased,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,2|203691|203692|136|2845253|157,Complete,NA
Study 477,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero MP, Cuadrat RRC, Vidal I, Andrade BGN, Molina-Pardines C, Haro-Moreno JM, Coutinho FH, Merino E, Regitano LCA, Silveira CB, Afli H, López-Pérez M , Rodríguez JC",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,Experiment 2,Spain,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,Severe COVID-19 patients requiring ICU,Patients with confirmed COVID-19 infection and severe symptoms who were admitted into the intensive care unit,18,19,NA,16S,34,Illumina,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Table S5,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of bacterial taxa between healthy controls and severe COVID-19 patients requiring ICU care,decreased,k__Eukaryota|s__uncultured phototrophic eukaryote,2759|172788,Complete,NA
Study 477,"cross-sectional observational, not case-control",33815323,10.3389/fmicb.2021.637430,NA,"Ventero MP, Cuadrat RRC, Vidal I, Andrade BGN, Molina-Pardines C, Haro-Moreno JM, Coutinho FH, Merino E, Regitano LCA, Silveira CB, Afli H, López-Pérez M , Rodríguez JC",Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19,Frontiers in microbiology,2021,Experiment 3,Spain,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,Patients with confirmed COVID-19 infection and severe symptoms who were hospitalized,19,18,NA,16S,34,Illumina,Linear Regression,0.25,TRUE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplemental Table S5,29 June 2021,Claregrieve1,Claregrieve1,Differential abundance of bacterial taxa between mild and severe COVID-19 cases,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,2|976|200643|171549|171552|838,Complete,NA
Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,Experiment 1,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,13 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HSID18069,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",2|201174|1760|85009|31957|2801844;2|201174|1760|2037|2049|2050;2|1239|186801|186802|186803|265975;2|1239|186801|186802|186803|265975|712414;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|2419515;2|201174|84998|1643822|1643826|84108;2|201174|1760|85009|31957|2801844|1750,Complete,NA
Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,Experiment 1,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4c,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus|s__Liquorilactobacillus nagelii",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|2767888|82688,Complete,NA
Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,Experiment 2,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Flu patients,COVID-19 patients,Confirmed COVID-19 cases,29,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4c,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and other flu patients,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HSID18069,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",2|201174|1760|85009|31957|2801844;2|1239|91061|186826|33958|2742598|1613;2|1239|186801|186802|186803|265975;2|1239|186801|186802|186803|265975|712414;2|976|200643|171549|171552|838|419005;2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|32207|2419515;2|201174|84998|1643822|1643826|84108;2|201174|1760|85009|31957|2801844|1750,Complete,NA
Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,Experiment 3,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,29,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 4c,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between flu patients and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus|s__Liquorilactobacillus nagelii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii",2|1239|909932|1843489|31977|29465;2|1239|91061|186826|33958|2767888|82688;2|1239|91061|186826|33958|2742598|1613;2|976|200643|171549|171552|838|419005,Complete,NA
Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,Experiment 3,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,29,31,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 4c,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between flu patients and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia sp. HSID18069,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp. oral taxon 108,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica",2|1239|186801|186802|186803|265975;2|201174|1760|85009|31957|2801844;2|201174|1760|85006|1268|32207;2|201174|1760|2037|2049|2050;2|201174|1760|85006|1268|32207|2419515;2|1239|186801|186802|186803|265975|712414;2|201174|1760|85009|31957|2801844|1750,Complete,NA
Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,Experiment 4,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a-b,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls by LefSe,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Cellulomonadaceae|g__Cellulomonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Cryptobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Promicromonosporaceae|g__Xylanimonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus",2|201174|1760|2037|2049|76833;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|118747;2|201174|1760|85006|85016|1707;2|201174|1760|85007|1653|1716;2|201174|84998|1643822|1643826|84162;2|1239|186801|186802|186804|44259;2|201174|1760|85006|2805426|57499;2|1239|186801|186802|186803|1164882;2|1239|186801|186802|543314|86331;2|1239|1737404|1737405|1570339|543311;2|201174|1760|85009|31957|1743;2|201174|1760|2037|2049|2529408;2|1239|909932|909929|1843491|970;2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207;2|1239|186801|186802|186803|265975;2|201174|1760|85006|85017|186188;2|201174|1760|85009|31957|2801844;2|1224|1236|135615|868|2717;2|201174|1760|2037|2049|184869;2|201174|1760|2037|2049|2050,Complete,NA
Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,Experiment 4,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Confirmed COVID-19 cases,28,31,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a-b,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and healthy controls by LefSe,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|186827|46123,Complete,NA
Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,Experiment 5,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,28,29,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2a,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between flu patients and healthy controls by LefSe,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Promicromonosporaceae|g__Xylanimonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum",2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|1654;2|201174|1760|85006|1268|32207;2|1239|186801|186802|186803|265975;2|201174|1760|85006|85017|186188;2|201174|1760|85009|31957|2801844;2|1224|1236|135615|868|2717;2|201174|1760|2037|2049|184869,Complete,NA
Study 478,"cross-sectional observational, not case-control",33986253,10.1038/s41392-021-00614-3,NA,"Ma S, Zhang F, Zhou F, Li H, Ge W, Gan R, Nie H, Li B, Wang Y, Wu M, Li D, Wang D, Wang Z, You Y , Huang Z",Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19,Signal transduction and targeted therapy,2021,Experiment 5,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,Flu patients,Patients with influenza B,28,29,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2a,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between flu patients and healthy controls by LefSe,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|909932|1843489|31977|906;2|1239|909932|1843489|31977|29465,Complete,NA
Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,Experiment 1,Italy,Homo sapiens,"nasopharynx,oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Healthy controls,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,10,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Table S1,30 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and ICU COVID-19 patients,decreased,"k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Deinococcus-Thermus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family III. Incertae Sedis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pelomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Tepidiphilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family III. Incertae Sedis|g__Thermoanaerobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Thermosinus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Firmicutes|c__Tissierellia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",2|95818;2|1297;2|1224|1236|135624|84642;2|1239|91061|1385|186823;2|1224|28211|204458|76892;2|1224|28216|206351|1499392;2|1297|188787|118964|183710;2|1224|29547|213849|72293;2|1224|2008785|119069|206349;2|201174|1760|85006|85021;2|1224|28216|80840|75682;2|201174|84995|84996|84997;2|1239|909932|909929|1843490;2|1239|186801|68295|186814;2|1239|186801|68295|543371;2|1224|1236|2887326|468|469;2|1224|1236|135624|84642|642;2|201174|1760|85006|1268|1663;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|1224|28216|80840|119060|32008;2|1239|186801|186802|186803|830;2|1239|186801|186802|31979|1485;2|1297|188787|118964|183710|1298;2|1239|186801|186802|186804|44259;2|1224|28216|206351|1499392|397456;2|1239|186801|186802|186803|43994;2|201174|1760|85006|85023|33882;2|1224|1236|135625|712|745;2|1224|28216|80840|80864|335058;2|1224|28216|80840|119060|48736;2|201174|84995|84996|84997|42255;2|1224|28216|206351|481|1193515;2|1224|2008785|119069|206349|203470;2|1239|186801|68295|186814|1754;2|1239|186801|68295|543371|28895;2|1239|909932|909929|1843490|261684;2|976|117743|200644|49546;2|544448|31969;2|1224|28216|206351;2|976|200643|171549|171551;2|1239|909932|909929|1843491;2|1239|1737404;2|1224|28216|80840|80864|34072,Complete,NA
Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,Experiment 1,Italy,Homo sapiens,"nasopharynx,oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Healthy controls,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,10,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Table S1,30 June 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and ICU COVID-19 patients,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|201174|1760|85006|85020;2|1224|1236|91347|1903409;2|201174|1760|85007|85025;2|1224|1236|91347|1903410;2|1224|29547|213849;2|1224|1236|135614|32033;2|1224|1236|91347|1903411;2|1224|1236|91347|543|547;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570;2|1239|186801|186802|186803|1506553;2|201174|1760|85007|2805586|1847725;2|201174|1760|85006|1268|1269;2|201174|84998|84999|1643824|133925;2|1239|91061|1385|186822|44249;2|1224|1236|91347|1903409|53335;2|201174|1760|85007|85025|1827;2|1224|1236|91347|543|590;2|201174|1760|85004|31953|196081;2|1224|1236|91347|1903411|613;2|1224|1236|135614|32033|40323;2|1239|186801|186802|543314;2|201174|1760|85007;2|1239|91061|186826|81852;2|1224|1236|72274|135621;2|1239|91061|1385|90964,Complete,NA
Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,Experiment 2,Italy,Homo sapiens,"nasopharynx,oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Healthy controls,Mild-moderate COVID-19 patients,COVID-19 patients with mild to moderate symptoms that were not admitted to an intensive care unit,10,11,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between healthy controls and mild-moderate COVID-19 cases,decreased,"k__Bacteria|p__Deinococcus-Thermus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Alicyclobacillaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family III. Incertae Sedis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Gulbenkiania,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Okadaella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pelomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Tepidiphilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacteraceae|g__Thermoanaerobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Thermoanaerobacterales|f__Thermoanaerobacterales Family III. Incertae Sedis|g__Thermoanaerobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Sporomusaceae|g__Thermosinus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Variovorax",2|1297;2|1239|91061|1385|186823;2|1224|28211|204458|76892;2|1224|28216|206351|1499392;2|1224|2008785|119069|206349;2|201174|1760|85006|85021;2|201174|1760|85006|85023;2|1224|28216|80840|75682;2|201174|84995|84996|84997;2|1239|909932|909929|1843490;2|1239|186801|68295|186814;2|1239|186801|68295|543371;2|1224|28216|80840;2|201174|1760|85006|1268|1663;2|1239|526524|526525|128827|118747;2|1224|28216|80840|119060|32008;2|1297|188787|118964|183710|1298;2|1224|28216|206351|1499392|397456;2|1239|186801|186802|186803|43994;2|201174|1760|85006|1268|57493;2|1239|91061|186826|1300|1357;2|1239|91061|186826|1300|948104;2|1224|28216|80840|80864|335058;2|1224|28216|80840|119060|48736;2|201174|84995|84996|84997|42255;2|1224|28216|206351|481|1193515;2|1224|2008785|119069|206349|203470;2|1239|186801|68295|186814|1754;2|1239|186801|68295|543371|28895;2|1239|909932|909929|1843490|261684;2|1224|28216|80840|119060;2|1239|186801|186802|31979;2|201174|1760|85007;2|1224|1236|91347|543;2|1224|29547;2|201174|1760|85009|31957;2|1239|909932|909929|1843491;2|1224|28216|80840|80864|34072,Complete,NA
Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,Experiment 2,Italy,Homo sapiens,"nasopharynx,oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Healthy controls,Mild-moderate COVID-19 patients,COVID-19 patients with mild to moderate symptoms that were not admitted to an intensive care unit,10,11,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between healthy controls and mild-moderate COVID-19 cases,increased,"k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Tenericutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halanaerobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Streptobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1297|188787|118964|183710;2|1224|28211|356|119045;2|1224|28211;2|1224|29547|213849;2|1224|29547;2|976|117743|200644;2|544448;2|1239|186801|53433|972|2330;2|1224|28211|356|119045|407;2|32066|203490|203491|1129771|34104;2|1239|186801|186802|543314;2|1239|91061|186826|81852;2|1239|186801|186802|186806;2|1224|1236|2887326|468;2|544448|31969|2085|2092;2|1239|91061|1385|90964,Complete,NA
Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,Experiment 3,Italy,Homo sapiens,"nasopharynx,oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Mild-Moderate COVID-19 patients,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,11,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 1,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between mild-moderate COVID-19 patients and ICU-admitted COVID-19 patients,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halanaerobium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Pasteurella,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Tenericutes,k__Bacteria|p__Firmicutes|c__Tissierellia",2|1224|1236|2887326|468|469;2|1224|1236|135624|84642;2|1224|1236|135624|84642|642;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|118747;2|1239|186801|186802|186803|830;2|95818;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186804|44259;2|976|117743|200644;2|1239|186801|53433|972;2|1239|186801|53433|972|2330;2|1224|29547|213849|72293;2|1224|28211|356|119045|407;2|544448|31969|2085|2092;2|1224|1236|135625|712|745;2|544448|31969|2085|2092;2|544448|31969;2|1224|1236|2887326|468;2|201174|1760|85006|1268;2|32066|203490|203491;2|32066|203490|203491|203492;2|976|117743|200644|49546;2|1239|186801|186802|186806;2|1224|29547;2|1224|28211;2|201174|1760|85004|31953;2|1224|28216|206351;2|976|200643|171549|171551;2|544448;2|1239|1737404,Complete,NA
Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,Experiment 3,Italy,Homo sapiens,"nasopharynx,oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Mild-Moderate COVID-19 patients,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,11,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,decreased,decreased,NA,NA,NA,Signature 2,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between mild-moderate COVID-19 patients and ICU-admitted COVID-19 patients,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Okadaella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae",2|1224|1236|91347|543|547;2|1224|1236|91347|1903409;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570;2|201174|1760|85006|1268|57493;2|1239|186801|186802|186803|1506553;2|1239|91061|186826|1300|1357;2|201174|1760|85007|2805586|1847725;2|201174|1760|85006|85023;2|201174|1760|85006|1268|1269;2|201174|1760|85007|85025;2|1239|91061|186826|1300|948104;2|201174|84998|84999|1643824|133925;2|1239|91061|1385|186822|44249;2|1224|1236|91347|1903409|53335;2|1224|1236|91347|1903410;2|201174|1760|85007|85025|1827;2|1224|1236|91347|543|590;2|201174|1760|85004|31953|196081;2|1224|1236|91347|1903411|613;2|1224|1236|135614|32033|40323;2|1224|1236|135614|32033;2|1224|1236|91347|1903411;2|201174|1760|85007|1653;2|201174|1760|85007;2|1224|1236|91347|543;2|201174|1760|85009|31957;2|1224|1236|72274|135621|286;2|1224|1236|135614|32033,Complete,NA
Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,Experiment 4,Italy,Homo sapiens,"nasopharynx,oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Patients infected with other human coronaviruses,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,8,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between non-COVID coronavirus patients and ICU COVID patients,decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Demequinaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Geodermatophilales|f__Geodermatophilaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Planococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Tissierellia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Arsenophonus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Geodermatophilales|f__Geodermatophilaceae|g__Blastococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Casaltella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Paracoccus,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Pedobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pelomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinobacteria|c__Rubrobacteria|o__Rubrobacterales|f__Rubrobacteraceae|g__Rubrobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Saccharopolyspora,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Snodgrassella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Intrasporangiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Xanthomonas",2|1224|28211|204441|433;2|1224|1236|135624|84642;2|1224|28216|80840|506;2|201174|1760|85006|85019;2|1224|28211|204458|76892;2|1224|1236|1706369|1706371;2|976|1853228|1853229|563835;2|1239|186801|186802|424536;2|201174|84998|84999|84107;2|201174|1760|85006|1042322;2|1224|28221|213115|194924;2|201174|1760|1643682|85030;2|201174|1760|85006|85021;2|1224|28211|356|119045;2|1224|1236|91347|1903414;2|201174|1760|85007|1762;2|201174|1760|85009|85015;2|976|200643|171549|1853231;2|1224|28216|80840|75682;2|1239|91061|1385|186818;2|201174|1760|85010|2070;2|1224|28211|356|82115;2|976|200643|171549|171550;2|201174|84995|84996|84997;2|976|117747|200666|84566;2|1224|28211|204457|41297;2|1224|28211;2|1224|28216|80840;2|1239|526524|526525;2|1239|526524;2|1239|1737404;2|1224|1236|2887326|468|469;2|1224|1236|135624|84642|642;2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|207244;2|1224|1236|91347|1903414|637;2|201174|1760|85006|1268|1663;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|201174|1760|1643682|85030|38501;2|1239|186801|186802|186803|572511;2|201174|1760|85006|85019|1696;2|1224|28211|204458|76892|41275;2|1224|28216|80840|119060|32008;2|1239|186801|186802|543314|1715793;2|1224|28211|204458|76892|75;2|976|117743|200644|2762318|59732;2|1239|186801|186802|31979|1485;2|1224|28216|80840|119060|106589;2|1239|186801|186802|186803|189330;2|1239|91061|186826|186827|66831;2|1239|186801|186802|186804|44259;2|1239|526524|526525|128827|1573535;2|201174|1760|85006|85021|53457;2|1224|28216|80840|75682|149698;2|1224|28211|356|119045|407;2|201174|1760|85006|85023|33882;2|201174|1760|85007|1762|1763;2|1239|909932|1843489|31977|909928;2|201174|1760|85009|85015|1839;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|1224|28211|204455|31989|265;2|976|117747|200666|84566|84567;2|1224|28216|80840|80864|335058;2|1224|28216|80840|119060|48736;2|1239|186801|186802|186803|841;2|201174|84995|84996|84997|42255;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1263;2|201174|1760|85010|2070|1835;2|1224|28216|206351|481|1193515;2|1224|28211|204457|41297|13687;2|1239|186801|186802|186803|1506577;2|201174|1760|2037|2049|1654|29317;2|201174|1760|2037;2|1239|91061|1385|186817;2|1224|28216|80840|119060;2|1239|186801|186802|31979;2|201174|1760|85006|85020;2|1239|526524|526525|128827;2|1239|186801|186802|186806;2|976|117743|200644|49546;2|201174|1760|85006|85021;2|201174|1760|85006|85023;2|201174|1760|85006|1268;2|1224|28216|206351;2|201174|1760|85007|85025;2|1239|1737404|1737405|1570339;2|1224|28211|204455|31989;2|1239|186801|186802|216572|1263;2|1224|28211|204457|41297;2|1224|1236|135614|32033|338,Complete,NA
Study 479,case-control,33672177,10.3390/ijerph18042174,NA,"Rueca M, Fontana A, Bartolini B, Piselli P, Mazzarelli A, Copetti M, Binda E, Perri F, Gruber CEM, Nicastri E, Marchioni L, Ippolito G, Capobianchi MR, Di Caro A , Pazienza V",Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing,International journal of environmental research and public health,2021,Experiment 4,Italy,Homo sapiens,"nasopharynx,oropharynx","UBERON:0001728,UBERON:0001729",COVID-19,MONDO:0100096,Patients infected with other human coronaviruses,ICU COVID-19 patients,COVID-19 patients admitted to intensive care unit,8,10,NA,16S,23456789,Ion Torrent,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,Table S1,1 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between non-COVID coronavirus patients and ICU COVID patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae",2|1239|91061|186826|1300|1357;2|1224|1236|91347|543|590;2|201174|1760|85004|31953|196081;2|1224|1236|91347|1903411|613;2|1224|29547|213849;2|1239|186801|186802|543314|2137877;2|1239|91061|186826|81852;2|1224|1236|72274|135621,Complete,NA
Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,Experiment 1,Brazil,Homo sapiens,vagina,UBERON:0000996,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign conditions,Confirmed endometriosis patients,Patients were assigned to the endometriosis group after endometriosis was confirmed via laparoscopic surgery and histology.,11,10,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,There was increased abundance of gemella and streptococcus when comparing the vaginal fluid of endometriosis patients to healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061|1385|1378;2|1239|91061|186826|1300|1301,Complete,NA
Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,Experiment 1,Brazil,Homo sapiens,vagina,UBERON:0000996,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign conditions,Confirmed endometriosis patients,Patients were assigned to the endometriosis group after endometriosis was confirmed via laparoscopic surgery and histology.,11,10,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,"There was decreased abundance of aerococcus in vaginal fluid of endometriosis patients compared to healthy controls. Atopobium, which is normally found in the lower female reproductive tract, was completely absent in vaginal fluid of endometriosis patients.",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",2|1239|91061|186826|186827|1375;2|201174|84998|84999|1643824|1380,Complete,NA
Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,Experiment 2,Brazil,Homo sapiens,endometrium,UBERON:0001295,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign conditions,Confirmed endometriosis patients,Patients were assigned to the endometriosis group after endometriosis was confirmed via laparoscopic surgery and histology.,11,10,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,There was increased abundance of bifidobacterium when comparing the endometrial lining of endometriosis patients to healthy controls,increased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,2|201174|1760|85004|31953|1678,Complete,NA
Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,Experiment 2,Brazil,Homo sapiens,endometrium,UBERON:0001295,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign conditions,Confirmed endometriosis patients,Patients were assigned to the endometriosis group after endometriosis was confirmed via laparoscopic surgery and histology.,11,10,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,"There was decreased abundance of atopobium, mobiluncus, campylobacter, chromohalobacter, and alcanivorax when comparing the endometrial lining of endometriosis patients to healthy controls",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Chromohalobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus",2|1224|1236|135619|224372|59753;2|201174|84998|84999|1643824|1380;2|1224|29547|213849|72294|194;2|1224|1236|135619|28256|42054;2|201174|1760|2037|2049|2050,Complete,NA
Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,Experiment 3,Brazil,Homo sapiens,endometrium,UBERON:0001295,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign conditions,Confirmed endometriosis patients,Patients were assigned to the endometriosis group after endometriosis was confirmed via laparoscopic surgery and histology.,11,10,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 1,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,"When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were increased: aerococcus, staphylococcus, sphingomonas, alishewanella, pseudomonas, and enterococcus",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alishewanella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|91061|186826|186827|1375;2|1239|91061|1385|90964|1279;2|1224|28211|204457|41297|13687;2|1224|1236|135622|72275|111142;2|1224|1236|72274|135621|286;2|1239|91061|186826|81852|1350,Complete,NA
Study 480,case-control,32192080,10.3390/diagnostics10030163,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151170/,"Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF , Podgaec S","Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion","Diagnostics (Basel, Switzerland)",2020,Experiment 3,Brazil,Homo sapiens,endometrium,UBERON:0001295,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign conditions,Confirmed endometriosis patients,Patients were assigned to the endometriosis group after endometriosis was confirmed via laparoscopic surgery and histology.,11,10,within 30 days prior to sample collection,16S,34,Illumina,DESeq2,0,FALSE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,unchanged,Signature 2,Figure 4B,1 July 2021,Samara.Khan,Samara.Khan,"When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were decreased: prevotella, atopobium, afipia, mobiluncus, campylobacter, and facklamia",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae|g__Afipia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia",2|976|200643|171549|171552|838;2|201174|84998|84999|1643824|1380;2|1224|28211|356|41294|1033;2|201174|1760|2037|2049|2050;2|1224|29547|213849|72294|194;2|1239|91061|186826|186827|66831,Complete,NA
Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,5,13,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3d,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between healthy controls and COVID-19 patients,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__Erysipelatoclostridium ramosum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 1_4_56FAA",2|1239|186801|186802|186803|2316020|33038;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|128827|1505663|1547;2|201174|84998|1643822|1643826|84111|84112;2|1239|186801|186802|186803|658082;2|1239|186801|186802|186803|658655,Complete,NA
Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,5,13,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3d,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between healthy controls and COVID-19 patients,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes ihumii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes indistinctus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis",2|976|200643|171549|171550|239759|1470347;2|1239|186801|186802|186803|841|166486;2|1224|28216|80840|469610;2|1239|186801|186802|186803|2569097|39488;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|171550|239759|626932;2|976|200643|171549|2005519|1348911|1099853;2|1239|186801|186802|186803|28050|39485;2|976|200643|171549|2030927;2|976|200643|171549|815|816|291644;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|171550|239759|328814;2|1239|186801|186802|216572|1263|40518;2|976|200643|171549|815|909656|204516,Complete,NA
Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Antibiotic-naive COVID-19 patients,Antibiotic-treated COVID-19 patients,Patients with COVID-19 treated with antibiotics,8,5,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3g,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and antibiotic-treated COVID-19 patients,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__Erysipelatoclostridium ramosum",2|1239|909932|1843489|31977|29465|29466;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|128827|1505663|1547,Complete,NA
Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Antibiotic-naive COVID-19 patients,Antibiotic-treated COVID-19 patients,Patients with COVID-19 treated with antibiotics,8,5,NA,WMS,NA,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 3g,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and antibiotic-treated COVID-19 patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2 1 46FAA,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",2|1239|186801|186802|216572|292632|2053618;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|186803|841|301301;2|1224|28216|80840|995019|577310|487175;2|1239|186801|186802|186803|2683689;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|33042|116085;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|815|909656|821,Complete,NA
Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,Patients with severe COVID-19,3,3,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between mild and severe COVID-19 patients,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium glucuronolyticum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus avium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc lactis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella|s__Weissella confusa,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella glucosivorans,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis",2|201174|1760|85007|1653|1716|61592;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|81852|1350|1352;2|1224|29547|213849|72294|194|824;2|201174|1760|85007|1653|1716|39791;2|201174|1760|85006|1268|32207|172042;2|201174|1760|85004|31953|419014|419015;2|1239|91061|186826|81852|1350|33945;2|1239|91061|186826|81852|1350|37734;2|1239|91061|186826|33958|1243|1246;2|1239|91061|186826|33958|46255|1583;2|1224|28216|80840|80864|80865;2|1224|28216|206351|481|538|2766967;2|1224|29547|213849|72294|194|199;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|570|548;2|1239|91061|186826|1300|1301|68892;2|1239|909932|1843489|31977|906|187326,Complete,NA
Study 481,case-control,33678150,10.1080/19490976.2021.1887722,NA,"Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J , Yang P",Integrated gut virome and bacteriome dynamics in COVID-19 patients,Gut microbes,2021,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,Patients with severe COVID-19,3,3,NA,WMS,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between mild and severe COVID-19 patients,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale,2|1239|186801|186802|186803|39491,Complete,NA
Study 482,"cross-sectional observational, not case-control",33850111,10.1038/s41421-021-00257-2,NA,"Zhong H, Wang Y, Shi Z, Zhang L, Ren H, He W, Zhang Z, Zhu A, Zhao J, Xiao F, Yang F, Liang T, Ye F, Zhong B, Ruan S, Gan M, Zhu J, Li F, Li F, Wang D, Li J, Ren P, Zhu S, Yang H, Wang J, Kristiansen K, Tun HM, Chen W, Zhong N, Xu X, Li YM, Li J , Zhao J",Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients,Cell discovery,2021,Experiment 1,China,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation,7,15,NA,WMS,NA,DNBSEQ-T7,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 2c,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between mild and severe COVID-19 patients,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|29465;2|1224|28216|206351|481|482;2|1239|91061|186826|1300|1301;2|976|200643|171549|171552|838,Complete,NA
Study 482,"cross-sectional observational, not case-control",33850111,10.1038/s41421-021-00257-2,NA,"Zhong H, Wang Y, Shi Z, Zhang L, Ren H, He W, Zhang Z, Zhu A, Zhao J, Xiao F, Yang F, Liang T, Ye F, Zhong B, Ruan S, Gan M, Zhu J, Li F, Li F, Wang D, Li J, Ren P, Zhu S, Yang H, Wang J, Kristiansen K, Tun HM, Chen W, Zhong N, Xu X, Li YM, Li J , Zhao J",Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients,Cell discovery,2021,Experiment 1,China,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation,7,15,NA,WMS,NA,DNBSEQ-T7,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 2c,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between mild and severe COVID-19 patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1239|91061|1385|90964|1279;2|1224|1236|91347|543|561,Complete,NA
Study 482,"cross-sectional observational, not case-control",33850111,10.1038/s41421-021-00257-2,NA,"Zhong H, Wang Y, Shi Z, Zhang L, Ren H, He W, Zhang Z, Zhu A, Zhao J, Xiao F, Yang F, Liang T, Ye F, Zhong B, Ruan S, Gan M, Zhu J, Li F, Li F, Wang D, Li J, Ren P, Zhu S, Yang H, Wang J, Kristiansen K, Tun HM, Chen W, Zhong N, Xu X, Li YM, Li J , Zhao J",Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients,Cell discovery,2021,Experiment 2,China,Homo sapiens,rectum,UBERON:0001052,COVID-19,MONDO:0100096,Mild COVID-19 patients,Severe COVID-19 patients,COVID-19 infected patients admitted to the ICU and requiring mechanical ventilation,7,15,NA,WMS,NA,DNBSEQ-T7,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S6b,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance in microbial taxa between mild and severe COVID-19 patients,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,2|976|200643|171549|2005525|375288,Complete,NA
Study 483,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS , Ng SC",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,"Uninfected controls, pneumonia patients, antibiotics treated COVID-19 patients",Antibiotic-naive COVID-19 patients,"COVID-19 patients hospitalized with SARS-CoV-2 infection confirmed by 2 consecutive RT-PCR tests, not treated with antibiotics",29,7,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and healthy controls,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces viscosus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium hathewayi CAG:224,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii",2|201174|1760|2037|2049|1654|1656;2|1239|186801|186802|31979|1485|1263067;2|976|200643|171549|815|816|291645,Complete,Chloe
Study 483,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS , Ng SC",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,"Uninfected controls, pneumonia patients, antibiotics treated COVID-19 patients",Antibiotic-naive COVID-19 patients,"COVID-19 patients hospitalized with SARS-CoV-2 infection confirmed by 2 consecutive RT-PCR tests, not treated with antibiotics",29,7,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 2,Table 2,11 August 2021,Chloe,Chloe,Differential abundance of microbial taxa between antibiotic-naive COVID-19 patients and healthy controls,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,2|1239|186801|186802|186806|1730|39496,Complete,Chloe
Study 483,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS , Ng SC",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,"Antibiotic-naive COVID-19 patients, pneumonia patients, uninfected controls",Antibiotic-treated COVID-19 patients,"COVID-19 patients hospitalized with SARS-CoV-2 infection confirmed by 2 consecutive RT-PCR tests, treated with antibiotics",28,8,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between antibiotic-naive and antibiotic-treated COVID-19 patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium rectale CAG:36,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus obeum CAG:39,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186806|1730|1263079;2|1239|186801|186802|216572;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|33042;2|1239|186801|186802|216572|1263|1263107;2|1239|186801|186802|186803|658089;2|1239|186801|186802|186806|1730|39496,Complete,Chloe
Study 483,case-control,32442562,10.1053/j.gastro.2020.05.048,NA,"Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS , Ng SC",Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization,Gastroenterology,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,"Uninfected controls, COVID-19 patients",Pneumonia controls,Patients hospitalized with community-acquired pneumonia,30,6,NA,WMS,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,"age,antibiotic exposure,comorbidity,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 2,2 July 2021,Claregrieve1,"Claregrieve1,Chloe",Differential abundance of microbial taxa between healthy controls and pneumonia controls,decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__Erysipelatoclostridium ramosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum",2|1239|526524|526525|2810280|100883;2|1239|91061|186826|81852|1350|1352;2|1239|526524|526525|128827|1505663|1547;2|1239|186801|186802|186803|658089;2|1239|186801|186802|186806|1730|39496,Complete,Chloe
Study 484,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J , Wei H",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,Experiment 1,China,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients with fever and cough,COVID-19 positive patients,COVID-19 positive patients with fever and cough symptoms,11,11,NA,WMS,NA,MGISEQ-2000,ANOVA,0.05,FALSE,NA,NA,NA,decreased,unchanged,NA,NA,NA,unchanged,Signature 1,Figure S2,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and non-COVID-19 patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella ruminicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.",2|1239|91061|186826|1300|1301|1759399;2|1239|91061|186826|1300|1301|1311;2|1239|91061|186826|1300|1301|1307;2|1224|29547|213849|72294|194|197;2|976|200643|171549|171552|838|839;2|976|200643|171549|171552|838|59823,Complete,NA
Study 484,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J , Wei H",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,Experiment 2,China,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Healthy controls,COVID-19 positive patients,COVID-19 positive patients with fever and cough symptoms,7,11,NA,WMS,NA,MGISEQ-2000,ANOVA,0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 484,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J , Wei H",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,Experiment 3,China,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Healthy controls,COVID-19 negative patients with fever and cough,COVID-19 negative patients with fever and cough,7,11,NA,WMS,NA,MGISEQ-2000,ANOVA,0.05,FALSE,NA,NA,NA,decreased,decreased,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 484,case-control,33978940,10.1007/s12250-021-00391-x,NA,"Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J , Wei H",Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19,Virologica Sinica,2021,Experiment 4,China,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative patients with fever and cough,COVID-19 positive patients,COVID-19 positive patients with fever and cough symptoms,11,11,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,FALSE,NA,NA,NA,decreased,unchanged,NA,NA,NA,unchanged,Signature 1,Supplemental Table S5,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and symptomatic non-COVID-19 patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus|s__Aerococcus sanguinicola,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter jejuni,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas gingivalis,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella ruminicola,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 299,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium pseudoperiodonticum,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix|s__Erysipelothrix sp. HDW6B,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema phagedenis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus troglodytae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix|s__Erysipelothrix larvae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HSISM1,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus suis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus ilei,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus|s__Vagococcus teuberi,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus koreensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. CNU G3,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema brennaborense,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella cardium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium camelliae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix|s__Brochothrix thermosphacta,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas cangingivalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus marmotae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium divergens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Fermentimonas|s__Fermentimonas caenicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oris,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium|s__Carnobacterium maltaromaticum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__Lachnoclostridium phytofermentans,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides heparinolyticus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter ureolyticus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus uberis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae",2|1239|91061|186826|1300|1301|1759399;2|1239|186801|186802|186803|28050|39485;2|1239|91061|186826|186827|1375|119206;2|1224|29547|213849|72294|194|197;2|1239|186801|186802|186803|1164882|617123;2|976|200643|171549|171551|836|837;2|1224|29547|213849|72294|194|199;2|1239|91061|186826|1300|1301|1156431;2|976|200643|171549|171552|838|839;2|1239|91061|186826|1300|1301|113107;2|1239|91061|1385|1378|1379;2|976|200643|171549|171552|838|652716;2|1239|909932|1843489|31977|29465|39777;2|32066|203490|203491|203492|848|2663009;2|1224|29547|213849|72294|194|204;2|1239|526524|526525|128827|1647|2714929;2|203691|203692|136|2845253|157|162;2|976|117743|200644|49546|1016|1019;2|1239|91061|186826|1300|1301|1111760;2|1239|526524|526525|128827|1647|1514105;2|1239|91061|186826|1300|1301|1316408;2|1239|91061|186826|1300|1301|1307;2|1239|91061|186826|1300|1301|1156433;2|1239|91061|186826|1300|1301|1318;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|81852|2737|519472;2|1239|91061|186826|1300|1301|2382163;2|1239|91061|186826|1300|1301|2698804;2|203691|203692|136|2845253|157|81028;2|976|117743|200644|2762318|59735|1585976;2|976|200643|171549|171552|838|28129;2|1239|91061|186826|1300|1301|1305;2|976|117743|200644|2762318|59732|1265445;2|1239|91061|1385|186820|2755|2756;2|976|200643|171549|171551|836|36874;2|1239|91061|186826|1300|1301|1825069;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|186828|2747|2748;2|976|200643|171549|2005520|1784836|1562970;2|976|200643|171549|171552|838|28135;2|1239|91061|186826|186828|2747|2751;2|1239|91061|186826|1300|1301|45634;2|1239|186801|186802|186803|1506553|66219;2|32066|203490|203491|1129771|32067|712357;2|976|200643|171549|171551|836|28123;2|976|200643|171549|815|816|28113;2|1224|29547|213849|72294|194|827;2|1239|91061|186826|1300|1301|1349;2|1239|91061|186826|1300|1301|1311,Complete,NA
Study 485,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y, Shi X, Fu W, Xiang F, He X, Yang B, Wang X , Ma WL",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure 2,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2759|4751|4890|4891|4892|4893|4930;2|1239|91061|186826|81852|1350,Complete,NA
Study 485,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y, Shi X, Fu W, Xiang F, He X, Yang B, Wang X , Ma WL",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure 2,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",2|1239|186801|186802|186803|207244;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|201174|84998|1643822|1643826|84111,Complete,NA
Study 485,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y, Shi X, Fu W, Xiang F, He X, Yang B, Wang X , Ma WL",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S5-7,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,increased,"k__Eukaryota|k__Fungi|p__Ascomycota,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecalis",2759|4751|4890;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|544;2759|4751|4890|4891|4892|4893|4930;2|1224|1236|135625|712|724;2|1239|186801|186802|186803|2719313|208479;2759|4751|4890|4891|4892|4893|4930|4932;2|1224|1236|135625|712|724|729;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|1896336;2|1239|91061|186826|81852|1350|1351,Complete,NA
Study 485,"cross-sectional observational, not case-control",34168484,10.2147/JIR.S311518,NA,"Zhou Y, Shi X, Fu W, Xiang F, He X, Yang B, Wang X , Ma WL",Gut Microbiota Dysbiosis Correlates with Abnormal Immune Response in Moderate COVID-19 Patients with Fever,Journal of inflammation research,2021,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,COVID-19 patients without fever,COVID-19 patients with fever,Symptomatic patients with confirmed COVID-19 (positive for COVID-19 nucleic acid by real-time RT-PCR from throat swab specimens) and fever (axillary temperature > 37.3 degrees Celsius),11,20,NA,WMS,NA,MGISEQ-2000,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Tables S5-7,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with fever and COVID-19 patients without fever,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__Erysipelotrichaceae bacterium 6_1_45,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides cellulosilyticus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|s__Burkholderiales bacterium 1_1_47,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 2_1_58FAA",2|1224|28216|80840|995019|577310;2|201174|84998|1643822|1643826|644652;2|976|200643|171549|171550|239759|328814;2|1239|186801|186802|186803|658087;2|1239|526524|526525|128827|469614;2|976|200643|171549|815|816|818;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|246787;2|976|200643|171549|815|816|371601;2|1239|186801|186802|186803|658086;2|1239|186801|186802|186806|1730|39490;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|815|909656|821;2|1239|186801|186802|186803|207244|649756;2|1224|28216|80840|469610;2|1239|186801|186802|186803|658089;2|1239|186801|186802|186803|658082,Complete,NA
Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,Experiment 1,India,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,Asymptomatic COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with no symptoms,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3a,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy volunteers and asymptomatic COVID-19 patients,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Diptera|f__Micropezidae|s__Calobatinae|g__Compsobata|s__Compsobata cibaria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Hemiptera|f__Aphididae|s__Aphidinae|g__Ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus",2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106|74426;2759|33208|6656|50557|7147|115293|115294|286452|1262234;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|543|547;2|1239|186801|186802|186803|2719313|358743;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958;2759|33208|6656|50557|7524|27482|133076|666060;2|976|200643|171549|2005525|375288|823;2|976|200643|171549|171551;2|1239|186801|186802|216572|1263;2|1224|1236|91347|543|620;2|1239|91061|186826|33958|46255;2|1239|186801|186802|186803|2316020|33038;2|1224|1236|91347|543;2|1224|1236|91347|543|620|622;2|1239|91061|186826|33958|1578|1587,Complete,NA
Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,Experiment 1,India,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,Asymptomatic COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with no symptoms,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3a,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy volunteers and asymptomatic COVID-19 patients,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis",2|1239|909932|1843488|909930|904;2|1224|1236|135624;2|1239|186801|186802|186803|207244;2|201174|1760|85004|31953|1678|1680;2|1224|29547|213849|72294|194;2|1224|29547|213849|72294;2|1224|29547|213849;2|1224|29547;2|1224|1236|135625|712|724|729;2|1239|186801|186802|186803|28050;2|1239|91061|186826|81850;2|1239|909932|1843489|31977|906;2|1239|909932|909929|1843491|52225;2|1239|909932|909929|1843491|52225|52226;2|201174|84998|84999|1643824|133925;2|1224|1236|135625|712;2|1224|1236|135625;2|976|200643|171549|171552|838|165179;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|841|301302;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|216572|1263|40519;2|1224|1236|135624|83763|83770;2|1224|1236|135624|83763;2|1239|909932|1843489|31977;2|1239|91061|186826|33958;2|1224|1236|135625|712;2|1239|909932|1843489|31977;2|1239|186801|186802|186803|2719313|1531,Complete,NA
Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,Experiment 2,India,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with mild symptoms and no requirement of oxygen support/ventilator,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,3 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy volunteers and mild COVID-19 patients,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus|s__Melissococcus plutonius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Eukaryota|k__Viridiplantae|p__Streptophyta,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae",2|1224|1236|91347|543;2759|33090|35493;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1224|1236|72274;2|1224|1236|91347|543|620;2|1224|1236|2887326|468;2|1239|91061|186826|81852|33969|33970;2|1239|91061|186826|81852|33969;2|1224|1236|2887326|468|469;2|1239|91061|186826|33958|1578|1587;2|1224|1236|2887326|468|469|106649;2|1224|1236|91347|543|620|624;2|1239|91061|186826|81850;2759|33090|35493;2|201174|1760|85006|1268;2|1239|91061|186826|33958|46255;2|1239|186801|186802|186803|2719313|358743,Complete,NA
Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,Experiment 2,India,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Asymptomatic COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with mild symptoms and no requirement of oxygen support/ventilator,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,4 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy volunteers and mild COVID-19 patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia",2|1239|186801;2|1239|91061|186826|33958;2|1239|186801|186802|216572|292632;2|1239|909932|909929|1843491|970;2|1239|186801|186802|186803|189330;2|201174|84998|84999|1643824|133925;2|1239|909932|1843488|909930|904;2|1239|186801|186802|186803|33042;2|1239|186801|186802|31979|1485;2|201174|84998|84999;2|201174|84998|84999|84107;2|1239|186801|186802|186803|2719313|1531;2|1239|186801|186802|31979;2|1224|1236|135625|712;2|1239|186801|186802|186803|207244;2|74201;2|1224|29547;2|1224|29547|213849;2|1239|909932|909929|1843491|52225;2|1224|1236|91347|543|547;2|976|200643|171549|171550;2|1224|1236|135625|712;2|1224|1236|135625;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|28050|28052;2|1239|909932|1843489|31977;2|1239|909932|1843489|31977|906;2|1239|186801|186802|186803|841;2|1224|29547|213849|72293;2|1239|186801|186802|186803|28050;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|216851;2|1224|1236|135624|83763|83770;2|1224|1236|135624|83763;2|1224|1236|135624;2|1239|909932|1843489|31977;2|1239|186801|186802|186803;2|1239|186801|186802;2|1239|186801,Complete,NA
Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,Experiment 3,India,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Severe COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with severe disease and requiring oxygen support/ventilator,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3c,4 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy volunteers and severe COVID-19 patients,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella dysenteriae",2|976|200643|171549|815|816;2|976|200643;2|976|200643|171549;2|976;2|1224|1236|91347|543;2|1224|1236|91347;2|1224|1236|91347|543;2|201174;2|201174|1760|85004;2|201174|1760|85004|31953;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81850;2;2|1224|1236|91347|543|620;2|1224|1236|91347|543|620|624;2|1239|91061|186826;2|1239|91061|186826|33958|1578|1587;2|201174|84998|84999|1643824|1380;2|1239|91061|186826|81852|33969;2|1239|186801|186802|186803|2719313|358743;2|1239|91061|186826|81852;2|1224|1236|91347|543|620|622,Complete,NA
Study 486,"cross-sectional observational, not case-control",34199203,10.3390/microorganisms9061292,NA,"Khan M, Mathew BJ, Gupta P, Garg G, Khadanga S, Vyas AK , Singh AK",Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19,Microorganisms,2021,Experiment 3,India,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Severe COVID-19 patients,COVID-19 patients (positive for SARS-CoV-2 in an RT-PCR diagnostic assay) with severe disease and requiring oxygen support/ventilator,10,10,NA,16S,34,NA,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3c,4 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy volunteers and severe COVID-19 patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Tenericutes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae|g__Succinivibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia",2|1239|186801|186802|31979|580596;2|1239|186801;2|544448|31969;2|1239|186801|186802|186803|189330;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|31979|1485;2|1239|909932|1843488|909930|904;2|1239|186801|186802|186803|2719313|1531;2|201174|84998|84999|84107;2|1224|1236|135625|712;2|1239|186801|186802|186803|33042;2|1239|186801|186802|31979;2|1239|91061|186826|33958;2|74201;2|1224|1236|91347|543|547;2|544448;2|1224|28216|80840|80864;2|1224|28216|80840|80864;2|1224|29547;2|1224|29547|213849;2|1239;2|1224|1236|135625;2|1224|1236|135625|712;2|1239|909932|1843489|31977|906;2|1224|29547|213849|72294;2|1224|29547|213849|72294|194;2|1239|909932|1843489|31977;2|1239|91061|186826|81850;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|28050|28052;2|1239|186801|186802|186803|28050;2|1239|186801|186802|216572;2|1239|186801|186802;2|1239|186801|186802|186803;2|1239|909932|1843489|31977|39948;2;2|1239|186801|186802|216572|216851;2|1224|1236|135624;2|1224|1236|135624|83763|83770;2|1224|1236|135624|83763;2|1239|186801|186802|541000;2|1239|186801|186802|186803;2|1239;2|1239|186801|186802;2|1239|186801,Complete,NA
Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Infected COVID-19 samples (respiratory positive),Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,12,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,increased,unchanged,NA,NA,NA,unchanged,Signature 1,Supplementary Table S1,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic compositions of gut microbiota between respiratory positive and respiratory negative COVID-19 samples,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976;2|976|200643;2|976|200643|171549,Complete,NA
Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,Experiment 1,South Korea,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Infected COVID-19 samples (respiratory positive),Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,12,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,increased,unchanged,NA,NA,NA,unchanged,Signature 2,Supplementary Table S1,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic compositions of gut microbiota between respiratory positive and respiratory negative COVID-19 samples,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,2|201174|1760|2037,Complete,NA
Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,unchanged,NA,NA,NA,increased,Signature 1,Supplementary Table S2,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic composition of gut microbiota in respiratory-negative recovered COVID-19 patients and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|s__rumen bacterium NK4A214,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Monoglobus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus",2|1239|909932;2|1239|909932|909929;2|1239|186801|186802|541000;2|1239|186801|186802|186803|877420;2|877428;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|207244;2|1239|186801|186802|216572|2039302;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|33042,Complete,NA
Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,Experiment 2,South Korea,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 samples (respiratory negative),Samples from symptomatic/mild COVID-19 patients collected on or after negative conversion for SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,unchanged,NA,NA,NA,increased,Signature 2,Supplementary Table S2,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic composition of gut microbiota in respiratory-negative recovered COVID-19 patients and healthy controls,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",2|201174;2|1224;2|201174|84998;2|1239|91061;2|1224|1236;2|201174|84998|84999;2|1239|91061|186826;2|1224|1236|91347;2|201174|84998|84999|84107;2|1239|91061|186826|81852;2|1239|91061|186826|81850;2|201174|84998|1643822|1643826;2|1239|91061|186826|1300;2|1239|186801|186802|186804;2|201174|1760|85004|31953;2|1224|1236|91347|543;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|216572|216851|1946507;2|1239|91061|186826|33958|1253;2|1224|1236|91347|543|544,Complete,NA
Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Infected COVID-19 samples (respiratory positive),Samples from symptomatic/mild COVID-19 patients collected on or before positive detection of SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,unchanged,Signature 1,Supplementary Table S2,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic composition of gut microbiota in respiratory-positive infected COVID-19 patients and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Marinilabiliales|f__Marinifilaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|s__rumen bacterium NK4A214,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Monoglobus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__uncultured Oscillospira sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",2|976;2|976|200643;2|1239|909932;2|976|200643|171549;2|1239|909932|909929;2|1239|186801|186802|541000;2|976|200643|171549|815;2|976|200643|171549|2005525;2|976|200643|1970189|1573805;2|976|200643|171549|171552;2|976|200643|171549|171550;2|976|200643|171549|2005519;2|1239|909932|1843489|31977;2|1239|186801|186802|186806|1730|290054;2|976|200643|171549|815|816;2|1239|186801|186802|216572|216851;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186803|877420;2|1224|28216|80840|995019|40544;2|877428;2|976|200643|171549|171550|239759;2|976|200643|171549|1853231|283168;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|207244;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|1766253;2|1239|186801|186802|186803|28050;2|1239|186801|186802|31979|580596;2|1239|186801|186802|216572|2039302;2|1239|186801|186802|1980681;2|976|200643|171549|171552|577309;2|976|200643|171549|1853231|574697;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|459786;2|1239|186801|186802|186803|28050|39485;2|1239|186801|186802|186803|33042;2|1239|186801|186802|216572|119852|512316;2|976|200643|171549|2005519|397864,Complete,NA
Study 487,time series / longitudinal observational,34200249,10.3390/microorganisms9061237,NA,"Kim HN, Joo EJ, Lee CW, Ahn KS, Kim HL, Park DI , Park SK",Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study,Microorganisms,2021,Experiment 3,South Korea,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Infected COVID-19 samples (respiratory positive),Samples from symptomatic/mild COVID-19 patients collected on or before positive detection of SARS-CoV-2 RNA from the respiratory tract,36,12,No history of antibiotics or probiotics,16S,34,Illumina,Linear Regression,0.05,TRUE,NA,NA,NA,decreased,decreased,NA,NA,NA,unchanged,Signature 2,Supplementary Table S2,4 July 2021,Claregrieve1,Claregrieve1,Comparison of taxonomic composition of gut microbiota in respiratory-positive infected COVID-19 patients and healthy controls,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Pediococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter",2|201174;2|1224;2|201174|84998;2|1239|91061;2|1224|1236;2|201174|84998|84999;2|1239|91061|186826;2|1239|1737404|1737405;2|201174|1760|85004;2|1224|1236|91347;2|1239|186801|186802;2|201174|84998|84999|84107;2|1239|91061|186826|81852;2|1239|91061|186826|33958;2|201174|84998|1643822|1643826;2|1239|91061|186826|1300;2|1239|186801|186802|186804;2|201174|1760|85004|31953;2|1224|1236|91347|543;2|1239|186801|186802|31979;2|201174|84998|84999|84107|102106;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303;2|1239|186801|186802|186804|1501226;2|1239|91061|186826|33958|1253;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|2569097|39488;2|1224|1236|91347|543|620;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186804|1505657,Complete,NA
Study 488,case-control,33663411,10.1186/s12876-021-01693-w,NA,"Mei L, Zhou J, Su Y, Mao K, Wu J, Zhu C, He L , Cui Y",Gut microbiota composition and functional prediction in diarrhea-predominant irritable bowel syndrome,BMC gastroenterology,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,"Aged from 20 to 64; and staple food of all participants were collected,
Inclusion criteria met the Rome IV diagnostic criteria [19] for IBS-D. Gender, age, BMI and staple food of all participants were collected",30,30,"Exclusion criteria for all subjects included: (1) taking antibiotics, probiotics, or other treatments, within 4 weeks; (2) inflammatory bowel disease, peptic ulcer, diverticulitis or infectious gastroenteritis; (3) pregnant, menstruating and lactating women; (4) any psychiatric comorbidity; (5) excessive physical exercise.",16S,4,Illumina,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 5,4 July 2021,Kwekuamoo,Kwekuamoo,"Distribution histogram of LDA score and cladogram of species: a IBS-D, b HCs. The length of the bar chart on the left represents the influence of different species. On the right, the circles radiating from the inside out represent taxonomic levels from phylum to genus (or species); each small circle at a different classification level represents a classification at that level, and the diameter of the small circle is proportional to the relative abundance. Coloring principle: red is the IBS-D, green is HCs, and yellow is the species with no significant difference",increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|201174;2|976|200643|171549|171552|1283313;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|28026;2|1239|186801;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|186802|216572|1263,Complete,NA
Study 488,case-control,33663411,10.1186/s12876-021-01693-w,NA,"Mei L, Zhou J, Su Y, Mao K, Wu J, Zhu C, He L , Cui Y",Gut microbiota composition and functional prediction in diarrhea-predominant irritable bowel syndrome,BMC gastroenterology,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,"Aged from 20 to 64; and staple food of all participants were collected,
Inclusion criteria met the Rome IV diagnostic criteria [19] for IBS-D. Gender, age, BMI and staple food of all participants were collected",30,30,"Exclusion criteria for all subjects included: (1) taking antibiotics, probiotics, or other treatments, within 4 weeks; (2) inflammatory bowel disease, peptic ulcer, diverticulitis or infectious gastroenteritis; (3) pregnant, menstruating and lactating women; (4) any psychiatric comorbidity; (5) excessive physical exercise.",16S,4,Illumina,"Mann-Whitney (Wilcoxon),T-Test",0.05,FALSE,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Figure 5,4 July 2021,Kwekuamoo,Kwekuamoo,"Distribution histogram of LDA score and cladogram of species: a IBS-D, b HCs. The length of the bar chart on the left represents the influence of different species. On the right, the circles radiating from the inside out represent taxonomic levels from phylum to genus (or species); each small circle at a different classification level represents a classification at that level, and the diameter of the small circle is proportional to the relative abundance. Coloring principle: red is the IBS-D, green is HCs, and yellow is the species with no significant difference",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|91061;2|976|200643|171549|815|816|817;2|1224|1236|91347|543;2|1224|1236|91347|543|561|562;2|1224|1236;2|1239|91061|186826;2|1224;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,NA
Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,Experiment 1,Italy,Homo sapiens,rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia control patients (COVID-negative),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",8,6,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Table S5, Table S8, Table S11",4 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between controls and ICU-admitted COVID-19 patients,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Ihubacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus rivorum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccalis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Candidatus Anaerococcus phoceensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuscaniense,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus helveticus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. IrT-R5M2-141,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S362,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus provencensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sundsvallense,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S4-8,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio crossotus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Gorbachella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. TM-40,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fusiformis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.",2|201174|1760|85006|85020;2|201174|1760|85006;2|201174|1760|85007|85025;2|1224|28211;2|201174;2|201174|1760|85010|2070;2|201174|1760|85011|2062;2|1239|526524|526525;2|201174|1760|85007|1762;2|1224|28211|356;2|1239|909932|1843489;2|1239|526524;2|1224|28211|204441|41295;2|201174|1760|85006|85019;2|1239|91061|1385|90964;2|201174|1760|85006|1268;2|1239|526524|526525|128827;2|1224|28216|80840;2|201174|1760|85006|85023;2|201174|1760|85007|1653;2|1239|91061|186826|186827;2|1239|909932;2|1239|91061|1385|186822;2|1239|91061;2|1239|91061|1385|186817;2|1239|91061|186826|81852;2|201174|1760|85006|1268|1663;2|1239|909932|1843489|31977|909928;2|201174|1760|85006|85020;2|1239|91061|186826|81852|2737;2|201174|84998|1643822|1643826|84108;2|201174|1760|85006;2|201174|1760|85006|1268|1269;2|201174|1760|85007|85025|1827;2|201174|1760|85006|1268|57493;2|976|117743|200644|49546;2|201174|1760|85011|2062|1883;2|1239|526524|526525|128827;2|544448|31969|186329|2146|33926;2|201174|1760|85007|1762|1763;2|1224|28216|80840|995019;2|1239|186801|186802|543314|86331;2|1239|526524;2|1239|186801|186802|216572|1935176;2|1239|186801|186802|404402;2|1239|186801|186802|31979|1434004;2|1224|1236|135625|712|724;2|1239|186801|186802|543314|1926667;2|201174|1760|85006|85019|1696;2|1239|91061|186826|81852|1350;2|201174|1760|85007|1653|1716;2|1239|91061|186826|186827|66831;2|1224|28216|80840;2|201174|1760|85007;2|1239|91061|1385|186822|44249;2|1239|91061|1385|186817|1386;2|1239|91061|186826|81852|1350|1352;2|201174|1760|85007|1653|1716|43765;2|1239|1737404|1737405|1570339|165779|54007;2|201174|1760|85007|1653|1716|156978;2|1239|91061|186826|186827|66831|178214;2|32066|203490|203491|203492|848|851;2|1239|91061|186826|81852|1350|1354;2|1239|91061|186826|81852|1350|762845;2|976|200643|171549|171552|838|28127;2|1239|1737404|1737405|1570339|165779|337317;2|1239|91061|186826|81852|2737;2|201174|1760|85007|1653|1716|302449;2|1239|91061|186826|33958|1578|1587;2|201174|1760|85007|1653|1716|146482;2|1239|1737404|1737405|1570339|162289|1647712;2|201174|84998|1643822|1643826|84108|2049041;2|201174|1760|85006|1268|1269|1270;2|1239|1737404|1737405|1570339|165779|938293;2|201174|1760|85007|1653|1716|161902;2|201174|1760|85007|1653|1716|38286;2|976|200643|171549|171552|838|1219629;2|1239|186801|186802|186803|830|45851;2|1239|186801|186802|216572|1935176;2|201174|1760|85004|31953;2|201174|1760|85007|85025|1827|1831;2|1239|186801|186802|216572|1935461;2|1224|28211|356;2|201174|84998|84999|84107|1473205|1473216;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|404402|404403;2|1239|91061|186826|81852|1350|37734;2|1224|1236|91347|543|570|571;2|1239|186801|186802|31979|1434004;2|1239|186801|186802|543314|86331;2|1239|186801|186802|31979|1485|371143;2|1224|28216|80840|995019|577310;2|1239|186801|186802|31979|1485|69833;2|1239|91061|186826|81852|1350|35783;2|201174|1760|85007|1653|1716|1720,Complete,NA
Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,Experiment 1,Italy,Homo sapiens,rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia control patients (COVID-negative),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",8,6,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Table S5, S8, S11",4 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between controls and ICU-admitted COVID-19 patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium deltae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides clarus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus|s__Butyricicoccus sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Halanaerobiales|f__Halanaerobiaceae|g__Halanaerobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira|s__Oscillospira guilliermondii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] spiroforme,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Caproiciproducens,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus gorbachii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. MC_18,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. DJF_RP53,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. NML96-0085,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S470,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. gpac007,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. BI-42,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobium|s__Anaerobium acetethylicum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans|s__Saccharofermentans acetigenes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. A9,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp. 992a,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. enrichment culture clone 7-14,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum cambriense,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 14505,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas sp. FSAA-17,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. BPY5,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon G70,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Caproiciproducens,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella",2|1239|186801|186802|216572|35829;2|976|200643|171549|171550|239759|28117;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|244127|169435;2|201174|84998|84999|1643824|1380|1393034;2|976|200643|171549|815|816|626929;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|291645;2|976|200643|171549|815|816|291644;2|976|200643|171549|815|816|29523;2|976|200643|171549|815|816|46506;2|1239|186801|186802|31979|580596|2049021;2|1239|91061|186826|186828;2|1239|186801|186802|990719;2|1224|1236|91347|543|544;2|1239|186801|186802|543314;2|1239|186801|186802|31979|1485|1506;2|201174|84998|84999|84107|102106;2|976|200643|171549|2005519|1348911;2|976|200643|171549|2005519|1348911|1099853;2|201174|84998|84999|84107;2|1224|28221|213115|194924|872;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|186803|1432051;2|1239|186801|186802|186803|2719313|208479;2|1239|186801|186802|186803|2719313|1531;2|1239|186801|186802|186803|2719313|460384;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|1686313;2|1239|186801|186802|1686313|938288;2|1239|186801|186802|216572|946234;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|186803|1407607;2|1239|91061|186826|186828|117563;2|1239|186801|53433|972|2330;2|1239|91061|186826|33958|1243;2|544448|31969|2085|2092|2093;2|544448|31969|2085|2092;2|1239|186801|186802|186803|265975;2|1239|186801|186802|186803|265975|1969407;2|1239|186801|186802|216572|119852|119853;2|1239|186801|186802|186807|2740;2|976|200643|171549|815|909656|204516;2|976|200643|171549|171552|838|28125;2|1239|186801|186802|216572|1017280;2|508458|649775|649776|649777|638847;2|508458|649775|649776|649777|638847|638849;2|1239|186801|186802|186803|588605;2|1224|1236|91347|543|590;2|1239|186801|186802|216572|292632;2|1224|1236|135623|641|662;2|1239|526524|526525|128827|1505663|29348;2|201174|84998|84999|84107;2|1239|186801|186802|216572;2|201174|84998;2|201174|1760|2037|2049|1653174;2|976|200643|171549|171552|1980689;2|976|200643|171549|171550;2|1239|186801|186802|186803|2005359;2|1239|186801|186802|216572|1738645;2|1239|1737404|1737405|1570339|162289|411567;2|976|200643|171549|171552|838|1755609;2|976|200643|171549|171552|838|537298;2|201174|1760|85007|1653|1716|598660;2|201174|1760|85007|1653|1716|702963;2|976|200643|171549|171552|1980689|1870999;2|1239|1737404|1737405|1570339|162289|1647714;2|1239|1737404|1737405|1570339|162289|361492;2|976|200643|171549|171552|838|243905;2|1239|186801|186802|186803|1855714|1619234;2|201174|1760|2037|2049|1653174|59505;2|1239|186801|186802|216572|1200657|319644;2|1239|186801|186802|31979|1649459;2|201174|84998|84999|84107|102106;2|976|200643|171549|1853231|574697;2|1239|186801|186802|31979|1485|397283;2|1239|186801|186802|186803|207244|1261637;2|1239|186801|186802|31979|1485|598552;2|1224|28221|213115|194924|872;2|201174|1760|2037|2049|184869|184870;2|1239|186801|186802|186803|1407607|1150298;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|31979|1485|169136;2|1239|186801|186802|1392389|1640371;2|1239|186801|186802|186803|1506577;2|976|200643|171549|815|816|338188;2|1239|186801|186802|186803|207244;2|1239|186801|186802|31979|1485|1572655;2|976|200643|171549|171552|838|712495;2|1239|186801|186802|216572|1738645;2|1224|1236|91347|543|570,Complete,NA
Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,Experiment 2,Italy,Homo sapiens,rectum,UBERON:0001052,COVID-19,MONDO:0100096,COVID-positive patients admitted to infectious disease ward (w-COVID-19),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",9,6,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 1,"Table S6, S9, S12",6 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19),increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales|f__Pseudonocardiaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Kocuria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae|g__Streptomyces,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Candidatus Phytoplasma,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Ihubacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. DJF_SLA47,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fusiformis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S362,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium aurimucosum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus provencensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium afermentans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus durans,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Nocardiaceae|g__Rhodococcus|s__Rhodococcus sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium tuscaniense,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S4-8,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. MANG,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio crossotus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia|s__Senegalimassilia anaerobia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Gorbachella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Howardella|s__Howardella ureilytica,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Fonticella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. TM-40,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis",2|1224|28216|80840;2|201174|1760|85007|85025;2|1224|28211;2|201174|1760|85010|2070;2|1239|526524|526525;2|201174|1760|85007|1762;2|1224|28211|356;2|1239|526524;2|1224|1236|135624|84642;2|1224|28211|204441|41295;2|201174|1760|85006|1268;2|201174|1760|85006|85019;2|201174|1760|85007|1653;2|1239|91061|1385|90964;2|201174|1760|85006|85023;2|1239|91061|1385|186822;2|201174|1760|85006|1268|1663;2|201174|1760|85006|1268;2|201174|84998|1643822|1643826|84108;2|1239|526524|526525|128827;2|1239|91061|186826|81852|2737;2|201174|1760|85006|85023|33882;2|1239|91061|1385|186822|44249;2|201174|1760|85006|1268|1269;2|201174|1760|85007|85025|1827;2|201174|1760|85007|1653;2|201174|1760|85006|1268|57493;2|201174|1760|85011|2062|1883;2|544448|31969|186329|2146|33926;2|976|117743|200644|49546;2|201174|1760|85007|1762|1763;2|1224|1236|135624|84642|642;2|1239|186801|186802|543314|86331;2|1239|186801|186802|404402;2|1239|186801|186802|31979|1434004;2|1224|1236|135625|712|724;2|1239|186801|186802|543314|1926667;2|1239|91061|1385|90964|1279;2|201174|1760|85007|1653|1716;2|201174|1760|85006|85019|1696;2|201174|1760|85007|1653|1716|156978;2|1239|91061|186826|81852|1350|537280;2|201174|84998|1643822|1643826|84108|2049041;2|32066|203490|203491|203492|848|68766;2|1239|91061|186826|33958|1578|1596;2|1239|186801|186802|31979|1485|69833;2|1239|1737404|1737405|1570339|162289|1647712;2|201174|1760|85007|1653|1716|169292;2|1239|1737404|1737405|1570339|165779|938293;2|1239|91061|1385|90964|1279|1280;2|201174|1760|85007|1653|1716|38286;2|1239|91061|186826|81852|1350|53345;2|201174|1760|85007|85025|1827|1831;2|201174|1760|85007|1653|1716|302449;2|1239|186801|186802|186803|2316020|46228;2|976|200643|171549|171552|838|1219629;2|976|200643|171549|815|816|298389;2|201174|1760|85004|31953;2|1239|186801|186802|186803|830|45851;2|201174|84998|84999|84107|1473205|1473216;2|1239|91061|186826|81852|2737;2|1239|186801|186802|216572|1935461;2|1239|186801|186802|404402|404403;2|1239|91061|186826|81852|1350|37734;2|1239|186801|186802|543314|86331;2|1239|186801|186802|31979|1434004;2|1239|186801|186802|31979|1485|371143;2|1224|28216|80840|995019|577310;2|1239|91061|1385|90964|1279|29387;2|1239|91061|1385|90964|1279|1282,Complete,NA
Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,Experiment 2,Italy,Homo sapiens,rectum,UBERON:0001052,COVID-19,MONDO:0100096,COVID-positive patients admitted to infectious disease ward (w-COVID-19),COVID-positive patients admitted to ICU (i-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in ICU",9,6,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,NA,NA,NA,Signature 2,"Table S6, S9, S12",6 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between ICU COVID-19 patients (i-COVID-19) and non-ICU COVID-19 patients (w-COVID-19),decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Alterileibacterium|s__Alterileibacterium massiliense,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus degeneri,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter|s__Coprobacter fastidiosus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria|s__Fenollaria massiliensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Kallipyga|s__Kallipyga massiliensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Lagierella|s__Lagierella massiliensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Metaprevotella|s__Metaprevotella massiliensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micromonosporales|f__Micromonosporaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola massiliensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella colorans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. DJF_RP53,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Varibaculum|s__Varibaculum anthropi,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Fenollaria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. DJF_B097,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus rogosae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella aerogenes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella enterica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. 1120,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bergensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S8 F8,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. C71,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp. 992a,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. Marseille-P328,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. BPY5,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. enrichment culture clone,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Marseillibacter|s__Marseillibacter massiliensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus sp.,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Moritellaceae|g__Moritella|s__Moritella abyssi,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. enrichment culture clone 7-14,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. Marseille-P2398,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. Marseille-P3260,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter cloacae",2|1239|91061|186826|186827|1375;2|1224|1236|135619|224372;2|1224|1236|135619|224372|59753;2|1239|186801|186802|543314|1980680|1870997;2|1239|1737404|1737405|1570339|165779|361500;2|1239|186801|186802|186803|207244|649756;2|1224|29547|213849|72294|194|76517;2|1239|91061|186826|186828;2|1224|1236|91347|543|544;2|1239|186801|186802|543314;2|201174|84998|84999|84107|102106;2|201174|84998|84999|84107|102106|74426;2|1239|526524|526525|2810280|100883;2|1239|526524|526525|2810280|100883|100884;2|976|200643|171549|2005519|1348911;2|976|200643|171549|2005519|1348911|1099853;2|201174|84998|84999|84107;2|201174|84998;2|1224|1236|91347|543|413496;2|1224|28221|213115|194924|872;2|1239|909932|1843489|31977|39948|309120;2|1239|186801|186802|186803|2719313|1531;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|1971605;2|1239|186801|186802|1686313;2|1239|186801|186802|1686313|938288;2|1239|186801|186802|216572|946234;2|1239|91061|186826|186828|117563;2|1239|526524|526525|128827|1937007;2|1239|1737404|1472763|1472764;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|28050|28052;2|1239|91061|186826|1300|1357;2|1239|1737404|1737405|1570339|1945592|1689303;2|976|200643|171549|171552|1980689;2|976|200643|171549|171552|1980689|1870999;2|201174|1760|85008|28056;2|1224|1236|135622|267891;2|1239|1737404|1737405|1570339|1161127;2|201174|84998|84999|1643824|133925;2|976|200643|171549|2005525|375288|387661;2|1224|1236|91347|1903410;2|976|200643|171549|815|909656|204516;2|976|200643|171549|171552|838|1703337;2|976|200643|171549|171552|838|28130;2|976|200643|171549|171552|838|537298;2|1239|186801|186802|186803|841|301302;2|1224|1236|91347|543|590;2|1239|909932|909929|1843491;2|1239|909932|909929|1843491|970;2|1239|186801|186802|216572|292632;2|1224|28216|80840|995019|40544;2|201174|1760|2037|2049|184869|1177728;2|1224|1236|135623|641|662;2|1239|186801|186802|216572|39492;2|1239|909932|1843488|909930;2|201174|84998|84999|84107;2|201174|84998;2|1224|28221;2|1239|186801|186802|1686313;2|1239|186801|186802|186804;2|1239|909932|1843488|909930|33024;2|976|200643|171549|815|816|537274;2|1239|91061|186826|33958|1578|706562;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171552|838|28125;2|1239|186801|186802|186803|841|2049040;2|1224|1236|91347|543|570|548;2|1224|1236|91347|543|590|28901;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|841|1227508;2|976|200643|171549|171552|838|242750;2|1239|91061|186826|1300|1301|1308;2|976|200643|171549|1853231|574697;2|1224|1236|91347|543|547;2|201174|84998|84999|84107|102106;2|1224|1236|91347|543|561;2|976|200643|171549|171552|838|1330241;2|1224|1236|91347|543|561|1299485;2|1239|186801|186802|186803|207244|1261637;2|1239|186801|186802|31979|1649459;2|1239|186801|186802|216572|1263|1816688;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|31979|1485|1572655;2|976|200643|171549|171550|239759|1648956;2|1224|1236|91347|1903409|53335|549;2|1224|1236|91347|543|620|624;2|1239|186801|186802|216572|1930587|1852369;2|1239|186801|186802|186803|33042|2049024;2|1224|28221|213115|194924|872;2|1224|1236|135622|267891|58050|111292;2|1239|186801|186802|31979|1485|598552;2|1239|91061|186826|186828|117563|2049028;2|1239|186801|186802|186803|572511|1805476;2|1239|186801|186802|186803|207244;2|1239|186801|186802|216572|459786|1871036;2|1224|1236|91347|543|547|550,Complete,NA
Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,Experiment 3,Italy,Homo sapiens,rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia controls (COVID-negative),COVID-positive patients admitted to infectious disease ward (w-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in infectious disease ward",8,9,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table S1, S4, S7, S10",4 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between non-COVID-19 patients and non-ICU COVID-19 patients,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Pectobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia,k__Bacteria|p__Proteobacteria|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Alcanivoracaceae|g__Alcanivorax,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Syntrophobotulus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Candidatus Syntrophonatronum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pacaella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Hespellia,k__Bacteria|p__Proteobacteria|c__Acidithiobacillia|o__Acidithiobacillales|f__Acidithiobacillaceae|g__Acidithiobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella colorans,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister micraerophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus octavius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides johnsonii,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Murdochiella|s__Murdochiella asaccharolytica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Alterileibacterium|s__Alterileibacterium massiliense,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. oral taxon 375,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S276,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp. DNF00912,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. DJF_B097,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus cateniformis,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella|s__Holdemanella biformis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus obesiensis,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Kallipyga|s__Kallipyga massiliensis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium|s__Atopobium sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia|s__Facklamia hominis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus hirae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. S8 F8,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia sp. C71,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. Marseille-P328,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium amycolatum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella|s__Shigella sonnei,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea|s__Pantoea agglomerans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Syntrophobotulus|s__Syntrophobotulus glycolicus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia sp. Marseille-P2398,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Candidatus Syntrophonatronum|s__Candidatus Syntrophonatronum acetioxidans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Angelakisella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera massiliensis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister succinatiphilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia marcescens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister sp. S7D,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pacaella|s__Pacaella massiliensis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Candidatus Peptoniphilus massiliensis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. Marseille-P3260,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas phoceensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp. enrichment culture clone,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas ruminantium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. IrT-R5M2-141,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus sp.",2|1224;2|1224|1236|135619|224372;2|201174;2|201174|1760|85006;2|1224|28221;2|1239|909932|1843488|909930;2|1239|909932|1843489|31977;2|1224|1236|91347|1903410;2|1239|186801|186802|68298;2|201174|1760|85011|2062;2|1239|909932|909929|1843491;2|201174|1760|85006|85020;2|976|117747;2|1224|1807140|225057|225058;2|1239|186801|186802|186804;2|1224|1236|91347|543;2|1239|909932;2|1239|91061|186826|186827;2|1239|91061|1385|90964;2|201174|84998|84999|1643824;2|1224|1236|135623|641;2|1224|1236|135619|224372|59753;2|1239|91061|186826|186827|1375;2|1224|28216|80840|995019|40544;2|1239|186801|186802|186807|51196;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|186804;2|201174|84998|84999|1643824|133925;2|201174;2|1224|28216|80840|995019;2|1239|909932|1843489|31977|909928;2|1239|91061|186826|1300|1357;2|1239|186801|186802|68298|1795789;2|1239|186801|186802|216572|1935176;2|1239|909932|1843488|909930|904;2|508458|649775|649776|649777|1931105;2|1239|909932|909929|1843491|970;2|1239|91061|186826|81852;2|1239|526524|526525|128827|1573535;2|1239|186801|186802|186803|241189;2|1224|1807140|225057|225058|119977;2|1239|909932|1843489|31977|906;2|1224|28221|213115|194924|35832;2|1224|1236|91347|543|561;2|1224|1236|91347|543;2|1239|91061|186826|1300;2|1224|1236|135623|641|662;2|976|200643|171549|171552|838|28130;2|976|200643|171549|171552|838|1703337;2|1239|909932|1843489|31977|39948|309120;2|1239|186801|186802|186804|1257|1261;2|1239|1737404|1737405|1570339|165779|54007;2|976|200643|171549|2005525|375288|387661;2|1239|1737404|1737405|1570339|1161127|507844;2|1239|186801|186802|543314|1980680|1870997;2|976|200643|171549|171550|239759|1288121;2|1239|1737404|1737405|1570339|162289|712430;2|1239|1737404|1737405|1570339|162289|1647711;2|1239|909932|1843489|31977|906|1285934;2|976|200643|171549|815|816|537274;2|1239|526524|526525|2810280|100883|100884;2|1239|526524|526525|128827|1573535|1735;2|1239|1737404|1737405|1570339|165779|1287640;2|1239|1737404|1472763|1472764;2|1239|909932|1843489|31977|906|2023260;2|1239|91061|186826|81852|1350|1352;2|201174|84998|84999|1643824|1380|1872650;2|976|200643|171549|171552|838|28127;2|1239|91061|186826|1300|1301|1308;2|1239|91061|186826|186827|66831|178214;2|1239|91061|186826|81852|1350|1354;2|976|200643|171549|171552|838|1330241;2|976|200643|171549|171551|836|28123;2|1224|1236|91347|543|561|1299485;2|1239|186801|186802|216572|1263|1816688;2|201174|1760|85007|1653|1716|43765;2|1224|1236|91347|543|620|624;2|1224|1236|91347|1903409|53335|549;2|1239|91061|186826|186827|66831;2|1239|186801|186802|186807|51196|51197;2|1239|186801|186802|186803|572511|1805476;2|1239|91061|1385|90964|1279|1290;2|1239|186801|186802|68298|1795789|1795816;2|1239|186801|186802|216572|1935176;2|1239|909932|1843489|31977|906|1232428;2|1239|909932|1843489|31977|39948|487173;2|1224|1236|91347|1903411|613|615;2|1239|909932|1843488|909930|904|187327;2|1239|909932|1843489|31977|39948|1577797;2|508458|649775|649776|649777|1931105|1871009;2|1239|1737404|1737405|1570339|162289|337315;2|1224|28216|80840|995019|40544;2|1239|186801|186802|216572|459786|1871036;2|1224|1236|91347|543|570|571;2|976|200643|171549|1853231|574697|1720203;2|976|200643|171549|171550|239759|1648956;2|976|200643|171549|171552|577309|454154;2|1239|909932|909929|1843491|970|971;2|201174|1760|85007|1653|1716|146482;2|1239|91061|186826|1300|1301|1328;2|1224|1236|91347|543|561;2|1224|1236|91347|543|547;2|1224|1236|91347|543|413496|28141;2|1239|186801|186802|186803|841|2049040;2|1239|186801|186802|186806|1730|290054;2|1239|91061|1385|90964|1279|29387,Complete,NA
Study 489,"cross-sectional observational, not case-control",33596245,10.1371/journal.pone.0247041,NA,"Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E , Pazienza V",16S rRNA gene sequencing of rectal swab in patients affected by COVID-19,PloS one,2021,Experiment 3,Italy,Homo sapiens,rectum,UBERON:0001052,COVID-19,MONDO:0100096,Pneumonia controls (COVID-negative),COVID-positive patients admitted to infectious disease ward (w-COVID-19),"COVID-19 patients with nasopharyngeal swab positive for SARS-CoV-2, > 18 years of age admitted in infectious disease ward",8,9,NA,16S,23456789,Ion Torrent,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table S1, S4, S7, S10",4 July 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between non-COVID-19 patients and non-ICU COVID-19 patients,decreased,"k__Bacteria|p__Spirochaetes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Caproiciproducens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Robinsoniella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp. S470,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus|s__Proteus mirabilis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. NML96-0085,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio|s__Acetivibrio cellulolyticus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobium|s__Anaerobium acetethylicum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum|s__Actinotignum schaalii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__Erysipelatoclostridium ramosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. A9,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp. MANG,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas sp. FSAA-17,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. 14505,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Candidatus Dorea massiliensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] scindens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__Mediterraneibacter glycyrrhizinilyticus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Caproiciproducens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas sp. S479,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon G70,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster lavalensis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides nordii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp. 653,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. enrichment culture,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans|s__Saccharofermentans acetigenes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Paenibacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella nexilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella massiliensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] viride,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena orotica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. ID5,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron",2|203691;2|32066;2|1224|1236|135624|84642;2|544448|31969|2085|2092;2|1239|186801|186802|543314;2|1224|28216|80840|119060;2|1224|1236|2887326|468;2|1224|28216|80840;2|1224|28211|204458|76892;2|201174|1760|85009|31957;2|1224|1236|91347|1903414|583;2|1224|1236|91347|1903414;2|201174|1760|85009|31957;2|201174|1760|2037|2049|1653174;2|201174|1760|85007|1653;2|1239|186801|186802|186803|1432051;2|201174|1760|85006|85023|33882;2|1239|186801|186802|186803|2005359;2|1239|186801|186802|216572|244127;2|1239|186801|186802|216572|1738645;2|1239|186801|186802|186807|2740;2|1239|186801|186802|186803|1407607;2|1239|526524|526525|128827;2|1239|186801|186802|216572|1017280;2|1239|91061|1385|186822|44249;2|1224|1236|135624|84642|642;2|1239|186801|186802|186803|588605;2|1239|186801|186802|216572|35829;2|1239|91061|186826|33958|1243;2|1239|186801|186802|216572|1905344;2|976|200643|171549|171550;2|1239|186801|186802|990719;2|1239|91061|186826|33958;2|544448|31969|2085|2092|2093;2|1239|91061|1385|1378;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|816|291644;2|201174|1760|85007|1653|1716|598660;2|976|200643|171549|171550|239759|28117;2|1239|1737404|1737405|1570339|162289|1647714;2|1224|1236|91347|1903414|583|584;2|1224|1236|91347|1903414|583;2|201174|1760|85007|1653|1716|702963;2|1239|186801|186802|216572|1200657;2|1239|186801|186802|216572|35829|35830;2|976|200643|171549|815|816|46506;2|1239|186801|186802|186803|1855714|1619234;2|201174|1760|2037|2049|1653174|59505;2|1239|186801|186802|216572|1263|438033;2|976|200643|171549|815|816|817;2|1239|526524|526525|128827|1505663|1547;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802|31979|1485|397283;2|976|200643|171549|815|816|298389;2|201174|1760|85006|85023|33882;2|1239|186801|186802|1392389|1640371;2|1239|186801|186802|31979|1485|169136;2|1239|186801|186802|186803|189330|1470355;2|1239|186801|186802|186803|1506553|29347;2|976|200643|171549|171550|239759|328814;2|1239|186801|186802|186803|2316020|342942;2|1239|186801|186802|186803|1506577;2|976|200643|171549|815|816|338188;2|1239|526524|526525|128827;2|1239|186801|186802|216572|1738645;2|1239|186801|186802|186803|1407607|1150298;2|1239|186801|186802|216572|244127|169435;2|1239|186801|186802|31979|580596;2|976|200643|171549|1853231|574697|1647678;2|976|200643|171549|171552|838|712495;2|1239|186801|186802|186803|2719313|460384;2|32066|203490|203491|203492|848|68766;2|976|200643|171549|815|816|29523;2|1239|186801|186802|216572|1905344|1550024;2|976|200643|171549|815|816|291645;2|1239|186801|186802|216572|1263|1227507;2|1239|186801|186802|31979|1485|1569942;2|1239|186801|186802|186803|2719313|208479;2|1239|186801|186802|216572|1200657|319644;2|1239|91061|1385|186822|44249;2|1239|186801|186802|186803|1432051|1924109;2|1239|186801|186802|186803|1506577|29361;2|1239|186801|186802|186803|1432051|1720294;2|1239|186801|186802|216572|47246;2|1239|186801|186802|186803|2005359|1544;2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|31979|1485|320882;2|1239|909932|1843489|31977|39948|39950;2|976|200643|171549|815|909656|357276;2|976|200643|171549|815|816|818,Complete,NA
Study 490,case-control,19903265,10.1111/j.1365-2982.2009.01427.x,NA,"Tana C, Umesaki Y, Imaoka A, Handa T, Kanazawa M , Fukudo S",Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2010,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"All patients were diagnosed with IBS after conducting a medical interview based on Rome II criteria and positive judgment by a Rome II modular questionnaire retrospectively and positively fulfilling Rome III criteria. According to Rome II criteria related to bowel habits, 11 subjects had constipation-predominant IBS (IBS-C), eight had diarrhoea-predominant IBS (IBS-D) and seven had mixed IBS (IBS-M).",26,26,"In the previous study, agents containing probiotics were administered to humans and stopped thereafter. On day 10 after stopping the administration of probiotics, levels of these bacteria returned to the levels before administration of probiotics. No subject received antibiotics during the abstention period.",WMS,NA,RT-qPCR,"ANOVA,Chi-Square,Mann-Whitney (Wilcoxon),Spearman Correlation,T-Test",0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,4 July 2021,Kwekuamoo,Kwekuamoo,"Comparison of GI microbiota between IBS patients and the
controls",increased,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,2|1239|909932|1843489|31977|29465,Complete,NA
Study 491,case-control,21741921,10.1053/j.gastro.2011.06.072,NA,"Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ , Versalovic J",Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Participants met Pediatric Rome III criteria for IBS7 (Table 1). Subtyping of IBS was based on previous recommendations for IBS in adults because no Pediatric Rome subtype criteria exist for children.,22,22,"Exclusion criteria included use of antibiotics, probiotics, or steroids (oral or nasal [inhaled]) within 6 months of sampling. Four children withdrew from the study (2 children declined after the home visit; 1 child consumed an antibiotic; 1 child took a probiotic).",16S,12345,"PhyloChip,Roche454",Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2; Supplementary Table 1A,8 July 2021,Kwekuamoo,Kwekuamoo,The pediatric gut microbiomes of children with IBS are characterized by greater abundance of �-proteobacteria. (A) Percentage of all bacterial classes represented. (B) Percentage of bacterial taxa found in lower abundance (�5% of total bacteria). Healthy children: 29 samples from 22 subjects; IBS: 42 samples from 22 patients. #Significantly different between IBS and healthy children (P < .05). Data were generated by 454 pyrosequencing (V1-V3 region).,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Coxiellaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Syntrophobacterales|f__Syntrophobacteraceae",2|1224|1236|135624|84642;2|1224|1236|135622|72275;2|1239|91061|1385|186817;2|1239|186801|186802|31979;2|1224|1236|118969|118968;2|1224|28221|213118|213119;2|1224|28221|213115|194924;2|1224|1236|91347|543;2|1224|1236|91347|543|561|562;2|1239|186801|186802|186806;2|1239|186801|186802|186803;2|1224|1236|135625|712;2|1239|186801|186802|186807|2740;2|1239|186801|186802|186804;2|976|200643|171549|171552;2|1224|28221|213462|213465,Complete,NA
Study 491,case-control,21741921,10.1053/j.gastro.2011.06.072,NA,"Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ , Versalovic J",Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Participants met Pediatric Rome III criteria for IBS7 (Table 1). Subtyping of IBS was based on previous recommendations for IBS in adults because no Pediatric Rome subtype criteria exist for children.,22,22,"Exclusion criteria included use of antibiotics, probiotics, or steroids (oral or nasal [inhaled]) within 6 months of sampling. Four children withdrew from the study (2 children declined after the home visit; 1 child consumed an antibiotic; 1 child took a probiotic).",16S,12345,"PhyloChip,Roche454",Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2; Supplementary Table 1B,8 July 2021,Kwekuamoo,Kwekuamoo,The pediatric gut microbiomes of children with IBS are characterized by greater abundance of �-proteobacteria. (A) Percentage of all bacterial classes represented. (B) Percentage of bacterial taxa found in lower abundance (�5% of total bacteria). Healthy children: 29 samples from 22 subjects; IBS: 42 samples from 22 patients. #Significantly different between IBS and healthy children (P < .05). Data were generated by 454 pyrosequencing (V1-V3 region).,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae",2|976|200643|171549|815;2|1239|186801|186802|186803;2|1239|91061|1385|186822;2|1239|91061|186826|1300,Complete,NA
Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,Experiment 1,India,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy,"Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy (T2D group); the T2DM cohort included subjects (a) positive for at least one of the three biochemical tests (HbA1c > 7%, fasting blood sugar > 120 mg% and post-prandial blood sugar > 200 mg%); (b) had history of taking anti-diabetic medications (Metformin or combinations of Metformin and / or Insulin) and (c) had no clinical signs of DR",30,25,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,increased,unchanged,NA,increased,Signature 1,"Table 2, Table 3",5 July 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Archaea|p__Crenarchaeota,k__Bacteria|p__Elusimicrobia,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|572511;2|1224|28216|80840|80864|283;2|1239|186801|186802|186803|33042;2157|28889;2|74152;2|32066;2|1224|1236|135625|712|724;2|1239|186801|186802|186803|28050;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|186803|841;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303,Complete,NA
Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,Experiment 1,India,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy,"Individuals having Type 2 Diabetes Mellitus without Diabetic Retinopathy (T2D group); the T2DM cohort included subjects (a) positive for at least one of the three biochemical tests (HbA1c > 7%, fasting blood sugar > 120 mg% and post-prandial blood sugar > 200 mg%); (b) had history of taking anti-diabetic medications (Metformin or combinations of Metformin and / or Insulin) and (c) had no clinical signs of DR",30,25,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,increased,unchanged,NA,increased,Signature 2,"Table 2, Table 3",5 July 2021,Madhubani Dey,Madhubani Dey,Increased abundance of microbial communities in individuals with Type 2 Diabetes compared to healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Lentisphaerae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Synergistetes,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|1239|909932|1843488|909930|904;2|976|200643|171549|1853231|574697;2|1224|1236|91347|543|547;2|1224|1236|91347|543|561;2157|28890;2|1239|186801|186802|186803|140625;2|256845;2157|28890|183925|2158|2159|2172;2|203691;2|508458;2|203691|203692|136|2845253|157;2|1239|91061|186826|33958|46255,Complete,NA
Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,Experiment 2,India,Homo sapiens,feces,UBERON:0001988,diabetic retinopathy,EFO:0003770,Healthy controls,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,30,28,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,unchanged,unchanged,NA,unchanged,Signature 1,"Table 2, Table 4",5 July 2021,Madhubani Dey,"Madhubani Dey,Fatima",Decreased abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared with healthy controls,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Archaea|p__Crenarchaeota,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Candidatus Saccharibacteria",2|201174;2|1239|909932|909929|1843491|82373;2|544448|31969|186332|186333|2152;2|976;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|572511;2|1239|526524|526525|128827|118747;2|1239|186801|186802|186803|830;2|1239|186801|186802|31979|1485;2|1224|28216|80840|80864|283;2157|28889;2|1224|28221|213115|194924|872;2|1224|1236|91347|1903409|551;2|1239|186801|186802|216572|216851;2|32066;2|1224|1236|135625|712|724;2|1239|186801|186802|186803|28050;2|1239|91061|186826|33958|1578;2|1239|909932|909929|1843491|52225;2|1239|186801|186802|186803|841;2|201174|1760|85006|1268|32207;2|203691;2|1239|91061|186826|1300|1301;2|1224|28216|80840|995019|40544;2|1239|526524|526525|2810281|191303;2|95818,Complete,NA
Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,Experiment 2,India,Homo sapiens,feces,UBERON:0001988,diabetic retinopathy,EFO:0003770,Healthy controls,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,30,28,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,increased,unchanged,unchanged,NA,unchanged,Signature 2,"Table 2, Table 4",5 July 2021,Madhubani Dey,"Madhubani Dey,Fatima",Increased abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared with healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Lentisphaerae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Synergistetes,k__Bacteria|p__Tenericutes,k__Bacteria|p__Verrucomicrobia",2|1239|909932|1843488|909930|904;2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|508458|649775|649776|649777|508459;2|1224|1236|91347|543|547;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2157|28890;2|256845;2|1239|909932|909929|1843491|158846;2|1224|28216|80840|75682|846;2|976|200643|171549|2005525|375288;2|1224|1236|91347|543|620;2|508458;2|544448;2|74201,Complete,NA
Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,Experiment 3,India,Homo sapiens,feces,UBERON:0001988,diabetic retinopathy,EFO:0003770,Individuals diagnosed with type 2 diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,24,28,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Table 2, Table 5",5 July 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared to individuals with only Type 2 Diabetes,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Anaerovibrio,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Anaeroplasmatales|f__Anaeroplasmataceae|g__Asteroleplasma,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium,k__Bacteria|p__Lentisphaerae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella",2|201174;2|1239|909932|909929|1843491|82373;2|544448|31969|186332|186333|2152;2|201174|1760|85004|31953|1678;2|1224|28221|213115|194924|872;2|1224|1236|91347|1903409|551;2157|28890;2|32066;2|1224|1236|135625|712|724;2|1224|1236|91347|543|570;2|1239|186801|186802|186803|140625;2|256845;2157|28890|183925|2158|2159|2172;2|1239|909932|909929|1843491|52225;2|203691;2|1239|91061|186826|1300|1301;2|203691|203692|136|2845253|157;2|1239|91061|186826|33958|46255,Complete,NA
Study 492,case-control,33531650,10.1038/s41598-021-82538-0,https://pubmed.ncbi.nlm.nih.gov/33531650/,"Das T, Jayasudha R, Chakravarthy S, Prashanthi GS, Bhargava A, Tyagi M, Rani PK, Pappuru RR, Sharma S , Shivaji S",Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy,Scientific reports,2021,Experiment 3,India,Homo sapiens,feces,UBERON:0001988,diabetic retinopathy,EFO:0003770,Individuals diagnosed with type 2 diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR),Individuals diagnosed with Type 2 Diabetes and clinically manifest Diabetic Retinopathy (DR); Subjects confirmed to having DR based on the fundus examination/photograph followed by fundus fluorescein angiography (FFA) and optical coherence tomography (OCT).,24,28,3 months,16S,34,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,diet,region,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Table 2, Table 5",5 July 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals diagnosed with Type 2 Diabetes and Diabetic Retinopathy (DR) compared to individuals with only Type 2 Diabetes,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Elusimicrobia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Synergistetes,k__Bacteria|p__Verrucomicrobia",2|74201|203494|48461|1647988|239934;2|976|200643|171549|171550|239759;2|508458|649775|649776|649777|508459;2|74152;2|1239|91061|186826|81852|1350;2|1239|909932|1843488|909930|33024;2|1224|1236|91347|543|620;2|508458;2|74201,Complete,NA
Study 493,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X, Wang L, Meng D, Wu L, Wang X, Zhang D, Luo Z, Pang Y , Liu G",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,Experiment 1,China,Homo sapiens,skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Vitiligo patients before narrowband UV (NBUVB) light irradiation in normal skin (NF group),Vitiligo patients after NBUVB irradiation on normal skin (NB group),"Vitiligo patients after NBUVB irradiation on normal skin (NB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,increased,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 493,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X, Wang L, Meng D, Wu L, Wang X, Zhang D, Luo Z, Pang Y , Liu G",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,Experiment 2,China,Homo sapiens,skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Normal skin of Vitiligo patients before narrowband UV (NBUVB) light irradiation (NF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 493,case-control,31917273,10.1016/j.micpath.2019.103943,https://pubmed.ncbi.nlm.nih.gov/31917273/,"Yuan X, Wang L, Meng D, Wu L, Wang X, Zhang D, Luo Z, Pang Y , Liu G",The impact of NBUVB on microbial community profiling in the lesional skin of vitiligo subjects,Microbial pathogenesis,2020,Experiment 3,China,Homo sapiens,skin of body,UBERON:0002097,Vitiligo,EFO:0004208,Lesional skin of Vitiligo patients before irradiation (DF group),Lesional skin of Vitiligo patients after NBUVB irradiation (DB group),"Lesional skin of Vitiligo patients after NBUVB irradiation (DB group); Vitiligo patients recruited from Weifang Medical University Hospital, Shandong, China, from February 2018 to January 2019.",15,15,6 months,16S,34,Illumina,T-Test,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 494,case-control,32214153,10.1038/s41598-020-62224-3,https://pubmed.ncbi.nlm.nih.gov/32214153/,"Li Q, Chang Y, Zhang K, Chen H, Tao S , Zhang Z",Implication of the gut microbiome composition of type 2 diabetic patients from northern China,Scientific reports,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; T2D subjects were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) 7 mmol/L or greater and/or 2-h fasting oral glucose tolerance test (OGTT) 11.1 mmol/L or greater35; (ii) no previously received pharmacologic treatment; and (iii) body mass index (BMI) > 18.0 kg/m2.,40,20,2 months,16S,45,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 1,Figure 2b,5 July 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls,decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|74201|203494|48461|1647988|239934;2|976;2|201174|1760|85004|31953|1678;2|976|200643|171549|2005525|375288,Complete,NA
Study 494,case-control,32214153,10.1038/s41598-020-62224-3,https://pubmed.ncbi.nlm.nih.gov/32214153/,"Li Q, Chang Y, Zhang K, Chen H, Tao S , Zhang Z",Implication of the gut microbiome composition of type 2 diabetic patients from northern China,Scientific reports,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; T2D subjects were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) 7 mmol/L or greater and/or 2-h fasting oral glucose tolerance test (OGTT) 11.1 mmol/L or greater35; (ii) no previously received pharmacologic treatment; and (iii) body mass index (BMI) > 18.0 kg/m2.,40,20,2 months,16S,45,Illumina,NA,0.05,TRUE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,NA,Signature 2,Figure 2b,5 July 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals with Type 2 Diabetes compared to healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|186803|189330;2|32066|203490|203491|203492|848;2|1239;2|1239|91061|186826|1300|1301,Complete,NA
Study 495,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z, Tian T, Chen Z, Liu L, Luo T , Dai J",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; Participants with T2DM were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) ≥7 mmol/L and/or 2-h fasting oral glucose tolerance test (OGTT) ≥11.1 mmol/L; and (ii) all cases of T2DM were newly diagnosed.,60,60,2 months,16S,45,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,5 July 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals with type 2 diabetes compared to healthy controls,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552|1283313;2|1239|909932|1843489|31977|906;2|1239|909932;2|976|200643|171549|171552|838,Complete,NA
Study 495,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z, Tian T, Chen Z, Liu L, Luo T , Dai J",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Healthy controls,Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; Participants with T2DM were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) ≥7 mmol/L and/or 2-h fasting oral glucose tolerance test (OGTT) ≥11.1 mmol/L; and (ii) all cases of T2DM were newly diagnosed.,60,60,2 months,16S,45,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 3,5 July 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals with type 2 diabetes compared to healthy controls,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella",2|976|200643|171549|815|816;2|976|200643|171549|171552|577309,Complete,NA
Study 495,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z, Tian T, Chen Z, Liu L, Luo T , Dai J",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,prediabetes syndrome,EFO:1001121,Healthy controls,Individuals with Prediabetes (PreDM),Individuals with Prediabetes (PreDM); PreDM was defined as FBG of 6.1–7.0 mmol/L or HbA1c levels of 6.0%–6.5%.,60,60,2 months,16S,45,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,NA,5 July 2021,Madhubani Dey,Madhubani Dey,Increased abundance of microbial communities in individuals with prediabetes compared to healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria",2|1239|909932|1843489|31977|906;2|1224,Complete,NA
Study 495,case-control,33828910,10.7717/peerj.10952,https://pubmed.ncbi.nlm.nih.gov/33828910/,"Zhang Z, Tian T, Chen Z, Liu L, Luo T , Dai J",Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes,PeerJ,2021,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,type II diabetes mellitus,MONDO:0005148,Individuals with Prediabetes (PreDM),Individuals diagnosed with Type 2 Diabetes Mellitus,Individuals diagnosed with Type 2 Diabetes Mellitus; Participants with T2DM were required to meet the following inclusion criteria: (i) fasting blood glucose test (FBG) ≥7 mmol/L and/or 2-h fasting oral glucose tolerance test (OGTT) ≥11.1 mmol/L; and (ii) all cases of T2DM were newly diagnosed.,60,60,2 months,16S,45,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,16 August 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals with type 2 diabetes compared to healthy controls,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA
Study 496,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J , Zhu S",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,40,62,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 1E,7 July 2021,Claregrieve1,"Claregrieve1,Fatima",Differential microbial abundance between healthy controls and COVID-19 patients (LDA>2),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|2037|2049|1654;2|1239|526524|526525|128827|174708;2|1239|1737404|1737405|1570339|165779;2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|526524|526525|128827|118747;2|1239|186801|186802|31979|1485;2|201174|1760|85007|1653|1716;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1224|29547|213849|72293|209;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|437755;2|1239|186801|186802|186803|265975;2|1224|1236|91347|1903414|583;2|201174|1760|85006|1268|32207;2|201174|1760|85004|31953|196081;2|1239|186801|186802|186803|177971;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 496,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J , Zhu S",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with COVID-19,40,62,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 1E,7 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and COVID-19 patients (LDA>2),decreased,"k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|256845|1313211|278082|255528|172900;2|1239|526524|526525|128827|61170;2|1224|1236|91347|1903411|629;2|976|200643|171549|1853231|283168;2|976|200643|171549|171550|239759;2|1239|186801|186802|31979|1485;2|976|200643|171549|1853231|574697;2|1224|28216|80840|80864|283;2|1239|186801|186802|186803|207244;2|1224|28216|80840|119060|32008;2|1224|28216|206351|481|482;2|1224|28216|80840|119060|106589;2|1224|28216|80840|119060|48736;2|1239|186801|186802|186803|189330;2|976|200643|171549|171552|838;2|1239|186801|186802|216572|119852;2|1239|186801|186802|186803|28050;2|976|200643|171549|2005525|375288;2|1239|186801|186802|216572|1263;2|1224|28216|80840|995019|40544;2|1239|186801|186802|186803|33042;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|841,Complete,NA
Study 496,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J , Zhu S",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Seasonal flu patients,COVID-19 patients,Patients with COVID-19,33,62,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 1G,7 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between seasonal flu patients and COVID-19 patients (LDA>2),increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium",2|1224|1236|91347|543|561;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485;2|1239|91061|186826|1300|1301;2|976|200643|171549|2005525|375288;2|1239|909932|1843489|31977|29465;2|1224|28216|80840|995019|40544;2|32066|203490|203491|203492|848,Complete,NA
Study 496,prospective cohort,34173452,10.1016/j.medmic.2020.100023,NA,"Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J , Zhu S",Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18,Medicine in microecology,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Seasonal flu patients,COVID-19 patients,Patients with COVID-19,33,62,NA,16S,4,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 1G,7 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between seasonal flu patients and COVID-19 patients (LDA>2),decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Shuttleworthia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Ralstonia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia",2|1239|909932|1843488|909930|33024;2|1239|186801|186802|186803|572511;2|1224|1236|135625|712|724;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|119852;2|201174|1760|2037|2049|1654;2|1224|1236|135614|32033|40323;2|1224|29547|213849|72293|209;2|1239|186801|186802|186803|177971;2|1224|28216|80840|119060|106589;2|1224|28216|80840|119060|32008;2|1239|186801|186802|186806|1730;2|1239|91061|186826|33958|1243;2|1224|28216|80840|119060|48736;2|1239|186801|186802|186803|437755;2|508458|649775|649776|649777|638847;2|1224|1236|135625|712|416916;2|1239|186801|186802|186803|265975;2|1239|526524|526525|128827|118747,Complete,NA
Study 498,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Rajagopala SV, Turner JH , Das SR",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,Experiment 1,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Asymptomatic uninfected controls,COVID-19 patients,"Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized",21,38,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,unchanged,increased,Signature 1,Figure 3B,10 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between non-COVID controls and COVID-19 infected patients,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium imitans,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella sp.,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium spiritivorum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus",2|1224|28211|204458|76892|41275|1871086;2|201174|1760|85007|1653|1716|156978;2|201174|1760|85007|1653|1716|1720;2|1239|91061|186826|186828|117563|2049028;2|1239|1737404|1582879;2|1239|1737404|1737405|1570339|162289|33031;2|1224|29547|213849|72294|194|76517;2|976|117747|200666|84566|28453|258;2|1239|1737404|1737405|1570339|165779|1872515;2|1239|1737404|1737405|1570339|162289|1971214;2|976|200643|171549|171552|838|165179;2|976|200643|171549|815|909656|821,Complete,NA
Study 498,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Rajagopala SV, Turner JH , Das SR",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,Experiment 1,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Asymptomatic uninfected controls,COVID-19 patients,"Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized",21,38,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,unchanged,increased,Signature 2,Figure 3B,10 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between non-COVID controls and COVID-19 infected patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens",2|1239|186801|186802|186803;2|1224|28216|206351|481|482|192066;2|1239|186801|186802|186803|207244|649756;2|201174|1760|85007|1653|1716|1720;2|1239|91061|1385|90964|1279|1283;2|976|200643|171549|171552|838|28130,Complete,NA
Study 498,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Rajagopala SV, Turner JH , Das SR",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,Experiment 2,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 patients with low viral load,COVID-19 patients with high viral load,"Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized,  with high viral load (quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1)",NA,NA,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Figure 4b,10 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with high viral load and patients with low viral load,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus sp.,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus sp.,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter hominis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri",2|1224|28216|206351|481;2|1239|1737404|1737405|1570339|165779|1872515;2|1239|1737404|1737405|1570339|162289|1971214;2|1224|29547|213849|72294|194|76517;2|1239|91061|186826|81852|1350|35783;2|201174|1760|85007|1653|1716|1720;2|1224|1236|91347|543;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|171552|838|165179,Complete,NA
Study 498,case-control,33577896,10.1016/j.jaci.2021.02.001,NA,"Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Rajagopala SV, Turner JH , Das SR",SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome,The Journal of allergy and clinical immunology,2021,Experiment 2,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 patients with low viral load,COVID-19 patients with high viral load,"Confirmed symptomatic mild to moderate COVID-19 patients > age 18, nonhospitalized,  with high viral load (quantitative reverse transcription PCR cycle threshold value
below the median for the detection of SARS-CoV-2 nucleocapside gene region 1)",NA,NA,2 weeks,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,"age,sex",NA,unchanged,NA,NA,unchanged,unchanged,Signature 2,Figure 4b,10 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients with high viral load and patients with low viral load,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum pigrum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella disiens,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus haemolyticus",2|1239|91061|186826|1300|1301|1306;2|1239|91061|186826|186828|29393|29394;2|1224|1236|135614|32033|40323;2|1224|1236|2887326|468|469;2|201174|1760|85007|1653|1716|1720;2|976|200643|171549|171552|838|28130;2|1224|28216|206351|481|482|192066;2|1239|91061|186826|186828|117563|137732;2|1239|91061|1385|90964|1279|1283,Complete,NA
Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-A,IBS patients fulfilled the Rome II criteria. Alternating IBS (IBS-A),46,19,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,"Differences Between Intestinal Microbiota in Healthy and IBS.
NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816|820;2|1239|186801|186802|216572|216851;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656|821;2|976|200643|171549|2005525|195950,Complete,Lwaldron
Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-A,IBS patients fulfilled the Rome II criteria. Alternating IBS (IBS-A),46,19,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,"Differences Between Intestinal Microbiota in Healthy and IBS.
NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora sphenoides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus callidus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella nexilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Firmicutes|c__Clostridia|s__uncultured Clostridia bacterium",2|1239|186801|186802|186803|572511;2|1239|186801|186802|186804|1870884|1496;2|1239|186801|186802|186803|33042|33043;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|2719231|29370;2|1239|186801|186802|186803|248744;2|1239|186801|186802|216572|100175;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|40519;2|1239|91061|186826|1300|1301|1338;2|1239|186801|186802|186803|1506577|29361;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186803|2316020|46228;2|1239|186801|244328,Complete,Lwaldron
Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,IBS patients fulfilled the Rome II criteria. Constipation-predominant IBS (IBS-C),46,18,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oralis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella ruminicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidetes|s__uncultured Bacteroidetes bacterium",2|976|200643|171549|171550|239759;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|816|820;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|838|28134;2|976|200643|171549|171552|838|839;2|976|200643|171549|2005525|195950;2|976|152509,Complete,Lwaldron
Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 2,Finland,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,IBS patients fulfilled the Rome II criteria. Constipation-predominant IBS (IBS-C),46,18,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella nexilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] cellulosi,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus",2|1239|186801|186802|216572|244127;2|1239|186801|186802|543314|109326;2|1239|91061|1385|186822|55079;2|1239|186801|186802|186804|1870884|1496;2|1239|186801|186802|186803|33042|33043;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|248744;2|1239|186801|186802|216572|100175;2|1239|186801|186802|186807|2740;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|44748;2|1239|186801|186802|186803|1506577|29361;2|1239|186801|186802|216572|29343;2|1239|186801|186802|216572|1535;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|2316020|33038,Complete,Lwaldron
Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 3,Finland,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,IBS patients fulfilled the Rome II criteria. Diarrhea-predominant IBS (IBS-D),46,25,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oralis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|815|816|329854;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|976|200643|171549|171552|838|28134;2|976|200643|171549|2005525|195950,Complete,Lwaldron
Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 3,Finland,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,IBS patients fulfilled the Rome II criteria. Diarrhea-predominant IBS (IBS-D),46,25,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella nexilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",2|1239|186801|186802|186803|830;2|1239|186801|186802|186804|1870884|1496;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186807|2740;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|1506577|29361;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186803|2316020|46228,Complete,Lwaldron
Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 4,Finland,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS (All patients),IBS patients fulfilled the Rome II criteria. All IBS patients.,46,62,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oralis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella ruminicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidetes|s__uncultured Bacteroidetes bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|s__uncultured Clostridia bacterium",2|201174|1760|85004|31953|1678;2|976|200643|171549|171550|239759;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|816|28116;2|976|200643|171549|815|816|46506;2|976|200643|171549|815|816|820;2|976|200643|171549|815|909656|310297;2|976|200643|171549|815|909656|821;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|838|28134;2|976|200643|171549|171552|838|839;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|2005525|195950;2|976|152509;2|1239|186801|244328,Complete,Lwaldron
Study 499,"case-control,prospective cohort",21820992,10.1053/j.gastro.2011.07.043,NA,"Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA, Tims S , de Vos WM",Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,Gastroenterology,2011,Experiment 4,Finland,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS (All patients),IBS patients fulfilled the Rome II criteria. All IBS patients.,46,62,NA,16S,NA,Human Intestinal Tract Chip,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1.,15 July 2021,Kwekuamoo,Kwekuamoo,Differences Between Intestinal Microbiota in Healthy and IBS. NOTE. Genus-like phylogenetic groups for which the hybridization signal differed significantly between the healthy subjects and (one of the subtypes of) IBS patients are indicated. Gray shading represents phylogenetic groups with a decreased signal in IBS patients. a) Significant (q < .05) correlation. b) Strongly significant (q < .01) correlation.,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Anaerovorax,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__Tyzzerella nexilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris",2|1239|91061|1385|186822|55079;2|1239|91061|186826|1300|1301|1338;2|1239|186801|186802|216572|1535;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|216572|100175;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186807|2740;2|1239|186801|186802|543314|109326;2|1239|186801|186802|186804|1870884|1496;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|248744;2|1239|186801|186802|186803|1506577|29361;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|33042|33043;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186803|2316020|46228,Complete,Lwaldron
Study 500,case-control,33980943,10.1038/s41598-021-89516-6,NA,"Gaibani P, Viciani E, Bartoletti M, Lewis RE, Tonetti T, Lombardo D, Castagnetti A, Bovo F, Horna CS, Ranieri M, Viale P, Re MC , Ambretti S",The lower respiratory tract microbiome of critically ill patients with COVID-19,Scientific reports,2021,Experiment 1,Italy,Homo sapiens,lung,UBERON:0002048,COVID-19,MONDO:0100096,Non-COVID-19 pneumonia patients,COVID-19 patients,Patients positive for SARS-CoV-2 by RT-PCR on nasopharyngeal swabs or lower respiratory tract samples,24,24,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 1,Figure 3,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 positive patients and non-COVID pneumonia patients by LEfSe,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter schindleri,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptacetobacter|s__Peptacetobacter hiranonis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas alcaligenes",2|1224|1236|91347|543;2|1224|1236|2887326|468|469;2|1224|1236|2887326|468|469|108981;2|976|117747|200666|84566|28453;2|1239|186801|186802|186804|2743582|89152;2|1224|1236|72274|135621|286|43263,Complete,NA
Study 500,case-control,33980943,10.1038/s41598-021-89516-6,NA,"Gaibani P, Viciani E, Bartoletti M, Lewis RE, Tonetti T, Lombardo D, Castagnetti A, Bovo F, Horna CS, Ranieri M, Viale P, Re MC , Ambretti S",The lower respiratory tract microbiome of critically ill patients with COVID-19,Scientific reports,2021,Experiment 1,Italy,Homo sapiens,lung,UBERON:0002048,COVID-19,MONDO:0100096,Non-COVID-19 pneumonia patients,COVID-19 patients,Patients positive for SARS-CoV-2 by RT-PCR on nasopharyngeal swabs or lower respiratory tract samples,24,24,NA,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,unchanged,NA,unchanged,unchanged,Signature 2,Figure 3,14 July 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 positive patients and non-COVID pneumonia patients by LEfSe,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus influenzae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|186803|43996;2|1239|186801|186802|186803|265975;2|976|200643|171549|2005525|195950;2|1239|186801|186802|186803|437755;2|1239|909932|909929|1843491|970;2|201174|84998|84999|1643824|1380;2|1224|1236|135625|712|724|729;2|1239|909932|1843489|31977|29465;2|1224|29547|213849|72294|194;2|1239|91061|1385|1378;2|976|200643|171549|171552|838|425941;2|976|200643|171549|171552|838|60133;2|1239|909932|1843489|31977|906;2|976|200643|171549|171552|838;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|33958|2759736|57037;2|32066|203490|203491|1129771|32067;2|1239|909932|1843489|31977|29465|29466;2|976|200643|171549|171552;2|976|200643|171549|171552|838|28132;2|976|117743|200644|49546|1016;2|976|200643|171549|171551|836;2|201174|1760|2037|2049|1654;2|1224|28216|206351|481|482;2|1239|91061|186826|186828|117563;2|1239|909932|1843489|31977|29465|39778;2|1224|1236|135625|712|724|727;2|1239|91061|186826|1300|1301,Complete,NA
Study 501,"cross-sectional observational, not case-control",NA,https://doi.org/10.21767/2476-1974.100036,https://reproductive-immunology.imedpub.com/reproductive-microbiomes-using-the-microbiome-as-a-novel-diagnostic-tool-for-endometriosis.php?aid=20437,NA,NA,NA,NA,Experiment 1,United States of America,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Women scheduled for laparoscopic surgery for benign uterine/ ovarian conditions as well as women with Stage I or Stage II endometriosis,One (1) Stage III Endometriosis patient,One (1) Stage III Endometriosis patient was diagnosed via laparoscopic surgery and categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,17,1,None,16S,345,Illumina,PERMANOVA,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,8 August 2021,Samara.Khan,Samara.Khan,"In this experiment, 9 patients had stage I, II or III endometriosis. The nine patients in the control group were undergoing laparoscopic surgery for other gynecological reasons, for a total of 18 patients.

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

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

It should also be noted that multiple unidentified species of Barnesiella were reported to be significantly different, but researchers did not specify which species so these were excluded from curation. There were also multiple unidentified species of Ruminococcus and Clostridium.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Marinilabiliales|f__Marinilabiliaceae|g__Alkalitalea,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|1239|186801|186802|216572|35829;2|1224|28216|80840|506|222;2|976|200643|1970189|558415|1193324;2|1239|526524|526525|128827|174708;2|1239|186801|186802|216572|244127;2|976|200643|171549|815|816;2|1239|186801|186802|31979|580596;2|1239|526524|526525|2810280|100883;2|1239|186801|186802|186803|33042;2|1239|186801|186802|216572|946234;2|1239|91061|186826|33958|1578;2|976|200643|171549|2005525|375288;2|201174|1760|85009|31957|1743;2|32066|203490|203491|1129771|168808;2|1239|91061|1385|90964|1279;2|1239|526524|526525|2810281|191303,Complete,NA
Study 502,randomized controlled trial,22713265,10.4161/gmic.21009,NA,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,Experiment 1,NA,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Fulfilled the Rome III criteria for the diagnosis of IBS.,24,19,"Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.",16S,NA,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus|s__Alkalihalobacillus clausii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus buchneri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|1239|91061|1385|186817|2675234|79880;2|1239|91061|1385|186817|1386|1396;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|216816;2|1224|29547|213849|72294|194;2|1239|186801|186802|186804|1870884|1496;2|1224|1236|91347|543;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958;2|1239|91061|186826|33958|2767893|1581;2|1239|91061|186826|33958|2767887|1624;2|1239|186801|186802|186804;2|1239|186801|186802|186803|39491,Complete,NA
Study 502,randomized controlled trial,22713265,10.4161/gmic.21009,NA,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,Experiment 1,NA,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,Fulfilled the Rome III criteria for the diagnosis of IBS.,24,19,"Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.",16S,NA,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|1283313;2|976|200643|171549|815|816;2|1239|909932|1843489|31977|29465,Complete,NA
Study 502,randomized controlled trial,22713265,10.4161/gmic.21009,NA,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,Experiment 2,NA,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,Fulfilled the Rome III criteria for the diagnosis of IBS. Constipation IBS (IBS-C),24,4,"Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.",16S,NA,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus|s__Alkalihalobacillus clausii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae",2|1239|91061|1385|186817|2675234|79880;2|201174|1760|85004|31953,Complete,NA
Study 502,randomized controlled trial,22713265,10.4161/gmic.21009,NA,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,Experiment 2,NA,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,Fulfilled the Rome III criteria for the diagnosis of IBS. Constipation IBS (IBS-C),24,4,"Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.",16S,NA,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|171552|1283313;2|976|200643|171549|815|816,Complete,NA
Study 502,randomized controlled trial,22713265,10.4161/gmic.21009,NA,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,Experiment 3,NA,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Fulfilled the Rome III criteria for the diagnosis of IBS. Diarrhea IBS (IBS-D).,24,10,"Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.",16S,NA,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus|s__Alkalihalobacillus clausii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus cereus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus salivarius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|1239|91061|1385|186817|2675234|79880;2|1239|91061|1385|186817|1386|1396;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|1678|216816;2|1239|186801|186802|186804|1870884|1496;2|1224|1236|91347|543;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958;2|1239|91061|186826|33958|2767887|1624;2|1239|186801|186802|186804;2|1239|186801|186802|186803|39491,Complete,NA
Study 502,randomized controlled trial,22713265,10.4161/gmic.21009,NA,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,Experiment 3,NA,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,Fulfilled the Rome III criteria for the diagnosis of IBS. Diarrhea IBS (IBS-D).,24,10,"Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.",16S,NA,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976|200643|171549|171552|1283313;2|976|200643|171549|815|816,Complete,NA
Study 502,randomized controlled trial,22713265,10.4161/gmic.21009,NA,"Maccaferri S, Candela M, Turroni S, Centanni M, Severgnini M, Consolandi C, Cavina P , Brigidi P",IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation,Gut microbes,2012,Experiment 4,NA,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-M,Fulfilled the Rome III criteria for the diagnosis of IBS. Mixed IBS (IBS-M).,24,5,"Exclusion criteria included pregnancy or lactation, chronic intestinal disease (i.e., inflammatory bowel disease or celiac disease) or severe systemic disorders, lactose intolerance or food allergies. Patients who in the 2 mo prior to study entry had taken medication, such as antibiotics, corticosteroids or functional foods containing pre or probiotics, were also excluded from the study.",16S,NA,HTF-Microbi.Array,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Table 1.,18 July 2021,Kwekuamoo,Kwekuamoo,"Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus|s__Alkalihalobacillus clausii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus|s__Lentilactobacillus buchneri",2|1239|91061|1385|186817|2675234|79880;2|201174|1760|85004|31953;2|1224|29547|213849|72294|194;2|1224|1236|91347|543;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958|2767893|1581,Complete,NA
Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,Experiment 1,United States of America,Homo sapiens,breast,UBERON:0000310,neoplasm,EFO:0000616,BNH with TNBC normal tissue,BNH with TNBC tumor tissue,Tumor tissue from black non-hispanic patients with triple negative breast cancer,7,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 6a,26 July 2021,Itslanapark,"Itslanapark,Chloe","Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.",decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae",2|201174;2|1224|28211|356|41294,Complete,Chloe
Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,Experiment 2,United States of America,Homo sapiens,breast,UBERON:0000310,neoplasm,EFO:0000616,WNH with TNBC normal tissue,WNH with TNBC normal tissue,Tumor tissue from white non-hispanic patients with triple negative breast cancer,6,6,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),NA,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 6,26 July 2021,Itslanapark,Itslanapark,"Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.",increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,Chloe
Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,Experiment 3,United States of America,Homo sapiens,breast,UBERON:0000310,neoplasm,EFO:0000616,WNH with TNBC normal tissue (second set),WNH with TNBC normal tissue (second set),Tumor tissue from white non-hispanic patients with triple negative breast cancer,10,10,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),NA,FALSE,NA,NA,NA,NA,increased,increased,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,Experiment 4,United States of America,Homo sapiens,breast,UBERON:0000310,neoplasm,EFO:0000616,TPBC normal tissue,TPBC tumor tissue,Tumor tissue from patients with triple positive breast cancer,10,10,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),NA,FALSE,NA,NA,NA,NA,NA,increased,NA,NA,NA,Signature 1,Table 6,26 July 2021,Itslanapark,Itslanapark,"Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.",increased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|32066;2|1239|91061|186826|1300|1301,Complete,Chloe
Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,Experiment 5,United States of America,Homo sapiens,breast,UBERON:0000310,EFO:0001799,NA,WNH,BNH,Normal tissue from black non-hispanic patients with breast cancer,6,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 8,26 July 2021,Itslanapark,Itslanapark,"Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Planococcaceae,2|1239|91061|1385|186818,Complete,Chloe
Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,Experiment 5,United States of America,Homo sapiens,breast,UBERON:0000310,EFO:0001799,NA,WNH,BNH,Normal tissue from black non-hispanic patients with breast cancer,6,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figure 8,26 July 2021,Itslanapark,Itslanapark,"Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",decreased,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,2|1224|28211|204458|76892|20,Complete,Chloe
Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,Experiment 6,United States of America,Homo sapiens,breast,UBERON:0000310,"ethnic group,Rapid Amplification of cDNA Ends","EFO:0001799,EFO:0004182",WNH,BNH,Tumor tissue from black non-hispanic patients with breast cancer,6,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Figure 8,27 July 2021,Itslanapark,Itslanapark,"Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Phyllobacterium",2|1239|909932|1843489|31977|29465;2|1224|28211|356|69277|28100,Complete,Chloe
Study 504,case-control,32839514,10.1038/s41598-020-71102-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445256/,"Thyagarajan S, Zhang Y, Thapa S, Allen MS, Phillips N, Chaudhary P, Kashyap MV , Vishwanatha JK",Comparative analysis of racial differences in breast tumor microbiome,Scientific reports,2020,Experiment 6,United States of America,Homo sapiens,breast,UBERON:0000310,"ethnic group,Rapid Amplification of cDNA Ends","EFO:0001799,EFO:0004182",WNH,BNH,Tumor tissue from black non-hispanic patients with breast cancer,6,7,"Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.",16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Figure 8,27 July 2021,Itslanapark,Itslanapark,"Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.",decreased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Phenylobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1224|28211|204458|76892|20;2|1239|91061|186826|33958|1578,Complete,Chloe
Study 505,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K , Akkermans LM",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,Experiment 1,Netherlands,Homo sapiens,"feces,mucosa of small intestine","UBERON:0001988,UBERON:0001204",irritable bowel syndrome,EFO:0000555,Healthy Control,IBS,"Twelve male and 29 female IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as diarrhea predominant (IBS-D), constipation predominant (IBS-C) or alternating IBS subgroup (IBS-A)",26,41,"Subjects taking medication known to influence bacterial composition and gastrointestinal motility, especially antimicrobial medications and/or probiotics were excluded from the study.",NA,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Tables 2 and 3,19 July 2021,Kwekuamoo,"Kwekuamoo,Chloe","Real time PCR analysis of fecal bifidobacteria in HS, IBS patients and IBS subgroups",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia lituseburensis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|201174|1760|85004|31953|1678|1686;2|1239|186801|186802|186804|1501226|1537;2|201174|1760|85004|31953|1678,Complete,Chloe
Study 505,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K , Akkermans LM",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,Experiment 2,Netherlands,Homo sapiens,"feces,mucosa of small intestine","UBERON:0001988,UBERON:0001204",irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as diarrhea predominant (IBS-D),26,14,"Subjects taking medication known to influence bacterial composition and gastrointestinal motility, especially antimicrobial medications and/or probiotics were excluded from the study.",NA,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 505,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K , Akkermans LM",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,Experiment 3,Netherlands,Homo sapiens,"feces,mucosa of small intestine","UBERON:0001988,UBERON:0001204",irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-A,IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as  alternating IBS subgroup (IBS-A),26,16,"Subjects taking medication known to influence bacterial composition and gastrointestinal motility, especially antimicrobial medications and/or probiotics were excluded from the study.",NA,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 505,case-control,19533811,10.3748/wjg.15.2887,NA,"Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K , Akkermans LM",Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients,World journal of gastroenterology,2009,Experiment 4,Netherlands,Homo sapiens,"feces,mucosa of small intestine","UBERON:0001988,UBERON:0001204",irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-C,IBS patients included in this study fulfilled the Rome II criteria for IBS and were categorized as  constipation predominant (IBS-C),26,11,"Subjects taking medication known to influence bacterial composition and gastrointestinal motility, especially antimicrobial medications and/or probiotics were excluded from the study.",NA,NA,RT-qPCR,T-Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 506,case-control,22356587,10.1111/j.1365-2982.2012.01893.x,NA,"Duboc H, Rainteau D, Rajca S, Humbert L, Farabos D, Maubert M, Grondin V, Jouet P, Bouhassira D, Seksik P, Sokol H, Coffin B , Sabaté JM",Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome,Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society,2012,Experiment 1,NA,Homo sapiens,feces,UBERON:0001988,irritable bowel syndrome,EFO:0000555,Healthy Control,IBS-D,The diagnosis of IBS-D was defined by the Rome 3 criteria,18,14,"Patients with lactose intolerance and organic diseases, including inflammatory
bowel diseases, liver disease, pregnancy, and significant systemic diseases, were excluded.
Patients were free of any previous treatment, including probiotics, antibiotics, steroids, immunosuppressors, transit modulators, and antipsychotics, during the 3 months preceding inclusion.",NA,NA,RT-qPCR,"Mann-Whitney (Wilcoxon),T-Test",0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,19 July 2021,Kwekuamoo,Kwekuamoo,"Comparison of fecal counts (A) in all bacteria, Faecalibacterium prausnitzii, lactobacillus and bifidobacterium and (B) of the main fecal bacterial groups that transform bile acid (coccoides, bacteroides, Escherichia coli, and leptum) in feces of healthy subjects (white bar) and diarrhea predominant IBS patients (gray bar) by quantitative polymerase chain reaction. All results are expressed in log10 bacteria per gram of stool.",increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,2|1224|1236|91347|543|561|562,Complete,NA
Study 507,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani FR, Scaldaferri F, Petito V, Paroni Sterbini F, Pecere S, Lopetuso LR, Palladini A, Gerardi V, Masucci L, Pompili M, Cammarota G, Sanguinetti M , Gasbarrini A",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients after Rifaximin treatment,"Patients affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively treated with 1,200 mg of Rifaximin daily for 10 days.",20,20,1 month,16S,123,Roche454,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,21 July 2021,Gina,Gina,Differential abundance analysis of bacterial genera compared by Rifaximin treatment at time a versus time b.,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|135625|712|724;2|1239|186801|186802|186803|841;2|1239|909932|1843489|31977|29465,Complete,Chloe
Study 507,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani FR, Scaldaferri F, Petito V, Paroni Sterbini F, Pecere S, Lopetuso LR, Palladini A, Gerardi V, Masucci L, Pompili M, Cammarota G, Sanguinetti M , Gasbarrini A",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients after Rifaximin treatment,"Patients affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively treated with 1,200 mg of Rifaximin daily for 10 days.",20,20,1 month,16S,123,Roche454,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2021,Gina,Gina,Differential abundance analysis of bacterial genera compared by Rifaximin treatment at time a versus time b.,increased,NA,NA,Complete,Chloe
Study 507,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani FR, Scaldaferri F, Petito V, Paroni Sterbini F, Pecere S, Lopetuso LR, Palladini A, Gerardi V, Masucci L, Pompili M, Cammarota G, Sanguinetti M , Gasbarrini A",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients 1 month after Rifaximin treatment,"Patients 1 month after Rifaximin treatment affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively.",20,20,1 month prior to Rifaximin treatment.,16S,123,Roche454,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,21 July 2021,Gina,Gina,Differential abundance analysis of bacterial genera compared by Rifaximin treatment time a versus time c.,increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,Chloe
Study 507,time series / longitudinal observational,27027301,10.1159/000443361,NA,"Ponziani FR, Scaldaferri F, Petito V, Paroni Sterbini F, Pecere S, Lopetuso LR, Palladini A, Gerardi V, Masucci L, Pompili M, Cammarota G, Sanguinetti M , Gasbarrini A",The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin,"Digestive diseases (Basel, Switzerland)",2016,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Patients before Rifaximin treatment,Patients 1 month after Rifaximin treatment,"Patients 1 month after Rifaximin treatment affected by ulcerative colitis, Chron's disease, Irritable Bowel Syndrome, diverticular disease, and liver cirrhosis with hepatic encephalopathy consecutively.",20,20,1 month prior to Rifaximin treatment.,16S,123,Roche454,metagenomeSeq,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,21 July 2021,Gina,Gina,Differential abundance analysis of bacterial genera compared by rifaximin treatment at time a versus time c,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,2|1239|186801|186802|186803|841,Complete,Chloe
Study 510,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa JD, Fernandes GR, Calderaro DC, Mendonça SMS, Silva JM, Albiero ML, Cunha FQ, Xiao E, Ferreira GA, Teixeira AL, Mukherjee C, Leys EJ, Silva TA , Graves DT",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,Experiment 1,Brazil,Homo sapiens,subgingival dental plaque,UBERON:0016484,periodontitis,EFO:0000649,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,20,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 1,"Figure 3b, text",29 July 2021,Tislam,"Tislam,Fatima",OTUs with different relative abundance based on LEfSe among subjects with periodontitis,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter actinomycetemcomitans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium|s__Mogibacterium timidum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multisaccharivorax,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella salivae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas artemidis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp.",2|1224|1236|135625|712|416916|714;2|1239|186801|186802|543314|86331|35519;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|162289|33031;2|976|200643|171549|171552|838|52227;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|310514;2|976|200643|171549|171552|838|228604;2|1224|1236|72274|135621|286|287;2|1239|909932|909929|1843491|970|671224;2|1224|1236|135625|712|416916|1872413,Complete,Fatima
Study 510,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa JD, Fernandes GR, Calderaro DC, Mendonça SMS, Silva JM, Albiero ML, Cunha FQ, Xiao E, Ferreira GA, Teixeira AL, Mukherjee C, Leys EJ, Silva TA , Graves DT",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,Experiment 1,Brazil,Homo sapiens,subgingival dental plaque,UBERON:0016484,periodontitis,EFO:0000649,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,20,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 2,"Figure 3b, text",29 July 2021,Tislam,"Tislam,Fatima",OTUs with different relative abundance based on LEfSe among subjects with periodontitis,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella marshii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema sp.",2|976|200643|171549|171552|838|189722;2|201174|1760|2037|2049|2529408|52773;2|1239|91061|186826|1300|1301|1328;2|203691|203692|136|2845253|157|166,Complete,Fatima
Study 510,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa JD, Fernandes GR, Calderaro DC, Mendonça SMS, Silva JM, Albiero ML, Cunha FQ, Xiao E, Ferreira GA, Teixeira AL, Mukherjee C, Leys EJ, Silva TA , Graves DT",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,Experiment 2,Brazil,Homo sapiens,subgingival dental plaque,UBERON:0016484,rheumatoid arthritis,EFO:0000685,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,27,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 1,"Figure 3a, text",29 July 2021,Tislam,"Tislam,Fatima",Differential abundance based on LEfSe among subjects without periodontitis,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella rava,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus|s__Anaeroglobus geminatus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium|s__Mogibacterium neglectum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium|s__Mogibacterium timidum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella buccae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella dentalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella maculosa,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella multisaccharivorax,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oulorum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella salivae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella shahii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Scardovia|s__Scardovia wiggsiae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas flueggei,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sp. oral clone DO042,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas sputigena,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella sp. oral taxon 808",2|976|200643|171549|171552|1283313|671218;2|1239|909932|1843489|31977|156454|156456;2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1689;2|976|117743|200644|49546|1016|1018;2|201174|1760|85007|1653|1716|43768;2|201174|84998|84999|1643824|2767353|1383;2|32066|203490|203491|1129771|32067|157688;2|32066|203490|203491|1129771|32067|157691;2|32066|203490|203491|1129771|32067|157687;2|1239|909932|909929|1843491|52225;2|1239|186801|186802|543314|86331|114528;2|1239|186801|186802|543314|86331|35519;2|976|200643|171549|171552|838|28126;2|976|200643|171549|171552|838|52227;2|976|200643|171549|171552|838|28129;2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|439703;2|976|200643|171549|171552|838|28132;2|976|200643|171549|171552|838|310514;2|976|200643|171549|171552|838|28133;2|976|200643|171549|171552|838|28136;2|976|200643|171549|171552|838|60133;2|976|200643|171549|171552|838|228604;2|976|200643|171549|171552|838|228603;2|1224|1236|72274|135621|286|287;2|201174|1760|85004|31953|196081|230143;2|1239|909932|909929|1843491|970|135080;2|1239|909932|909929|1843491|970|135083;2|1239|909932|909929|1843491|970|163583;2|1239|909932|909929|1843491|970|69823;2|976|200643|171549|2005525|195950|712711,Complete,NA
Study 510,"cross-sectional observational, not case-control",31182740,10.1038/s41598-019-44674-6,NA,"Corrêa JD, Fernandes GR, Calderaro DC, Mendonça SMS, Silva JM, Albiero ML, Cunha FQ, Xiao E, Ferreira GA, Teixeira AL, Mukherjee C, Leys EJ, Silva TA , Graves DT",Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients,Scientific reports,2019,Experiment 2,Brazil,Homo sapiens,subgingival dental plaque,UBERON:0016484,rheumatoid arthritis,EFO:0000685,patients with no rheumatoid arthritis,patients with rheumatoid arthritis,patients with rheumatoid arthritis,27,21,3 months,16S,4,Illumina,LEfSe,0.05,TRUE,NA,"age,sex",NA,NA,increased,NA,increased,NA,increased,Signature 2,"Figure 3, text",29 July 2021,Tislam,Tislam,subjects without periodontitis,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella elegans,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Pelomonas|s__Pelomonas puraquae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pleuritidis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral clone BR014,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Pyramidobacter|s__Pyramidobacter piscolens,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia meyeri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral clone ASCB04",2|1224|28216|80840|80864|80865|180282;2|1239|91061|186826|186828|117563|137732;2|1224|28216|206351|481|32257|505;2|1224|28216|80840|80864|335058|431059;2|976|200643|171549|171552|838|407975;2|976|200643|171549|171552|838|163559;2|508458|649775|649776|649777|638847|638849;2|201174|1760|85006|1268|32207|172042;2|201174|1760|2037|2049|2529408|52773;2|1239|91061|186826|1300|1301|1328;2|1239|91061|186826|1300|1301|325787,Complete,NA
Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,Experiment 1,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,44,140,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Figure 2D,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and COVID-19 patients,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor",2|1224|1236|135625|712|724|729;2|1239|909932|1843489|31977|29465;2|1224|29547|213849|72294|194;2|201174|1760|85006|1268|32207|43675;2|1239|91061|186826|186828|117563;2|1224|28216|206351|481|482|28449;2|1224|28216|206351|481|32257;2|1239|186801|186802|186804|44259,Complete,NA
Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,Experiment 1,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,44,140,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Figure 2D,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and COVID-19 patients,decreased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum",2|1224|28216|206351|481|482;2|201174|1760|85007|1653|1716;2|1224|1236|135625|712|713;2|1239|186801|186802|186803|437755;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|838|28131;2|203691|203692|136|2845253|157;2|1224|1236|72274|135621|286;2|203691|203692|136|2845253|157|59892,Complete,NA
Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,Experiment 2,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,COVID-19 patients (mild/moderate),COVID-19 patients (severe/critical),Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests deemed to have severe/critical disease,30,22,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Supplementary Table 3,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between mild/moderate and severe/critical COVID-19 patients,decreased,"k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema amylovorum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus",2|203691|203692|136|2845253|157;2|1224|1236|135625|712|416916;2|1224|1236|135625|712|416916|739;2|976|200643|171549|171552|838|28131;2|1239|91061|186826|1300|1301|1328;2|1239|909932|909929|1843491|970;2|1239|186801|186802|186804|44259;2|203691|203692|136|2845253|157|59892;2|1239|186801|186802|186807|2740,Complete,NA
Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,Experiment 3,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,44,17,No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 3,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus",2|1224|28216|206351|481|482|28449;2|1239|91061|186826|186828|117563;2|1239|909932|1843489|31977|29465;2|1224|29547|213849|72294|194;2|201174|1760|85006|1268|32207|43675;2|1239|909932|1843489|31977|29465|39778;2|1239|1737404|1737405|1570339|162289,Complete,NA
Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,Experiment 3,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,44,17,No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 3,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia",2|1239|186801|186802|186803|437755;2|203691|203692|136|2845253|157;2|976|200643|171549|171552|838|28131,Complete,NA
Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,32,81,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 1,Supplementary Table 4,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and COVID-19 patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella",2|1239|91061|186826|1300|1301;2|1239|91061|186826|33958|46255;2|1239|91061|186826|81852|1350;2|1239|186801|186802|186803|2719313|358743;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85006|1268|32207|43675;2|201174|1760|85006|1268|32207;2|1239|91061|186826|33958|1578;2|201174|1760|2037|2049|1654;2|1239|91061|186826|186828|117563,Complete,NA
Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests,32,81,No antibiotics or probiotics within 8 weeks prior to COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,decreased,Signature 2,Supplementary Table 4,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between healthy controls and COVID-19 patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus",2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|33042;2|976|200643|171549|815|816|47678;2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|186803|1506577|36835;2|201174|84998|84999|84107|102106;2|976|200643|171549|815|909656|387090,Complete,NA
Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,32,13,No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium",2|1239|91061|186826|1300|1301;2|1239|186801|186802|186803|2719313|358743;2|1239|1737404|1737405|1570339|165779;2|1239|91061|186826|1300|1301|1328;2|1239|1737404|1737405|1570339|162289;2|1224|29547|213849|72294|194;2|201174|84998|84999|1643824|1380,Complete,NA
Study 511,"cross-sectional observational, not case-control",34294722,10.1038/s41522-021-00232-5,NA,"Wu Y, Cheng X, Jiang G, Tang H, Ming S, Tang L, Lu J, Guo C, Shan H , Huang X",Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization,NPJ biofilms and microbiomes,2021,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,COVID-19 patients not treated with antibiotics,Patients with confirmed COVID-19 infection per 2 sequential positive RT-PCR tests who were not treated with antibiotics,32,13,No antibiotics or probiotics within 8 weeks prior to or during COVID-19 infection (also true for controls),16S,34,Illumina,"LEfSe,Linear Regression",0.05,TRUE,2,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,2 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who were not treated with antibiotics and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides eggerthii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola coprophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia producta,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|33042;2|976|200643|171549|815|816|28111;2|976|200643|171549|815|909656|387090;2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|186803|572511|33035;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|1506577|36835;2|1224|28216|206351|481|482,Complete,NA
Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,Experiment 1,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls and healthcare workers,COVID-19 positive patients,Patients positive for SARS-CoV-2,66,68,NA,16S,4,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2a,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and non-COVID patients (COVID negative patients and healthcare workers),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|201174|1760|85006|1268|32207;2|201174|1760|85006|1268|1269;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|286;2|1224|1236|2887326|468|475,Complete,NA
Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,Experiment 2,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients positive for SARS-CoV-2,21,68,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,increased,Signature 1,Figures 2b-h,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 positive and COVID-19 negative patients,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1239|91061|1385|186817|150247;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|286;2|1224|1236|72274|135621|286|287,Complete,NA
Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,Experiment 3,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative healthcare workers (controls),COVID-19 positive patients,Patients positive for SARS-CoV-2,45,68,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 1,Figures 2b-h,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa",2|1239|91061|1385|186817|150247;2|1224|1236|72274|135621|286|287,Complete,NA
Study 512,case-control,34031657,https://doi.org/10.1101/2021.05.20.445008,NA,"Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I , Messaoudi I",Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including <i>Pseudomonas Aeruginosa</i>,bioRxiv : the preprint server for biology,2021,Experiment 3,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative healthcare workers (controls),COVID-19 positive patients,Patients positive for SARS-CoV-2,45,68,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,decreased,Signature 2,Figures 2b-h,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 positive and COVID-19 negative healthcare workers,decreased,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia|s__Burkholderia cepacia,2|1224|28216|80840|119060|32008|292,Complete,NA
Study 513,"cross-sectional observational, not case-control",NA,https://doi.org/10.3390/applmicrobiol1020014,NA,NA,NA,NA,NA,Experiment 1,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 negative controls,COVID-19 positive patients,Patients who were confirmed PCR positive for SARS-CoV-2,20,79,NA,WMS,NA,Illumina,Fisher's Exact Test,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S5,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients and non-COVID-19 patients,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1224|1236|91347|1903411|613;2|1239|909932|1843489|31977|29465,Complete,NA
Study 513,"cross-sectional observational, not case-control",NA,https://doi.org/10.3390/applmicrobiol1020014,NA,NA,NA,NA,NA,Experiment 2,United States of America,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,COVID-19 positive patients without breathing assistance,COVID-19 positive patients with breathing assistance,"Patients who were confirmed PCR positive for SARS-CoV-2 and had treatment with oxygen mask, non-rebreather mask, nasal cannula, BiPAP, CPAP, or ventilator",67,12,NA,WMS,NA,Illumina,NA,0.05,FALSE,NA,NA,NA,NA,unchanged,NA,NA,unchanged,unchanged,Signature 1,Table S5,6 August 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 patients who had breathing assistance and those who did not,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia",2|1224|1236|91347|543|547;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1224|1236|91347|1903411|613,Complete,NA
Study 514,"cross-sectional observational, not case-control",31087436,10.1111/aji.13147,NA,"Akiyama K, Nishioka K, Khan KN, Tanaka Y, Mori T, Nakaya T , Kitawaki J",Molecular detection of microbial colonization in cervical mucus of women with and without endometriosis,"American journal of reproductive immunology (New York, N.Y. : 1989)",2019,Experiment 1,Japan,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Women scheduled for laparoscopic surgery for benign uterine/ ovarian conditions,Stage 3/4 endometriosis patients,Women were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,39,30,No antibiotics were taken 6 months prior to sample collection,16S,56,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Figure 4,8 August 2021,Samara.Khan,Samara.Khan,Enterobactericeae and streptococcus were significantly higher in the cervical mucus of the endometriosis group than the control group.,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1224|1236|91347|543;2|1239|91061|186826|1300|1301,Complete,NA
Study 515,"cross-sectional observational, not case-control",29771400,10.26355/eurrev_201805_14899,NA,"Wang XM, Ma ZY , Song N","Inflammatory cytokines IL-6, IL-10, IL-13, TNF-α and peritoneal fluid flora were associated with infertility in patients with endometriosis",European review for medical and pharmacological sciences,2018,Experiment 1,China,Homo sapiens,uterovesical pouch,UBERON:0011049,endometriosis,EFO:0001065,Non-endometriosis patients with infertility,Endometriosis patients with infertility,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,30,55,None,16S,45,Ion Torrent,T-Test,0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 and Results section,8 August 2021,Samara.Khan,Samara.Khan,"There was no difference in the abundance of the following bacteria in the peritoneal fluid of patients with endometriosis and infertility compared to patients with infertility but not endometriosis: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Fusobacterium, Tenericutes",NA,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Tenericutes",2|1224;2|1239;2|201174;2|976;2|32066|203490|203491|203492|848;2|544448,Complete,NA
Study 516,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M, Li D, Zhang Z, Sun H, An M , Wang G",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,Experiment 1,China,Mus musculus,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,8,NA,N/A,16S,4,Illumina,T-Test,0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,8 August 2021,Samara.Khan,"Samara.Khan,Fatima","Researchers used t-tests to calculate the differences in microbiota at the taxon level between the control and experimental groups.

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

The following bacterial taxa were less abundant in mice with simulated endometriosis than in mice without endometriosis.",decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976;2|976|200643;2|976|200643|171549,Complete,Fatima
Study 516,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M, Li D, Zhang Z, Sun H, An M , Wang G",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,Experiment 2,China,Mus musculus,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,8,NA,N/A,16S,4,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 4,14 March 2022,Fatima,"WikiWorks,Fatima",LDA coupled with effect size measurements identified the most differentially abundant taxa between the two groups,increased,k__Bacteria|p__Firmicutes,2|1239,Complete,Fatima
Study 516,laboratory experiment,29462324,10.1093/humrep/dex372,NA,"Yuan M, Li D, Zhang Z, Sun H, An M , Wang G",Endometriosis induces gut microbiota alterations in mice,"Human reproduction (Oxford, England)",2018,Experiment 2,China,Mus musculus,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy mice,Mice who were injected with endometrial tissues,Researchers induced endometriosis models by intraperitoneal injection of endometrial tissues to mimic endometriosis formation in humans.,8,NA,N/A,16S,4,Illumina,LEfSe,0.05,NA,4,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 4,11 April 2022,NA,NA,LDA coupled with effect size measurements identified the most differentially abundant taxa between the two groups,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes",2|976|200643|171549|171552|1283313;2|976|200643;2|976|200643|171549;2|976,Complete,NA
Study 517,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan KN, Fujishita A, Masumoto H, Muto H, Kitajima M, Masuzaki H , Kitawaki J",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,Experiment 1,Japan,Homo sapiens,endometrium,UBERON:0001295,endometriosis,EFO:0001065,Fertile women being operated on for other gynecological issues,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). 16 of the control patients and 16 of the endometriosis patients received GnRHa (gonadotropin releasing hormone agonist) treatment for 4-6 months.,32,32,None,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,8 August 2021,Samara.Khan,Samara.Khan,"Regardless of GnRHa treatment, patients with endometriosis had higher levels of streptococcaceae and moraxellaceae than those without endometriosis.",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae",2|1239|91061|186826|1300;2|1224|1236|2887326|468,Complete,NA
Study 517,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan KN, Fujishita A, Masumoto H, Muto H, Kitajima M, Masuzaki H , Kitawaki J",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,Experiment 2,Japan,Homo sapiens,endometrium,UBERON:0001295,endometriosis,EFO:0001065,Endometriosis patients not treated with GnRHa,Endometriosis patients treated with GnRHa,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). 16 of the 32 endometriosis patients received GnRHa (gonadotropin releasing hormone agonist) treatment for 4-6 months.,16,16,None,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4,8 August 2021,Samara.Khan,Samara.Khan,"Streptococcaceae, Staphylococaceae, Enterobacteriaceae were significantly increased (p<0.05 for each) in GnRHa-treated women with endometriosis than in GnRHa-untreated women.",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1224|1236|91347|543;2|1239|91061|186826|1300;2|1239|91061|1385|90964,Complete,NA
Study 517,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan KN, Fujishita A, Masumoto H, Muto H, Kitajima M, Masuzaki H , Kitawaki J",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,Experiment 2,Japan,Homo sapiens,endometrium,UBERON:0001295,endometriosis,EFO:0001065,Endometriosis patients not treated with GnRHa,Endometriosis patients treated with GnRHa,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). 16 of the 32 endometriosis patients received GnRHa (gonadotropin releasing hormone agonist) treatment for 4-6 months.,16,16,None,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 4,8 August 2021,Samara.Khan,Samara.Khan,Lactobacillaceae was significantly decreased (p<0.01) in GnRHa-treated women with endometriosis compared to GnRHa-untreated women with endometriosis,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,2|1239|91061|186826|33958,Complete,NA
Study 517,case-control,26901400,10.1016/j.ejogrb.2016.01.040,NA,"Khan KN, Fujishita A, Masumoto H, Muto H, Kitajima M, Masuzaki H , Kitawaki J",Molecular detection of intrauterine microbial colonization in women with endometriosis,"European journal of obstetrics, gynecology, and reproductive biology",2016,Experiment 3,Japan,Homo sapiens,ovary,UBERON:0000992,endometriosis,EFO:0001065,Patients with non-endometrioma cysts,Patients with ovarian endometrioma cysts,Patients with ovarian endometrioma had endometrial cysts in their ovaries. Researchers took samples of the fluid inside these cysts. Ovarian endometrioma is one of the many ways endometriosis manifests in the female reproductive system.,8,8,None,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,8 August 2021,Samara.Khan,Samara.Khan,There was a significantly higher percentage of Streptococcaceae (p<0.01) and Staphylococaceae (p<0.05) in the cystic fluid derived from women with ovarian endometrioma comparing to that in cystic fluid collected from non-endometrioma cysts.,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1239|91061|186826|1300;2|1239|91061|1385|90964,Complete,NA
Study 518,case-control,33839907,10.1007/s00404-021-06057-z,NA,"Shan J, Ni Z, Cheng W, Zhou L, Zhai D, Sun S , Yu C",Gut microbiota imbalance and its correlations with hormone and inflammatory factors in patients with stage 3/4 endometriosis,Archives of gynecology and obstetrics,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,12,12,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 1,"Figure 2, Figure 3 and Results section",9 August 2021,Samara.Khan,Samara.Khan,Patients with endometriosis demonstrated a significantly higher abundance of the following taxa compared to control patients. There were 36 taxa unique to endometriosis patients that were completely absent in control patients. Some taxa were excluded because they had an unidentified genus/ species,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae",2|201174;2|201174|1760|2037|2049|1654;2|1224|28211;2|1239|186801|186802|186803|2569097|39488;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|189330;2|201174|84998|1643822|1643826|84111;2|1239|91061|186826|81852|1350;2|32066;2|1224|28211|356;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|976|200643|171549|2005473;2|1224|28216|206389|75787;2|1224|28216|206389;2|1239|186801|186802|216572|1508657;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|186801|186802|543314|35517;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|31979|1485;2|201174|1760|85007|1653|1716;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|186801|186802|31979;2|1239|91061;2|1239|91061|186826|81852;2|1239|91061|186826|33958,Complete,NA
Study 518,case-control,33839907,10.1007/s00404-021-06057-z,NA,"Shan J, Ni Z, Cheng W, Zhou L, Zhai D, Sun S , Yu C",Gut microbiota imbalance and its correlations with hormone and inflammatory factors in patients with stage 3/4 endometriosis,Archives of gynecology and obstetrics,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy controls,Stage 3/4 endometriosis patients,Women were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,12,12,None,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,NA,unchanged,NA,decreased,Signature 2,"Figure 2, Figure 3 and Results section",9 August 2021,Samara.Khan,Samara.Khan,The following taxa were decreased in endometriosis patients and increased in the control group. There were 11 genera unique to the control group. Some taxa were excluded because they had an unidentified genus/ species,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|28050|39485;2|976|200643|171549|1853231|283168;2|1224|28216|80840|995019|577310;2|1239|186801|186802|216572|1508657;2|1239|186801|186802|216572|1263|41978;2|1224|28216;2|1224|28216|80840;2|1224|28216|80840|506;2|1224|28216|80840|995019|40544;2|976|200643|171549|171551,Complete,NA
Study 519,laboratory experiment,31037294,10.1093/humrep/dez041,NA,"Chadchan SB, Cheng M, Parnell LA, Yin Y, Schriefer A, Mysorekar IU , Kommagani R",Antibiotic therapy with metronidazole reduces endometriosis disease progression in mice: a potential role for gut microbiota,"Human reproduction (Oxford, England)",2019,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,endometriosis,EFO:0001065,Non-endo mice,Endo mice,"Uterine tissue was transplanted onto the peritoneal wall in order to induce endometriosis in these mice. In this experiment, there were 4 more mice that were labelled Endo-VNMA mice. These mice were treated with antibiotics to see if their gut microbiota would have been altered. These mice were not included in the curated experiment.",5,5,Mice had never been given antibiotics prior to the start of the experiment,16S,NA,Illumina,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,9 August 2021,Samara.Khan,Samara.Khan,Fecal samples from mice with simulated endometriosis had higher levels of Bacteroidetes and Firmicutes than non-endo mice. The bacteroides genera was absent in non-endo mice but present in endo mice.,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|976;2|1239;2|976|200643|171549|815|816,Complete,NA
Study 520,"cross-sectional observational, not case-control",32046455,10.1007/s43032-019-00113-5,NA,"Perrotta AR, Borrelli GM, Martins CO, Kallas EG, Sanabani SS, Griffith LG, Alm EJ , Abrao MS",The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study,"Reproductive sciences (Thousand Oaks, Calif.)",2020,Experiment 1,Brazil,Homo sapiens,vagina,UBERON:0000996,endometriosis,EFO:0001065,Stage 1/2 Endometriosis patients,Stage 3/4 Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM). This study was comparing patients with different stages of endometriosis to each other.,21,14,Participants were excluded if they had taken antibiotics within the past 3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),NA,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4 and Discussion section,9 August 2021,Samara.Khan,Samara.Khan,Patients with stage 3/4 endometriosis had a higher abundance of Anaerococcus than those with stage1/2 endometriosis. Other signatures could not be reported because the rest of the paper grouped OTUs into community state types (CSTs).,increased,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,2|1239|1737404|1737405|1570339|165779,Complete,NA
Study 521,case-control,33925708,10.3390/ijms22094608,NA,"Lee SR, Lee JC, Kim SH, Oh YS, Chae HD, Seo H, Kang CS , Shin TS",Altered Composition of Microbiota in Women with Ovarian Endometrioma: Microbiome Analyses of Extracellular Vesicles in the Peritoneal Fluid,International journal of molecular sciences,2021,Experiment 1,South Korea,Homo sapiens,uterovesical pouch,UBERON:0011049,endometriosis,EFO:0001065,Surgical controls,Stage 3/4 endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,45,45,Patients were excluded if they had taken antibiotics 12 weeks prior to sample collection,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Table 1 and Results section,9 August 2021,Samara.Khan,Samara.Khan,There was a significant decrease in the following taxa in the peritoneal fluid among women with endometriosis when compared to surgical controls.,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|201174;2|201174|1760|2037;2|1239|909932|1843489|31977;2|201174|1760|85009|31957;2|201174|1760|2037|2049;2|201174|1760|85009|31957|1743;2|201174|1760|85006|1268|32207;2|201174|1760|2037|2049|1654,Complete,NA
Study 521,case-control,33925708,10.3390/ijms22094608,NA,"Lee SR, Lee JC, Kim SH, Oh YS, Chae HD, Seo H, Kang CS , Shin TS",Altered Composition of Microbiota in Women with Ovarian Endometrioma: Microbiome Analyses of Extracellular Vesicles in the Peritoneal Fluid,International journal of molecular sciences,2021,Experiment 1,South Korea,Homo sapiens,uterovesical pouch,UBERON:0011049,endometriosis,EFO:0001065,Surgical controls,Stage 3/4 endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,45,45,Patients were excluded if they had taken antibiotics 12 weeks prior to sample collection,16S,34,Illumina,T-Test,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,Table 1 and Results section,9 August 2021,Samara.Khan,Samara.Khan,There was a significant increase in the following taxa in the peritoneal fluid of endometriosis patients compared to those without endometriosis.,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter",2|1224|1236|72274;2|1224|1236|72274|135621;2|1224|1236|2887326|468|469;2|1224|1236|72274|135621|286;2|1239|91061|186826|1300|1301;2|1224|28211|356|212791,Complete,NA
Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,Experiment 1,China,Homo sapiens,lower part of vagina,UBERON:0015243,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign tumors,Endometriosis patients,This experiment only curates unknown species up to the genus level so it needs to be deleted.,14,36,This experiment only curates unknown species up to the genus level so it needs to be deleted.,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 and Results section,9 August 2021,Samara.Khan,Samara.Khan,Created in error - this figure only curates unidentified species up to the genus level. This experiment needs to be deleted.,increased,NA,NA,Complete,NA
Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,Experiment 2,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,14,36,Patients were excluded if they had taken antibiotics within 6 months before the study,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 and Results section,9 August 2021,Samara.Khan,Samara.Khan,Lactobacillus iners was decreased in the posterior fornix of the vagina of endometriosis patients compared to controls.,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,2|1239|91061|186826|33958|1578|147802,Complete,NA
Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,Experiment 2,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,14,36,Patients were excluded if they had taken antibiotics within 6 months before the study,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2 and Results section,9 August 2021,Samara.Khan,Samara.Khan,Created in error - this signature only curates unidentified species up to the genus level. This signature needs to be deleted.,increased,NA,NA,Complete,NA
Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,Experiment 3,China,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,14,36,Patients were excluded if they had taken antibiotics within 6 months before the study,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 and Results section,9 August 2021,Samara.Khan,Samara.Khan,The following taxa were increased in the cervical mucus of endometriosis patients compared to control patients.,increased,"k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viridiflava",2|1224|28211|204458|76892;2|1224|28216|80840|80864;2|1239|526524|526525|128827;2|1239|91061|186826|33958|1578|147802;2|32066|203490|203491|1129771;2|1224|1236|72274|135621;2|1224|1236|72274|135621|286|33069,Complete,NA
Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,Experiment 3,China,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,14,36,Patients were excluded if they had taken antibiotics within 6 months before the study,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2 and Results section,9 August 2021,Samara.Khan,Samara.Khan,The following taxa were decreased in the cervical mucus of endometriosis patients compared to controls. Some species were unidentified and were excluded from curation,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viridiflava",2|201174|1760|85006|1268;2|1224|1236|72274|135621|286|33069,Complete,NA
Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,Experiment 4,China,Homo sapiens,endometrium,UBERON:0001295,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,14,36,Patients were excluded if they had taken antibiotics within 6 months before the study,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 and Results section,9 August 2021,Samara.Khan,Samara.Khan,The following taxa were increased in the endometrium of endometriosis patients compared to controls.,increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus casseliflavus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus|s__Macrococcus caseolyticus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viridiflava,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|201174|84998|84999|84107;2|1239|91061|186826|81852|1350|37734;2|1239|91061|1385|33986;2|1224|28211|356;2|32066|203490|203491|1129771;2|1239|91061|1385|90964|69965|69966;2|976|200643|171549|171552|838|165179;2|1224|1236|72274|135621|286|33069;2|1224|28211|204455|31989;2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|31979|1485,Complete,NA
Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,Experiment 4,China,Homo sapiens,endometrium,UBERON:0001295,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,14,36,Patients were excluded if they had taken antibiotics within 6 months before the study,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2 and Results section,9 August 2021,Samara.Khan,Samara.Khan,The following taxa were decreased in the endometrium of endometriosis patients compared to controls.,decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Tissierellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas|s__Stenotrophomonas acidaminiphila",2|1239|526524|526525|128827;2|1239|1737404|1737405|1737406;2|1224|1236|135614|32033|40323|128780,Complete,NA
Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,Experiment 5,China,Homo sapiens,peritoneal fluid,UBERON:0001268,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,14,36,Patients were excluded if they had taken antibiotics within 6 months before the study,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2 and Results section,9 August 2021,Samara.Khan,Samara.Khan,The following taxa were increased in the peritoneal fluid of endometriosis patients compared to controls.,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter guillouiae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas viridiflava,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae|g__Sphingobacterium|s__Sphingobacterium multivorum",2|1224|1236|2887326|468|469|106649;2|1239|186801|186802|31979|1485;2|1224|1236|91347|543;2|201174|1760|85006|1268;2|1224|1236|72274|135621;2|1224|1236|72274|135621|286|33069;2|976|117747|200666|84566|28453|28454,Complete,NA
Study 522,"cross-sectional observational, not case-control",32299442,10.1186/s12941-020-00356-0,NA,"Wei W, Zhang X, Tang H, Zeng L , Wu R",Microbiota composition and distribution along the female reproductive tract of women with endometriosis,Annals of clinical microbiology and antimicrobials,2020,Experiment 5,China,Homo sapiens,peritoneal fluid,UBERON:0001268,endometriosis,EFO:0001065,Controls undergoing laparoscopic surgery for benign tumors,Endometriosis patients,Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).,14,36,Patients were excluded if they had taken antibiotics within 6 months before the study,16S,45,Ion Torrent,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2 and Results section,9 August 2021,Samara.Khan,Samara.Khan,The following taxa were decreased in the peritoneal fluid of endometriosis patients compared to controls.,decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas fragi,2|1224|1236|72274|135621|286|296,Complete,NA
Study 523,laboratory experiment,32681566,10.1111/aji.13307,NA,"Ni Z, Sun S, Bi Y, Ding J, Cheng W, Yu J, Zhou L, Li M , Yu C",Correlation of fecal metabolomics and gut microbiota in mice with endometriosis,"American journal of reproductive immunology (New York, N.Y. : 1989)",2020,Experiment 1,China,Mus musculus,feces,UBERON:0001988,endometriosis,EFO:0001065,Non-endo mice,Endo mice,Endometriosis was induced in female mice via transplantation of endometrial fragments.,6,6,N/A,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3 and Results section,9 August 2021,Samara.Khan,Samara.Khan,There was decreased abundance of the following taxa in the feces of mice with simulated endometriosis compared to controls.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes",2|976|200643|171549|815|816;2|1239|186801|186802|186803|572511;2|1239;2|1239|186801|186802|186803|877420;2|1239|91061|186826|33958|1578;2|976|200643|171549|171552;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|1506577;2|1239|526524|526525|128827|1573534;2|1239|186801|186802|186803|1432051;2|201174|84998|1643822|1643826|644652;2|1239|186801|186802|186803|207244,Complete,NA
Study 523,laboratory experiment,32681566,10.1111/aji.13307,NA,"Ni Z, Sun S, Bi Y, Ding J, Cheng W, Yu J, Zhou L, Li M , Yu C",Correlation of fecal metabolomics and gut microbiota in mice with endometriosis,"American journal of reproductive immunology (New York, N.Y. : 1989)",2020,Experiment 1,China,Mus musculus,feces,UBERON:0001988,endometriosis,EFO:0001065,Non-endo mice,Endo mice,Endometriosis was induced in female mice via transplantation of endometrial fragments.,6,6,N/A,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 3,9 August 2021,Samara.Khan,Samara.Khan,The abundance of the following taxa were increased in mice with simulated endometriosis compared to controls.,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|1224;2|74201;2|1239|526524|526525|128827|174708;2|74201|203494|48461|1647988|239934;2|1224|28216|80840|995019|577310;2|976|200643|171549|171550|28138;2|1224|1236|91347|543|544;2|976|200643|171549|2005525|375288,Complete,NA
Study 524,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI , Valdes AM",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,Experiment 1,United Kingdom,Homo sapiens,feces,UBERON:0001988,non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis),"Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis); The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation",76,40,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,11 August 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis),increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae",2|201174|1760|2037|2049|1654;2|201174|84998|84999|84107|102106;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|31979|1649459;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|1898203;2|1224|28211|204441|41295,Complete,NA
Study 524,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI , Valdes AM",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,Experiment 1,United Kingdom,Homo sapiens,feces,UBERON:0001988,non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis),"Individuals diagnosed with  Nonalcoholic steatohepatitis (without cirrhosis); The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation",76,40,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,11 August 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (without cirrhosis),decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NC2004,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptoclostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Terrisporobacter",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|1224|28221|213115|194924|872;2|1239|186801|186802|186803|1410626;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|2485925;2|976|200643|171549|2005525|375288;2|976|200643|171549|171552|577309;2|1224|28216|80840|995019|577310;2|1239|186801|186802|186804|1481960;2|976|200643|171549|171551;2|1239|186801|186802|186804|1505652,Complete,NA
Study 524,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI , Valdes AM",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,Experiment 2,United Kingdom,Homo sapiens,feces,UBERON:0001988,non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,"Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis; The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation; Fibrosis was scored following the CRN grading system54 by a single pathologist.",76,25,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Figure 4,11 August 2021,Madhubani Dey,Madhubani Dey,Increased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium",2|201174|1760|2037|2049|1654;2|201174|84998|84999|84107|102106;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|31979|1649459;2|1239|186801|186802|186803|1506553,Complete,NA
Study 524,prospective cohort,31696774,10.1080/19490976.2019.1681861,https://pubmed.ncbi.nlm.nih.gov/31696774/,"Astbury S, Atallah E, Vijay A, Aithal GP, Grove JI , Valdes AM",Lower gut microbiome diversity and higher abundance of proinflammatory genus <i>Collinsella</i> are associated with biopsy-proven nonalcoholic steatohepatitis,Gut microbes,2020,Experiment 2,United Kingdom,Homo sapiens,feces,UBERON:0001988,non-alcoholic steatohepatitis,EFO:1001249,Healthy controls,Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,"Individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis; The Fatty Liver Inhibition of Progression (FLIP) Consortium algorithm was used as a diagnostic indicator where the histological diagnosis of NASH requires the presence of steatosis, ballooning, and lobular inflammation; Fibrosis was scored following the CRN grading system54 by a single pathologist.",76,25,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Figure 4,11 August 2021,Madhubani Dey,Madhubani Dey,Decreased abundance of bacterial communities in individuals diagnosed with Nonalcoholic steatohepatitis (NASH) with cirrhosis,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|976|200643|171549|171550|239759;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|976|200643|171549|1853231|283168;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186804|1481960;2|1239|186801|186802|216572|1508657|2053608;2|1239|186801|186802|186804|1505652;2|976|200643|171549|171551,Complete,NA
Study 525,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X, Liu Y, Fan Q, Shi H, Wang S , Lang J",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,Experiment 1,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,Patients were excluded if they had taken antibiotics within 14 days prior to sampling,16S,4,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,11 August 2021,Samara.Khan,Samara.Khan,The following taxa were found to be decreased in women with endometriosis associated CPPS.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus reuteri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|1239|91061|186826|33958|2742598|1598;2|1239|91061|186826|33958|1578,Complete,NA
Study 525,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X, Liu Y, Fan Q, Shi H, Wang S , Lang J",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,Experiment 1,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,Patients were excluded if they had taken antibiotics within 14 days prior to sampling,16S,4,Illumina,T-Test,0.05,FALSE,NA,age,NA,NA,NA,NA,NA,NA,increased,Signature 2,Figure 4,11 August 2021,Samara.Khan,Samara.Khan,The following taxa were found to be increased in women with endometriosis associated CPPS.,increased,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia|s__Delftia tsuruhatensis,2|1224|28216|80840|80864|80865|180282,Complete,NA
Study 525,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X, Liu Y, Fan Q, Shi H, Wang S , Lang J",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,Experiment 2,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,Patients were excluded if they had taken antibiotics within 14 days prior to sampling,16S,4,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 2,11 August 2021,Samara.Khan,Samara.Khan,The following taxa were increased in women with endometriosis associated CPPS pain,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia|s__Alloscardovia omnicolens,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis",2|201174|1760|85004|31953|419014;2|201174|1760|85004|31953|419014|419015;2|1224|1236|135614|32033|40323;2|1239|909932|1843489|31977|29465;2|1239|909932|1843489|31977|29465|187328,Complete,NA
Study 525,case-control,34268384,10.21037/atm-20-4586,NA,"Chao X, Liu Y, Fan Q, Shi H, Wang S , Lang J",The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis,Annals of translational medicine,2021,Experiment 2,China,Homo sapiens,posterior fornix of vagina,UBERON:0016486,endometriosis,EFO:0001065,Women without CPPS presenting for routine examinations,Women with EM-associated CPPS,Thirty-seven women with endometriosis-associated chronic pelvic pain syndrome (CPPS) confirmed  by exploratory laparoscopy or surgical pathology,66,37,Patients were excluded if they had taken antibiotics within 14 days prior to sampling,16S,4,Illumina,LEfSe,0.05,FALSE,4,age,NA,NA,NA,NA,NA,NA,increased,Signature 2,Table 2,11 August 2021,Samara.Khan,Samara.Khan,The following taxa were decreased in women with endometriosis associated CPPS pain,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus iners,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia|s__Sneathia vaginalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus jensenii",2|1239|91061|186826|33958|1578|147802;2|1239|909932|1843489|31977|906;2|32066|203490|203491|1129771|168808|187101;2|1239|91061|186826|33958|1578|109790,Complete,NA
Study 526,"cross-sectional observational, not case-control",33313185,10.21037/atm-20-1309,NA,"Chen S, Gu Z, Zhang W, Jia S, Wu Y, Zheng P, Dai Y , Leng J",Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study,Annals of translational medicine,2020,Experiment 1,China,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Endometriosis patients,Endometriosis/ adenomyosis patients,All participants were diagnosed with endometriosis and/or adenomyosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery,25,14,No antibiotic use within 30 days,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6,11 August 2021,Samara.Khan,Samara.Khan,The following taxa were increased in patients with endometriosis and adenomyosis compared to those with just endometriosis,increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|201174|84998|84999|1643824|1380;2|1224|29547|213849|72294|194;2|1239|1737404|1582879;2|1239|186801|186802|216572|216851;2|1224|1236|91347|543|1940338;2|1224|29547|213849|72294;2|201174|84998|84999|84107,Complete,NA
Study 526,"cross-sectional observational, not case-control",33313185,10.21037/atm-20-1309,NA,"Chen S, Gu Z, Zhang W, Jia S, Wu Y, Zheng P, Dai Y , Leng J",Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study,Annals of translational medicine,2020,Experiment 2,China,Homo sapiens,uterine cervix,UBERON:0000002,endometriosis,EFO:0001065,Patients without endometriosis,Endometriosis/ adenomyosis patients,All participants were diagnosed with endometriosis and/or adenomyosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery,67,14,No antibiotic use within 30 days,16S,NA,Illumina,LEfSe,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,Figure 6,11 August 2021,Samara.Khan,Samara.Khan,The following taxa had increased abundance in patients with endometriosis and adenomyosis compared to those without endometriosis or adenomyosis.,increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae",2|201174|84998|84999|1643824|1380;2|1224|29547|213849|72294|194;2|1239|1737404|1582879;2|1239|186801|186802|216572|216851;2|1224|1236|91347|543|1940338;2|1224|29547|213849|72294;2|201174|84998|84999|84107,Complete,NA
Study 527,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A, Brunkwall L, Roth B, Orho-Melander M , Ohlsson B",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"The main inclusion criteria were to have a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,None but a sensitivity analysis was done excluding those who had taken antibiotics in the last 6 months in a separate experiment.,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Table 2,11 August 2021,Samara.Khan,Samara.Khan,The following taxa were decreased among those with endometriosis compared to healthy controls.,decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter",2|201174|84998|1643822|1643826|447020;2|976|200643|171549;2|201174|84998|84999|84107;2|1239|186801|186802|186803|28050;2|976|200643|171549|171552|577309;2|1239|526524|526525|2810281|191303,Complete,NA
Study 527,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A, Brunkwall L, Roth B, Orho-Melander M , Ohlsson B",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,Experiment 1,Sweden,Homo sapiens,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"The main inclusion criteria were to have a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,None but a sensitivity analysis was done excluding those who had taken antibiotics in the last 6 months in a separate experiment.,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Table 2,11 August 2021,Samara.Khan,Samara.Khan,The following taxa were increased among those with endometriosis compared to healthy controls after a false-discovery rate adjustment,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides",2|976|200643|171549|815|816;2|1239|186801|186802|186803|33042;2|1224|1236|91347|543;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288,Complete,NA
Study 527,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A, Brunkwall L, Roth B, Orho-Melander M , Ohlsson B",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,Experiment 2,Sweden,Homo sapiens,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"The main inclusion criteria were to have a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,This experiment was a sensitivity analysis excluding those who had taken antibiotics in the last 6 months,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 2,11 August 2021,Samara.Khan,Samara.Khan,The following taxa were decreased in endometriosis patients after a sensitivity analysis and adjustment for false-discovery rate.,decreased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,2|976|200643|171549,Complete,NA
Study 527,case-control,33660232,10.1007/s43032-021-00506-5,NA,"Svensson A, Brunkwall L, Roth B, Orho-Melander M , Ohlsson B",Associations Between Endometriosis and Gut Microbiota,"Reproductive sciences (Thousand Oaks, Calif.)",2021,Experiment 2,Sweden,Homo sapiens,feces,UBERON:0001988,endometriosis,EFO:0001065,Healthy controls taken from a larger cohort study,Endometriosis patients,"The main inclusion criteria were to have a diagnosis of endometriosis, confirmed by laparoscopy or laparotomy.",198,66,This experiment was a sensitivity analysis excluding those who had taken antibiotics in the last 6 months,16S,123,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex,smoking status",NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 2,11 August 2021,Samara.Khan,Samara.Khan,The following taxa were increased in endometriosis patients after a sensitivity analysis and adjustment for false-discovery rate.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1239|186801|186802|186803|28050;2|1239|186801|186802|216572|119852,Complete,NA
Study 528,laboratory experiment,31887116,10.1371/journal.pone.0226835,NA,"Hantschel J, Weis S, Schäfer KH, Menger MD, Kohl M, Egert M , Laschke MW",Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation,PloS one,2019,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,endometriosis,EFO:0001065,Non-endo mice,Endo mice,Endometrial tissue was transplanted into the peritoneal cavity to simulate endometriosis,8,8,"None were given prior to the start of the experiment. It should be noted that this experiment found no significant differences of any of the taxa examined on both the genus and family level. Thus, there are no relevant signatures to report.",16S,45,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 529,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L , Zhang",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,"EFO:0000685,MONDO:0005178","EFO:0000685,MONDO:0005178",healthy controls,arthritis patient,arthritis,155,177,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 2, text",16 August 2021,Tislam,Tislam,"(c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).",increased,"k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|32066|203490|203491|203492|848;2|1224|28216|80840|119060|47670;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|186828|117563;2|201174|1760|2037|2049|1654;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|1224|1236|135625|712|724;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838|28132;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,Chloe
Study 529,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L , Zhang",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,Experiment 1,China,Homo sapiens,saliva,UBERON:0001836,"EFO:0000685,MONDO:0005178","EFO:0000685,MONDO:0005178",healthy controls,arthritis patient,arthritis,155,177,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 2, text",16 August 2021,Tislam,Tislam,"(c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Wautersiella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas|s__Brevundimonas diminuta,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas yabuuchiae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Mycoplana",2|1224|1236|2887326|468|469;2|976|117743|200644|2762318|59732;2|1224|1236|72274|135621|286;2|1224|28211|356|212791;2|1224|1236|135614|32033|40323;2|1224|28211|204457|41297|13687;2|976|117743|200644|2762318|343873;2|1224|28211|204458|76892|41275|293;2|976|200643|171549|815|816;2|1224|28216|80840|80864|283;2|1224|28211|204457|41297|13687|172044;2|1224|28211|356|118882|13159,Complete,Chloe
Study 529,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L , Zhang",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,EFO:0000685,EFO:0000685,Osteoarthritis,rheumatoid arthritis,patient with rheumatoid arthritis,67,110,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, text",17 August 2021,Tislam,Tislam,"c) Histogram of the LDA scores, where
the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Actinobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria",2|1224|1236|135625|712|724|735;2|1224|1236|135625|712|713;2|1224|1236|135625|712|416916;2|976|200643|171549|171552|1283313|76122;2|32066|203490|203491|203492|848;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838;2|1239|909932|1843489|31977|29465|39778;2|1224|1236|135625|712|724;2|1224|1236|135625|712|724|729;2|1224|28216|206351|481|482|28449;2|1224|28216|206351|481|482,Complete,Chloe
Study 529,case-control,30459400,10.1038/s41598-018-35473-6,NA,"Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L , Zhang",Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening,Scientific reports,2018,Experiment 2,China,Homo sapiens,saliva,UBERON:0001836,EFO:0000685,EFO:0000685,Osteoarthritis,rheumatoid arthritis,patient with rheumatoid arthritis,67,110,NA,16S,NA,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 2,17 August 2021,Tislam,Tislam,"(c) Histogram of the LDA scores, where the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1239|91061|186826|1300|1301;2|201174|1760|2037|2049|1654;2|1224|28216|80840|119060|47670;2|201174|1760|85006|1268|32207;2|1239|91061|186826|186828|117563;2|201174|1760|85006|1268|32207|2047;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|265975;2|1239|186801|186802|186803|2316020|33038;2|1239|91061|186826|186827|46123,Complete,Chloe
Study 532,case-control,27102666,10.1186/s13073-016-0299-7,NA,"Chen J, Wright K, Davis JM, Jeraldo P, Marietta EV, Murray J, Nelson H, Matteson EL , Taneja V",An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis,Genome medicine,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patient,rheumatoid arthritis patient,32,40,"Any patient or control on antibiotics, consuming probiotics, or having a known history of inflammatory bowel disease or other autoimmune diseases like diabetes and multiple sclerosis were excluded.",16S,345,Illumina,LEfSe,NA,TRUE,2,"age,sex",NA,unchanged,decreased,unchanged,unchanged,unchanged,decreased,Signature 1,"Figure 3, text",16 August 2021,Tislam,"Tislam,Rimsha","Patients with RA are characterized by expansion of rare microbial lineages. a, b LefSe analysis was performed to identify differentially abundant taxa, which are highlighted on the phylogenetic tree in cladogram format (a) and for which the LDA scores are shown (b)",increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae,k__Bacteria|p__Actinobacteria",2|201174;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049;2|201174|1760|2037;2|1239|91061;2|201174|84998|84999|84107;2|201174|84998|84999;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347|1903409|551;2|1239|186801|186802|186806;2|1239|186801|186802|186806|1730;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301;2|1239|526524|526525|2810281|191303;2|1239|526524|526525|2810281;2|201174,Complete,NA
Study 532,case-control,27102666,10.1186/s13073-016-0299-7,NA,"Chen J, Wright K, Davis JM, Jeraldo P, Marietta EV, Murray J, Nelson H, Matteson EL , Taneja V",An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis,Genome medicine,2016,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patient,rheumatoid arthritis patient,32,40,"Any patient or control on antibiotics, consuming probiotics, or having a known history of inflammatory bowel disease or other autoimmune diseases like diabetes and multiple sclerosis were excluded.",16S,345,Illumina,LEfSe,NA,TRUE,2,"age,sex",NA,unchanged,decreased,unchanged,unchanged,unchanged,decreased,Signature 2,"Figure 3, text",16 August 2021,Tislam,"Tislam,Rimsha","LefSe analysis was performed to identify differentially abundant taxa, which are highlighted on the phylogenetic tree in cladogram format (a) and for which the LDA scores are shown (b).",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976|200643|171549|2005519;2|203691|203692|136|1643685;2|1239|186801|186802|216572|216851,Complete,NA
Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,Experiment 1,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects recieving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Figure 1a, 1b, 1c",10 September 2021,Mmarin,Mmarin,"Levels of (a) Bifidobacterium spp., (b) Lactobacillus spp. and (c) Enterobacteriaceae enumerated (log cfu/g faeces) from faecal samples from
185 elderly subjects, separated by antibiotic therapy (data for untreated subjects on left of figure and treated subjects on right) and residence location
[long-stay (LS), n¼32 and 16, light grey boxes; rehabilitation (RH), n¼14 and 10, white boxes; day hospital (DH), n¼33 and 7, white boxes with
horizontal lines; and community (CM), n¼64 and 9, dark grey boxes]. Circle with an enclosed cross¼mean; cross¼outlier; asterisk¼significant
difference between residence locations",decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,2|201174|1760|85004|31953|1678|41200,Complete,NA
Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,Experiment 1,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects recieving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Figure 1a, 1b, 1c",16 September 2021,Mmarin,Mmarin,". Levels of (a) Bifidobacterium spp., (b) Lactobacillus spp. and (c) Enterobacteriaceae enumerated (log cfu/g faeces) from faecal samples from
185 elderly subjects, separated by antibiotic therapy (data for untreated subjects on left of figure and treated subjects on right) and residence location
[long-stay (LS), n¼32 and 16, light grey boxes; rehabilitation (RH), n¼14 and 10, white boxes; day hospital (DH), n¼33 and 7, white boxes with
horizontal lines; and community (CM), n¼64 and 9, dark grey boxes]. Circle with an enclosed cross¼mean; cross¼outlier; asterisk¼significant
difference between residence locations",increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.",2|1224|1236|91347|543;2|1239|91061|186826|33958|1578|1591,Complete,NA
Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,Experiment 2,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects recieving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 1,16 September 2021,Mmarin,Mmarin,"comparison of microbiota for antibiotic-treated subjects versus antibiotic-untreated subjects, grouped by residence location; only significant differences are shown 

Long stay: Lachnospiraceae, Day Hospital: Blautia& Faecalibacterium, Community: Firmicutes & Proteobacteria",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria",2|1239|186801|186802|186803|572511;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|186802|186803;2|1224,Complete,NA
Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,Experiment 2,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects recieving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 1,16 September 2021,Mmarin,Mmarin,"Comparison of microbiota for antibiotic-treated subjects versus antibiotic-untreated subjects, grouped by residence location; only significant differences are shown

Day Hospital: Lactobacillus, Magibacterium, Moryella, Peptoniphilus, Victivallis & Weissella 

Community: Euryarchaeota, Rhodocyclaceae",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Moryella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Weissella,k__Bacteria|p__Bacteroidetes,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Rhodocyclaceae",2|1239|91061|186826|33958|1578;2|1239|186801|186802|543314|86331;2|1239|186801|186802|186803|437755;2|1239|1737404|1737405|1570339|162289;2|256845|1313211|278082|255528|172900;2|1239|91061|186826|33958|46255;2|976;2157|28890;2|1224|28216|206389|75787,Complete,NA
Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,Experiment 3,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects recieving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table S4,16 September 2021,Mmarin,Mmarin,Changes in the relative genus abundances in antibiotic-treated versus untreated subjects; only genera with significant changes are presented,decreased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira",2|1239|909932|1843488|909930|904;2|1239|186801|186802|186803|830;2|1239|186801|186802|186803|28050,Complete,NA
Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,Experiment 3,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects recieving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table S4,16 September 2021,Mmarin,Mmarin,Changes in the relative genus abundances in antibiotic-treated versus untreated subjects; only genera with significant changes are presented,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Penicillium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus",2|1239|1737404|1737405|1570339|165779;2|1239|91061|186826|33958|1578;2|1239|186801|186802|31979|420345;2|1239|909932|1843489|31977|906;2759|4751|4890|147545|5042|1131492|5073;2|1224|1236|91347|1903414|583,Complete,NA
Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,Experiment 4,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects recieving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure S2,16 September 2021,Mmarin,Mmarin,"Box plot representation of the numbers of Bifidobacterium spp., Lactobacillus spp. and Enterobacteriaceae (log cfu/g) recovered from 185 faecal samples from subjects treated (n=42) and untreated (n=143) with antibiotics, independent of residence location. Circle with an enclosed cross=mean; cross=outlier.",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae",2|201174|1760|85004|31953|1678;2|1224|1236|91347|543,Complete,NA
Study 535,"cross-sectional observational, not case-control",22949626,10.1093/jac/dks348,NA,"O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C , Ross RP",Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy,The Journal of antimicrobial chemotherapy,2013,Experiment 4,Ireland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Antibiotic untreated,Antibiotic treated,subjects recieving antibiotics within 1 month prior to visiting an ELDERMET Clinic,143,42,NA,16S,4,Roche454,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,TRUE,NA,age,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure S2,16 September 2021,Mmarin,Mmarin,"Box plot representation of the numbers of Bifidobacterium spp., Lactobacillus spp. and Enterobacteriaceae (log cfu/g) recovered from 185 faecal samples from subjects treated (n=42) and untreated (n=143) with antibiotics, independent of residence location. Circle with an enclosed cross=mean; cross=outlier.",increased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 536,randomized controlled trial,30478001,10.1016/j.ebiom.2018.11.035,NA,"Wei S, Mortensen MS, Stokholm J, Brejnrod AD, Thorsen J, Rasmussen MA, Trivedi U, Bisgaard H , Sørensen SJ","Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial",EBioMedicine,2018,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,azithromycin,CHEBI:2955,The group given a placebo,The group given an azithromycin oral solution,"1-3-year-olds diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Exclusion criteria included macrolide allergy, heart, liver, neurological, kidney disease, and or one or more clinical signs of pneumonia. Participants were prescribed a 3-day course of oral azithromycin solution of 10mg/kg per day.",33,39,none mentioned,16S,4,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,Supplementary table 2,24 September 2021,Gina,Gina,Short term effects: the relative abundance of significant taxa between groups at different phylogenetic levels.,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales,k__Bacteria|p__Firmicutes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__uncultured Bifidobacterium sp.",2|201174;2|201174|1760|85004;2|1239;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678|165187,Complete,NA
Study 536,randomized controlled trial,30478001,10.1016/j.ebiom.2018.11.035,NA,"Wei S, Mortensen MS, Stokholm J, Brejnrod AD, Thorsen J, Rasmussen MA, Trivedi U, Bisgaard H , Sørensen SJ","Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial",EBioMedicine,2018,Experiment 1,Denmark,Homo sapiens,feces,UBERON:0001988,azithromycin,CHEBI:2955,The group given a placebo,The group given an azithromycin oral solution,"1-3-year-olds diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Exclusion criteria included macrolide allergy, heart, liver, neurological, kidney disease, and or one or more clinical signs of pneumonia. Participants were prescribed a 3-day course of oral azithromycin solution of 10mg/kg per day.",33,39,none mentioned,16S,4,Illumina,Linear Regression,0.05,FALSE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 2,Supplementary table 2,24 September 2021,Gina,Gina,Short term effect: the relative abundance of significant taxa between groups at different phylogenetic levels.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor",2|1239|186801|186802|186803;2|1239|186801|186802|216572|946234,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with idiopathic parkinson's disease,Patients with idiopathic parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,1 month,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,increased,NA,NA,increased,Signature 1,"Supplementary table 3, Signature 1 is for increased abundance in those with Parkinson's",19 September 2021,Fcuevas3,"Fcuevas3,Fatima",Analysis of relative taxa abundance in controls and different disease groups.,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Firmicutes",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953;2|201174|1760|85004|31953|1678;2|1239|186801|186802|424536;2|201174|84998|84999|84107;2|1224|1236|91347|543;2|1239|91061|186826|81850;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|1224;2|74201;2|74201|203494|48461|203557;2|1239,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with idiopathic parkinson's disease,Patients with idiopathic parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,1 month,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,increased,NA,NA,increased,Signature 2,"Supplementary table 3, Signature 2 is for decreased abundance in those with Parkinson's",28 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in controls and different disease groups.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|186802|186803;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,the trend over Parkinson's disease progression,Patients with idiopathic Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance in different groups of Parkinson's disease patients.",20 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|74201;2|74201|203494|48461|203557,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 2,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,the trend over Parkinson's disease progression,Patients with idiopathic Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,193,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance in different groups of Parkinson's disease patients.",28 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,2|1239|186801|186802|186803,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 3,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with MSA(multiple system atrophy) disease,Patients diagnosed with synucleinopathy multiple system atrophy (MSA),113,22,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,increased,NA,NA,increased,Signature 1,"Supplementary table 3, signature 1 is for increased abundance in those with MSA",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in controls and different disease groups.,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934;2|1239|91061|186826|33958;2|976|200643|171549|2005525|375288;2|74201;2|74201|203494|48461|203557,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 3,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with MSA(multiple system atrophy) disease,Patients diagnosed with synucleinopathy multiple system atrophy (MSA),113,22,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,increased,NA,NA,increased,Signature 2,"Supplementary table 3, Signature 2 is for decreased abundance in those with MSA",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in controls and different disease groups.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|1239|186801|186802|216572|216851;2|976|200643|171549|171552,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 4,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with PSP(progressive supranuclear palsy) disease,Patients diagnosed with tauopathy progressive supranuclear palsy (PSP),113,22,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,increased,NA,NA,increased,Signature 1,"Supplementary table 3, Signature 1 is for increased abundance in those with PSP",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in controls and different disease groups,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|424536;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|74201;2|74201|203494|48461|203557,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 4,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with PSP(progressive supranuclear palsy) disease,Patients diagnosed with tauopathy progressive supranuclear palsy (PSP),113,22,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,increased,NA,NA,increased,Signature 2,"Supplementary table 3, Signature 2 is for decreased abundance in those with PSP",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in controls and different disease groups,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|186803;2|1239|186801|186802|186803|841;2|1239|91061|186826|1300;2|1239|91061|186826|1300|1301,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 5,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with De-novo Parkinson's disease,Patients with de novo Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,39,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for decreased taxa abundance in patients with De novo parkinson's",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,2|1239|186801|186802|186803,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 6,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's disease,patients with early Parkinson's disease,Patients with early Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,57,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance among patients with early Parkinson's",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|424536;2|1224|1236|91347|543;2|74201;2|74201|203494|48461|203557,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 6,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's disease,patients with early Parkinson's disease,Patients with early Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,57,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance among participants with early Parkinson's",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,2|1239|186801|186802|186803,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 7,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with mid stage Parkinson's,Patients with mid stage Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,53,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance among participants w/mid stage Parkinson's Analysis of relative taxa abundance in different groups of Parkinson’s disease patients",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934;2|1239|186801|186802|424536;2|1224|1236|91347|543;2|1224;2|74201;2|74201|203494|48461|203557,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 7,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with mid stage Parkinson's,Patients with mid stage Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,53,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance among those w/ mid stage Parkinson's",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,2|1239|186801|186802|186803,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 8,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with advanced stage Parkinson's,Patients with advanced stage Parkinson&#039;s disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,44,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,"Supplementary table 4, Signature 1 is for increased taxa abundance among those with advanced Parkinson's",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae",2|74201|203494|48461|1647988|239934;2|1224|1236|91347|543;2|1224;2|74201;2|74201|203494|48461|203557,Complete,NA
Study 537,case-control,30576008,10.1002/mds.27581,NA,"Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C , Pezzoli G",Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism,Movement disorders : official journal of the Movement Disorder Society,2019,Experiment 8,Italy,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with advanced stage Parkinson's,Patients with advanced stage Parkinson&#039;s disease with stage diagnosed according to UK Brain Bank Criteria(1996),113,44,NA,16S,34,Illumina,Negative Binomial Regression,0.05,NA,NA,"age,geographic area","age,breast feeding,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,"Supplementary table 4, Signature 2 is for decreased taxa abundance among those with advanced Parkinson's",30 September 2021,Fcuevas3,Fcuevas3,Analysis of relative taxa abundance in different groups of Parkinson’s disease patients,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239;2|1239|186801|186802|186803,Complete,NA
Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,Experiment 1,Switzerland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,baseline of the ciprofloxacin treated,ciprofloxacin treated,UTI patients treated with ciprofloxacin 500mg twice daily,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,23 September 2021,Mmarin,Mmarin,"Families and genera differentially represented between before and after antibiotic treatment. Boxes were coloured red and blue to indicate decrease and increase, respectively. CP: ciprofloxacin group, CRL: control group; CTCP: household members of ciprofloxacin group; NF: nitrofurantoin group",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|201174|1760|85004|31953;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|119852;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572,Complete,NA
Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,Experiment 1,Switzerland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,baseline of the ciprofloxacin treated,ciprofloxacin treated,UTI patients treated with ciprofloxacin 500mg twice daily,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3,23 September 2021,Mmarin,Mmarin,"Families and genera differentially represented between before and after antibiotic treatment. Boxes were coloured red and blue to indicate decrease and increase, respectively. CP: ciprofloxacin group, CRL: control group; CTCP: household members of ciprofloxacin group; NF: nitrofurantoin group",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia",2|976|200643|171549|815;2|1239|186801|186802|186803|572511;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186806|1730;2|1239|186801|186802|186803;2|1239|186801|186802|186803|841,Complete,NA
Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,Experiment 2,Switzerland,Homo sapiens,feces,UBERON:0001988,NA,NA,Baseline of the Nitrofurantoin treated,Nitrofurantoin treated,UTI patients treated with nitrofurantoin macrocrystals 100mg twice daily,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3,23 September 2021,Mmarin,Mmarin,"Families and genera differentially represented between before and after antibiotic treatment. Boxes were coloured red and blue to indicate decrease and increase, respectively. CP: ciprofloxacin group, CRL: control group; CTCP: household members of ciprofloxacin group; NF: nitrofurantoin group",decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,2|1239|186801|186802|31979,Complete,NA
Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,Experiment 2,Switzerland,Homo sapiens,feces,UBERON:0001988,NA,NA,Baseline of the Nitrofurantoin treated,Nitrofurantoin treated,UTI patients treated with nitrofurantoin macrocrystals 100mg twice daily,10,10,2 months,16S,34,Roche454,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 3,23 September 2021,Mmarin,Mmarin,"Families and genera differentially represented between before and after antibiotic treatment. Boxes were coloured red and blue to indicate decrease and increase, respectively. CP: ciprofloxacin group, CRL: control group; CTCP: household members of ciprofloxacin group; NF: nitrofurantoin group",increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,2|1239|186801|186802|216572|216851,Complete,NA
Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,Experiment 6,Switzerland,Homo sapiens,feces,UBERON:0001988,urinary tract infection,EFO:0003103,CRL2,CP2,"ciprofloxacin group, between antibiotic treatment",10,10,NA,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table S2,15 October 2021,Mmarin,Mmarin,Median values of taxa abundance.Taxa with median proportion >0.5% in at least one of two significantly different (P<0.05) groups of samples are presented. The statistical analysis method used was a Wilcoxon signed-rank test ('paired') and Wilcoxon rank sum ('non paired').,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae",2|976|200643|171549|171550|239759;2|1239|186801|186802|186803;2|1239|186801|186802|216572|119852;2|976|200643|171549|2005525|375288;2|976|200643|171549|171551;2|976|200643|171549|171550;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263;2|1239|909932|1843489|31977,Complete,NA
Study 538,prospective cohort,25658522,10.1016/j.cmi.2014.11.016,NA,"Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S , Lazarevic V",Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota,Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases,2015,Experiment 7,Switzerland,Homo sapiens,feces,UBERON:0001988,urinary tract infection,EFO:0003103,CRL2,NF2,nitrofurantoin group between antibiotic treatment,10,10,NA,16S,34,NA,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table S2,15 October 2021,Mmarin,Mmarin,Median values of taxa abundance.Taxa with median proportion >0.5% in at least one of two significantly different (P<0.05) groups of samples are presented. The statistical analysis method used was a Wilcoxon signed-rank test ('paired') and Wilcoxon rank sum ('non paired').,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|976|200643|171549|171550|239759;2|976|200643|171549;2|976;2|976|200643;2|1239|186801|186802|216572|216851;2|976|200643|171549|171550,Complete,NA
Study 541,case-control,32235826,10.1038/s41467-020-15457-9,NA,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,"Schizophrenic patients (ARSCZ, FESCZ)","Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,90,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina",Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,diet,sex",NA,NA,increased,NA,NA,NA,increased,Signature 1,Figure 1 + Supplementary Data 5A,22 September 2021,Titas,Titas,"The gut microbiota in schizophrenic patients harbored the following facultative anaerobes, which are rare in a healthy gut.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus|s__Alkaliphilus oremlandii,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum",2|1239|186801|186802|31979|114627|461876;2|1224|1236|91347|543|413496|28141;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|33958|2742598|1613,Complete,Lwaldron
Study 541,case-control,32235826,10.1038/s41467-020-15457-9,NA,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,"Schizophrenic patients (ARSCZ, FESCZ)","Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,90,NA,WMS,NA,"BGISEQ-500 Sequencing,Illumina",Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,diet,sex",NA,NA,increased,NA,NA,NA,increased,Signature 2,Figure 1 + Supplementary Data 5A,23 September 2021,Titas,Titas,"Bacteria that are often present in the oral cavity (the following species), were more abundant in patients with schizophrenia than in healthy controls, indicating a close association between the oral and the gut microbiota in schizophrenia.",increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris",2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|201174|1760|85004|31953|1678|1689;2|1239|909932|1843489|31977|39948|218538;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|33958|2742598|1632,Complete,NA
Study 541,case-control,32235826,10.1038/s41467-020-15457-9,NA,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,"Schizophrenic patients (ARSCZ, FESCZ)","Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,90,NA,NA,NA,NA,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 2a + 2d,22 September 2021,Titas,"Titas,Lwaldron","The schizophrenic patients have a significantly lower level of tryptophan in serum (p < 2.2e-16, Two-sided Wilcoxon rank-sum test). The following microbes are abundant in schizophrenic patients and have a negative correlation with serum tryptophan levels (spearman correlation, two-sided P< 0.05).",increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus|s__Acidaminococcus intestini,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus|s__Alkaliphilus oremlandii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus|s__Coprobacillus sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus oris,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gallolyticus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mutans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",2|1239|909932|1843488|909930|904|187327;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|31979|114627|461876;2|1239|186801|186802|216572|244127|169435;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1683;2|201174|1760|85004|31953|1678|1689;2|201174|1760|85004|31953|1678|216816;2|1239|186801|186802|1898207;2|1239|526524|526525|2810280|100883|2137881;2|1224|1236|91347|543|413496|28141;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|186803|189330|39486;2|1239|91061|186826|81852|1350|1352;2|1239|186801|186802|186803|1898203;2|1239|91061|186826|33958|1578|47770;2|1239|91061|186826|33958|2742598|1613;2|1239|91061|186826|33958|2742598|1632;2|1239|909932|1843489|31977|906|187326;2157|28890|183925|2158|2159|2172|2173;2|1239|186801|186802|216572|1017280|106588;2|1239|91061|186826|1300|1301|315405;2|1239|91061|186826|1300|1301|1309;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|1343;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|39778;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|216572|39492;2|976|200643|171549|815|909656|310297,Complete,NA
Study 541,case-control,32235826,10.1038/s41467-020-15457-9,NA,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,"Schizophrenic patients (ARSCZ, FESCZ)","Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,90,NA,NA,NA,NA,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 2a + 2d,22 September 2021,Titas,Titas,"The controls show an abundance of the following species and these species have a positive correlation with tryptophan levels in serum (spearman correlation, two-sidedP< 0.05).",decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc|s__Leuconostoc gelidum",2|1239|186801|186802|31979|1485|1502;2|1239|91061|186826|33958|1243|1244,Complete,NA
Study 541,case-control,32235826,10.1038/s41467-020-15457-9,NA,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,"Schizophrenic patients (ARSCZ, FESCZ)","Only acutely relapsed schizophrenic (ARSCZ) and first-episode schizophrenic (FESCZ) patients were recruited in this study. The current episode of ARSCZ patients was required to happen in the last three months. ARSCZ patients were free of treatment for at least six months. The current episode of FESCZ patients was required to happen in the last year. FESCZ patients did not take any antipsychotics, or their accumulative dosages of antipsychotics intake were much less than the effective dosage (generally less than 100 mg chlorpromazine equivalents in the last two weeks based on the transformation method).",81,90,NA,NA,NA,NA,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Supplementary Figure 2a + 2d,22 September 2021,Titas,Titas,"Schizophrenic patients have a higher level of kynurenic acid (KYNA) and the following microbial species. The species also show a positive correlation with KYNA (spearman correlation, two-sided P< 0.05).",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium angulatum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudocatenulatum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus fermentum",2|201174|1760|85004|31953|1678|1683;2|201174|1760|85004|31953|1678|1681;2|201174|1760|85004|31953|1678|1686;2|201174|1760|85004|31953|1678|216816;2|201174|1760|85004|31953|1678|28026;2|1239|909932|1843489|31977|906|187326;2|1239|91061|186826|1300|1301|1343;2|1239|909932|1843489|31977|29465|39777;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|33958|2742598|1613,Complete,NA
Study 541,case-control,32235826,10.1038/s41467-020-15457-9,NA,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,Schizophrenic patients,These new schizophrenic patients were taking antipsychotics.,45,45,NA,NA,NA,NA,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3b,22 September 2021,Titas,Titas,The following species show significant enrichment in schizophrenic patients.,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus|s__Alkaliphilus oremlandii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|31979|114627|461876;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|216816;2|1224|1236|91347|543|413496|28141;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|1300|1301|1343;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|216572|39492;2|976|200643|171549|815|909656|310297,Complete,NA
Study 541,case-control,32235826,10.1038/s41467-020-15457-9,NA,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,Schizophrenic patients,These new schizophrenic patients were taking antipsychotics.,45,45,NA,NA,NA,NA,Mann-Whitney (Wilcoxon),NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3b,22 September 2021,Titas,Titas,The following species show enrichment in healthy controls.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei",2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|329854;2|976|200643|171549|815|909656|357276,Complete,NA
Study 541,case-control,32235826,10.1038/s41467-020-15457-9,NA,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,Experiment 4,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,Baseline schizophrenic patients,These schizophrenic patients were selected from the 90 medication-free patients of experiment 1.,81,38,NA,NA,NA,NA,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,body mass index,diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3d + Supplementary data 10,23 September 2021,Titas,Titas,"Of the 26 identified microbial species, 20 species remained significantly changed between 81 controls and 38 baseline patients (P < 0.1, FDR = 0.44, Benjamini and Hochberg method).",NA,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus|s__Alkaliphilus oremlandii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus anthracis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|31979|114627|461876;2|1239|91061|1385|186817|1386|1392;2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|329854;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|216816;2|1224|1236|91347|543|413496|28141;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|1300|1301|1343;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|216572|39492;2|976|200643|171549|815|909656|310297,Complete,NA
Study 541,case-control,32235826,10.1038/s41467-020-15457-9,NA,"Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H , Ma X",Metagenome-wide association of gut microbiome features for schizophrenia,Nature communications,2020,Experiment 5,China,Homo sapiens,feces,UBERON:0001988,schizophrenia,MONDO:0005090,Healthy controls,Baseline schizophrenic patients,38 of the 90 patients had 3-months of treatment (27 with risperidone and 11 with other antipsychotics).,81,38,NA,NA,NA,NA,Mann-Whitney (Wilcoxon),0.1,TRUE,NA,"age,body mass index,diet,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3d + Supplementary data 10,23 September 2021,Titas,Titas,"After 3-months of treatment, the abundances of 12 of these 26 mOTUs remained significantly changed compared with the 81 controls (P < 0.1, FDR = 0.33, Benjamini and Hochberg method, Supplementary Data 10).",NA,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus|s__Alkaliphilus oremlandii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus anthracis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter sakazakii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus faecium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola plebeius",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|31979|114627|461876;2|1239|91061|1385|186817|1386|1392;2|976|200643|171549|815|816|329854;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|216816;2|1224|1236|91347|543|413496|28141;2|1239|91061|186826|81852|1350|1352;2|1239|91061|186826|1300|1301|1343;2|1239|909932|1843489|31977|29465|29466;2|1239|186801|186802|216572|39492;2|976|200643|171549|815|909656|310297,Complete,NA
Study 543,case-control,32415070,10.1038/s41467-020-16222-8,NA,"Vujkovic-Cvijin I, Sortino O, Verheij E, Sklar J, Wit FW, Kootstra NA, Sellers B, Brenchley JM, Ananworanich J, Loeff MSV, Belkaid Y, Reiss P , Sereti I",HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases,Nature communications,2020,Experiment 1,United Kingdom,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 544,case-control,30157754,10.1186/s12866-018-1232-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114884/,"Zhang Y, Yu X, Yu E, Wang N, Cai Q, Shuai Q, Yan F, Jiang L, Wang H, Liu J, Chen Y, Li Z , Jiang Q",Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study,BMC microbiology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,CRC patients,patients diagnosed with colorectal cancer,130,130,6 months,16S,34,Illumina,Spearman Correlation,0.01,TRUE,NA,"age,sex","age,alcohol drinking,body mass index,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 1,Table S1,20 January 2022,Itslanapark,Itslanapark,CRC-associated microbiota in CRC patients compared with controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter rectus",2|1239|186801|186802|186804|1257|341694;2|1239|1737404|1737405|1570339|543311|33033;2|1239|91061|1385|1378|29391;2|1239|909932|1843489|31977|39948|39950;2|976|200643|171549|171551|836|28123;2|1239|526524|526525|128827|123375|102148;2|32066|203490|203491|203492|848|851;2|201174|84998|1643822|1643826|84111|84112;2|1224|29547|213849|72294|194|203,Complete,NA
Study 544,case-control,30157754,10.1186/s12866-018-1232-6,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114884/,"Zhang Y, Yu X, Yu E, Wang N, Cai Q, Shuai Q, Yan F, Jiang L, Wang H, Liu J, Chen Y, Li Z , Jiang Q",Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study,BMC microbiology,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,controls,CRC patients,patients diagnosed with colorectal cancer,130,130,6 months,16S,34,Illumina,Spearman Correlation,0.01,TRUE,NA,"age,sex","age,alcohol drinking,body mass index,sex,smoking status",NA,NA,NA,NA,NA,NA,Signature 2,Table S1,20 January 2022,Itslanapark,Itslanapark,CRC-associated microbiota in CRC patients compared with controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Agathobaculum|s__Agathobaculum desmolans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",2|1239|186801|186802|186803|28050|39485;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|1407607|1150298;2|1239|186801|186802|186803|572511|871665;2|1239|186801|186802|186803|841|301302;2|1239|186801|186802|216572|2048137|39484;2|1239|91061|186826|1300|1301|1304,Complete,NA
Study 545,randomized controlled trial,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 10 days after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 5,27 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young mice after 10 days of antibiotic treatment,increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus",2|1239|91061|186826|81852;2|1239|91061|186826;2|1239|91061|186826|81852|1350,Complete,NA
Study 545,randomized controlled trial,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,Experiment 1,United States of America,Mus musculus,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 10 days after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 5,28 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 10 days of Abx treatment,decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|1239|526524|526525|128827|1470349;2|1239|186801|186802|543314|2137877;2|1239|526524|526525|128827;2|1239|526524|526525;2|1239|526524|526525|128827|1729679;2|1239|186801|186802|186804;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|1898207,Complete,NA
Study 545,randomized controlled trial,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,Experiment 2,United States of America,Mus musculus,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 6 months after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 1,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 6 months of recovery,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella",2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186804;2|1239|526524|526525|128827|1937008,Complete,NA
Study 545,randomized controlled trial,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,Experiment 2,United States of America,Mus musculus,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,7 week old (young) mice before antibiotic treatment,7 week old (young) mice 6 months after antibiotic treatments,7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,decreased,NA,decreased,NA,NA,Signature 2,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 6 months of recovery (lower panels),decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus",2|1239|186801|186802|543314|2137877;2|1239|526524|526525|128827|1470349,Complete,NA
Study 545,randomized controlled trial,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,Experiment 3,United States of America,Mus musculus,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 10 days after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 10 days of Abx treatment,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,2|976|200643|171549,Complete,NA
Study 545,randomized controlled trial,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,Experiment 3,United States of America,Mus musculus,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 10 days after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 10 days of Abx treatment.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales",2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186804;2|1239|526524|526525|128827|1729679;2|1239|526524|526525|128827;2|1239|526524|526525,Complete,NA
Study 545,randomized controlled trial,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,Experiment 4,United States of America,Mus musculus,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 6 months after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 1,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 6 months of recovery (lower panels).,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibaculum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|976|200643|171549;2|1239|526524|526525|128827|1729679;2|976|200643|171549|2005473;2|976|200643|171549|2005473|1918540;2|1239|186801|186802|186804;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|1898207,Complete,NA
Study 545,randomized controlled trial,33804656,10.3390/microorganisms9030647,NA,"Laubitz D, Typpo K, Midura-Kiela M, Brown C, Barberán A, Ghishan FK , Kiela PR",Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study),Microorganisms,2021,Experiment 4,United States of America,Mus musculus,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,40 week old (old) mice before antibiotic treatment,40 week old (old) mice 6 months after antibiotic treatments,40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.,5,5,Mice were not previously given antibiotics before the study,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,sex,NA,NA,NA,NA,NA,NA,Signature 2,Figure 5,29 September 2021,Gina,Gina,Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice after 6 months of recovery,increased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dubosiella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales",2|1239|526524|526525|128827|1937008;2|1239|526524|526525|128827;2|1239|526524|526525,Complete,NA
Study 546,"cross-sectional observational, not case-control",34425246,10.1016/j.micinf.2021.104880,NA,"Gupta A, Karyakarte R, Joshi S, Das R, Jani K, Shouche Y , Sharma A",Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types,Microbes and infection,2021,Experiment 1,India,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-infected controls,COVID-19 cases,COVID-19 infected individuals,26,63,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 1,Supplementary Info - Figure 1,27 September 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between infected and non-infected individuals,increased,k__Bacteria|p__Proteobacteria,2|1224,Complete,NA
Study 546,"cross-sectional observational, not case-control",34425246,10.1016/j.micinf.2021.104880,NA,"Gupta A, Karyakarte R, Joshi S, Das R, Jani K, Shouche Y , Sharma A",Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types,Microbes and infection,2021,Experiment 1,India,Homo sapiens,nasopharynx,UBERON:0001728,COVID-19,MONDO:0100096,Non-infected controls,COVID-19 cases,COVID-19 infected individuals,26,63,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,decreased,unchanged,NA,decreased,Signature 2,"Supplementary Info - Figure 1, Figure 2a-b",27 September 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between infected and non-infected individuals,decreased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239;2|976;2|976|200643|171549|171552;2|1239|909932|1843489|31977;2|1224|28216|206351|481;2|32066|203490|203491|1129771;2|32066|203490|203491|203492;2|1224|1236|135625|712|724;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482;2|1239|91061|186826|1300|1301,Complete,NA
Study 547,case-control,34382150,10.1007/s12275-021-1206-5,NA,"Zhou Y, Zhang J, Zhang D, Ma WL , Wang X",Linking the gut microbiota to persistent symptoms in survivors of COVID-19 after discharge,"Journal of microbiology (Seoul, Korea)",2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Health-care workers who recovered from COVID-19 and were discharged from the hospital between May and July 2020,14,15,3 months prior,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 1,Figure 4,27 September 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between recovered healthcare workers and healthy controls,increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__Erysipelatoclostridium ramosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster aldenensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae",2|201174;2|1224|1236|91347|543|561;2|1239|186801|186802|186804|1505657;2|1239|186801|186802|216572|946234;2|1224|1236|91347|543|561;2|1239|526524|526525|128827|1505663|1547;2|1239|186801|186802|186804|1505657|261299;2|1239|186801|186802|186803|2719313|358742;2|1239|186801|186802|186803|2719313|208479,Complete,NA
Study 547,case-control,34382150,10.1007/s12275-021-1206-5,NA,"Zhou Y, Zhang J, Zhang D, Ma WL , Wang X",Linking the gut microbiota to persistent symptoms in survivors of COVID-19 after discharge,"Journal of microbiology (Seoul, Korea)",2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,COVID-19,MONDO:0100096,Healthy controls,Recovered COVID-19 patients,Health-care workers who recovered from COVID-19 and were discharged from the hospital between May and July 2020,14,15,3 months prior,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,decreased,unchanged,NA,NA,unchanged,Signature 2,Figure 4,27 September 2021,Claregrieve1,Claregrieve1,Differential abundance of microbial taxa between recovered healthcare workers and healthy controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas|s__Intestinimonas butyriciproducens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia sedimentorum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus|s__Butyricicoccus pullicaecorum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella|s__[Clostridium] colinum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia faecis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans",2|1239|186801|186802|186803;2|1224|28221|213115|194924;2|1224|28221|213115|194924|35832;2|1239|186801|186802|1392389;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|216572|216851;2|1239|186801|186802|31979|580596;2|1239|186801|186802|186803|189330;2|1239|186801|186802|216572|1263;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|1407607;2|1224|28221|213115|194924|35832|35833;2|1239|909932|1843489|31977|39948|218538;2|1239|186801|186802|1392389|1297617;2|1239|186801|186802|186804|1501226|1368474;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|31979|580596|501571;2|1239|186801|186802|186803|1506577|36835;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|186803|572511|871665;2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|186803|841|360807;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|186803|1407607|1150298,Complete,NA
Study 548,prospective cohort,34423593,10.1002/advs.202102785,NA,"Gao M, Wang H, Luo H, Sun Y, Wang L, Ding S, Ren H, Gang J, Rao B, Liu S, Wang X, Gao X, Li M, Zou Y, Liu C, Yuan C, Sun J, Cui G , Ren Z",Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2021,Experiment 1,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Confirmed COVID-19 cases by RT-PCR,48,94,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 1,"Figure 3b, 3d",28 September 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 cases and healthy controls,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae|g__Halomonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria,k__Bacteria|p__Firmicutes",2|1224|1236|135619|28256|2745;2|1239|91061|186826|186828|117563;2|32066|203490|203491|1129771|32067;2|1239|91061|186826|1300|1301;2;2|1239,Complete,NA
Study 548,prospective cohort,34423593,10.1002/advs.202102785,NA,"Gao M, Wang H, Luo H, Sun Y, Wang L, Ding S, Ren H, Gang J, Rao B, Liu S, Wang X, Gao X, Li M, Zou Y, Liu C, Yuan C, Sun J, Cui G , Ren Z",Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2021,Experiment 1,China,Homo sapiens,oropharynx,UBERON:0001729,COVID-19,MONDO:0100096,Healthy controls,COVID-19 cases,Confirmed COVID-19 cases by RT-PCR,48,94,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2.5,"age,body mass index,sex",NA,NA,decreased,NA,decreased,NA,NA,Signature 2,"Figure 3b, 3d",28 September 2021,Claregrieve1,Claregrieve1,Differential microbial abundance between COVID-19 cases and healthy controls,decreased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Proteobacteria,k__Bacteria,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales,k__Bacteria|p__Synergistetes,k__Bacteria|p__Deferribacteres|c__Deferribacteres,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|976;2|1224;2;2|1224|29547;2|203691;2|1224|28221|213118;2|508458;2|200930|68337;2|74201;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838;2|976|200643|171549|171552|1283313;2|32066|203490|203491|203492|848;2|1224|1236|135625|712|724,Complete,NA
Study 550,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosèn A, Berstad JR, Flatø B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E , Al-Haroni M",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,Experiment 1,Norway,Homo sapiens,saliva,UBERON:0001836,juvenile idiopathic arthritis,EFO:0002609,healthy controls,JIA patients,children with juvenile idiopathic arthritis,34,59,Patients on antibiotics prior to sampling were excluded.,16S,123,Illumina,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 1,"Figure 3C, text",28 September 2021,Tislam,Tislam,"Differentially abundant taxa (C) Species that showed significant differences in relative abundance between the two study groups as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe) – 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum orale,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium|s__Mogibacterium diversum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sp.,k__Bacteria|p__Candidatus Saccharibacteria|s__TM7 phylum sp. oral taxon 352,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 417",2|976|200643|171549|171552|1283313|1872471;2|1239|186801|186802|186803|1164882|979627;2|201174|1760|85006|1268|32207|172042;2|1239|526524|526525|128827|123375|102148;2|1239|186801|186802|186803|1213720|796942;2|976|200643|171549|171552|838|425941;2|1239|186801|186802|543314|86331|114527;2|1239|909932|1843489|31977|29465|39777;2|976|117743|200644|49546|1016|44737;2|95818|713054;2|32066|203490|203491|1129771|32067|712365,Complete,NA
Study 550,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosèn A, Berstad JR, Flatø B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E , Al-Haroni M",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,Experiment 1,Norway,Homo sapiens,saliva,UBERON:0001836,juvenile idiopathic arthritis,EFO:0002609,healthy controls,JIA patients,children with juvenile idiopathic arthritis,34,59,Patients on antibiotics prior to sampling were excluded.,16S,123,Illumina,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,unchanged,unchanged,unchanged,NA,unchanged,Signature 2,"Figure 3C, text",28 September 2021,Tislam,Tislam,"Differentially abundant taxa. C) species that showed significant differences in relative abundance between the two study groups as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe) – 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus pittmaniae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella sp. oral taxon 807,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 314,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322",2|1224|1236|135625|712|724|729;2|32066|203490|203491|1129771|32067|712363;2|976|200643|171549|171552|838|28129;2|1224|1236|135625|712|724|249188;2|1239|91061|1385|186817|1386|1423;2|201174|84998|84999|1643824|133925|712411;2|1224|1236|135625|712|724|735;2|201174|1760|85006|1268|32207|2047;2|976|200643|171549|171552|838|712464;2|976|117743|200644|2762318|59735|712187,Complete,NA
Study 550,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosèn A, Berstad JR, Flatø B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E , Al-Haroni M",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,Experiment 2,Norway,Homo sapiens,saliva,UBERON:0001836,temporomandibular joint disorder,EFO:0005279,JIA patients without TMJ,JIA patients with TMJ,children with juvenile idiopathic arthritis,15,44,"Patients on antibiotics on the day of sampling were excluded, but previous antibiotic use were not recorded.",16S,123,Illumina,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 6C,",28 September 2021,Tislam,Tislam,"species that showed significant differences in relative abundance between the JIA subjects with and without TMJ involvement, as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe). 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 070,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus subtilis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|201174|1760|85006|1268|32207|43675;2|201174|84998|84999|1643824|2767353|1382;2|1239|186801|186802|186803|265975|237576;2|32066|203490|203491|1129771|2755140|157692;2|1239|91061|186826|1300|1301|671226;2|1239|91061|1385|186817|1386|1423;2|1224|1236|135625|712|724,Complete,NA
Study 550,"cross-sectional observational, not case-control",33251163,10.3389/fcimb.2020.602239,NA,"Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosèn A, Berstad JR, Flatø B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E , Al-Haroni M",Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study,Frontiers in cellular and infection microbiology,2020,Experiment 2,Norway,Homo sapiens,saliva,UBERON:0001836,temporomandibular joint disorder,EFO:0005279,JIA patients without TMJ,JIA patients with TMJ,children with juvenile idiopathic arthritis,15,44,"Patients on antibiotics on the day of sampling were excluded, but previous antibiotic use were not recorded.",16S,123,Illumina,LEfSe,0.1,TRUE,2.5,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 6C, text",28 September 2021,Tislam,Tislam,"species that showed significant differences in relative abundance between the JIA subjects with and without TMJ involvement, as identified by linear discriminant analysis (LDA) effect size analysis (LEfSe). 2.5 LDA score cutoff. OT, oral taxon. **FDR ≤ 0.1 (Benjamini-Hochberg method).",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas sp.,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 313,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 875,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium parvum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella shahii,k__Bacteria|p__Candidatus Absconditabacteria|s__SR1 bacterium oral taxon 874,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp.,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter sp. oral taxon 044,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nanceiensis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas pasteri,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae",2|976|200643|171549|171551|836|1924944;2|976|200643|171549|171552|838|652722;2|221235|1226342;2|1239|186801|186802|186803|265975|1501329;2|1224|28216|206351|481|538|539;2|976|200643|171549|171552|838|228603;2|221235|1226341;2|976|200643|171549|171552|1283313|1872471;2|1224|29547|213849|72294|194|712200;2|1224|28216|206351|481|32257|505;2|976|200643|171549|171552|838|425941;2|976|200643|171549|171551|836|1583331;2|1224|28216|206351|481|482|495;2|976|200643|171549|171552|838|60133;2|976|117743|200644|2762318|59735|1962306;2|1224|1236|135625|712|724|729,Complete,NA
Study 552,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen MA, Thorsen J, Dominguez-Bello MG, Blaser MJ, Mortensen MS, Brejnrod AD, Shah SA, Hjelmsø MH, Lehtimäki J, Trivedi U, Bisgaard H, Sørensen SJ , Stokholm J",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,Experiment 1,United States of America,Homo sapiens,vagina,UBERON:0000996,gestational age,EFO:0005112,Week 24,Week 36,Week 36.,56,57,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Figure 3,28 October 2021,Joyessa,"Joyessa,Fatima",Differentially abundant vaginal taxa at genus level between Week 24 vs. Week 36.,increased,"k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|1737404|1737405|1570339|165779|33037;2|1224|1236|2887326|468|475;2|1239|91061|186826|1300|1301,Complete,NA
Study 552,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen MA, Thorsen J, Dominguez-Bello MG, Blaser MJ, Mortensen MS, Brejnrod AD, Shah SA, Hjelmsø MH, Lehtimäki J, Trivedi U, Bisgaard H, Sørensen SJ , Stokholm J",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,Experiment 1,United States of America,Homo sapiens,vagina,UBERON:0000996,gestational age,EFO:0005112,Week 24,Week 36,Week 36.,56,57,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Figure 3,28 October 2021,Joyessa,"Joyessa,Fatima",Differentially abundant vaginal taxa at genus level between Week 24 vs. Week 36.,increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,2|1224|1236|91347|543,Complete,NA
Study 552,prospective cohort,32488167,10.1038/s41396-020-0686-3,https://pubmed.ncbi.nlm.nih.gov/32488167/,"Rasmussen MA, Thorsen J, Dominguez-Bello MG, Blaser MJ, Mortensen MS, Brejnrod AD, Shah SA, Hjelmsø MH, Lehtimäki J, Trivedi U, Bisgaard H, Sørensen SJ , Stokholm J",Ecological succession in the vaginal microbiota during pregnancy and birth,The ISME journal,2020,Experiment 2,United States of America,Homo sapiens,vagina,UBERON:0000996,gestational age,EFO:0005112,36,Birth,Week 36.,56,57,NA,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 3,15 November 2021,Joyessa,Joyessa,NA,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus",2|1224|1236|2887326|468|475;2|1239|91061|186826|1300|1301;2|1239|91061|1385|90964|1279;2|201174|1760|85007|1653|1716;2|1239|91061|186826|81852|1350;2|1239|91061|1385|1378;2|1224|1236|135625|712|724,Complete,NA
Study 553,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M, Bobdiwala S, Fourie H, Mannino R, Lee YS, Smith A, Marchesi JR, Timmerman D, Bourne T, Bennett PR , MacIntyre DA",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 1,United Kingdom,Homo sapiens,posterior fornix of vagina,UBERON:0016486,spontaneous abortion,EFO:1001255,Viable control pregnancy,First or second-trimester miscarriage,NA,81,77,NA,16S,12,Illumina,Chi-Square,0.05,NA,NA,"age,body mass index,gestational age",NA,NA,NA,NA,NA,increased,increased,Signature 1,Figure 2A,14 October 2021,Titas,Titas,NA,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,Fatima
Study 553,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M, Bobdiwala S, Fourie H, Mannino R, Lee YS, Smith A, Marchesi JR, Timmerman D, Bourne T, Bennett PR , MacIntyre DA",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 2,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,spontaneous abortion,EFO:1001255,Viable control pregnancy,First trimester miscarriage,NA,81,64,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,2D,14 October 2021,Titas,Titas,NA,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,Fatima
Study 553,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M, Bobdiwala S, Fourie H, Mannino R, Lee YS, Smith A, Marchesi JR, Timmerman D, Bourne T, Bennett PR , MacIntyre DA",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 2,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,spontaneous abortion,EFO:1001255,Viable control pregnancy,First trimester miscarriage,NA,81,64,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2D + interpretation,14 October 2021,Titas,Titas,Samples deplete of Lactobacillus spp. display increased richness and diversity and colonization by potential pathogens.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Ureaplasma,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister",2|976|200643|171549|171552|838|59823;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|162289;2|544448|31969|2085|2092|2129;2|1239|909932|1843489|31977|39948,Complete,Fatima
Study 553,case-control,31573753,10.1111/1471-0528.15972,NA,"Al-Memar M, Bobdiwala S, Fourie H, Mannino R, Lee YS, Smith A, Marchesi JR, Timmerman D, Bourne T, Bennett PR , MacIntyre DA",The association between vaginal bacterial composition and miscarriage: a nested case-control study,BJOG : an international journal of obstetrics and gynaecology,2020,Experiment 3,United Kingdom,Homo sapiens,Posterior fornix of vagina,UBERON:0016486,spontaneous abortion,EFO:1001255,missed miscarriage,complete/incomplete miscarriage,"A missed miscarriage is when a baby has died in the womb, but the mother hasn't had any symptoms, such as bleeding or pain.
A complete miscarriage has taken place when all the pregnancy tissue has left your uterus.",61,13,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,14 October 2021,Titas,"Titas,Fatima",Vaginal microbiota composition on the basis of incomplete and/or complete miscarriages,decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,2|1239|91061|186826|33958|1578|1591,Complete,Fatima
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with parkinson's disease,"Diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,4,age,NA,NA,increased,increased,increased,NA,decreased,Signature 1,Figure 2A: Phylum,18 October 2021,Fcuevas3,Fcuevas3,"Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.",increased,k__Bacteria|p__Verrucomicrobia,2|74201,Complete,NA
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with parkinson's disease,"Diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,4,age,NA,NA,increased,increased,increased,NA,decreased,Signature 2,Figure 2B: Class,18 October 2021,Fcuevas3,Fcuevas3,"Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae",2|1239|186801;2|1239|909932;2|74201|203494,Complete,NA
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with parkinson's disease,"Diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,4,age,NA,NA,increased,increased,increased,NA,decreased,Signature 3,Figure 2B: Class,18 October 2021,Fcuevas3,Fcuevas3,"Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels",decreased,k__Bacteria|p__Firmicutes|c__Bacilli,2|1239|91061,Complete,NA
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with parkinson's disease,"Diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,4,age,NA,NA,increased,increased,increased,NA,decreased,Signature 4,Figure 2C: Order,19 October 2021,Fcuevas3,Fcuevas3,"Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales",2|1239|186801|186802|543314|2137877;2|1239|909932|909929;2|74201|203494|48461,Complete,NA
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with parkinson's disease,"Diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,4,age,NA,NA,increased,increased,increased,NA,decreased,Signature 5,Figure 2C: Order,19 October 2021,Fcuevas3,Fcuevas3,"Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.",decreased,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,2|1239|91061|186826,Complete,NA
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with parkinson's disease,"Diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,4,age,NA,NA,increased,increased,increased,NA,decreased,Signature 6,Figure 2D: Family,19 October 2021,Fcuevas3,Fcuevas3,"Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae",2|1239|186801|186802|216572;2|1239|909932|1843489|31977;2|74201|203494|48461|203557;2|976|200643|171549|171551;2|976|200643|171549|171550;2|1239|909932|1843488|909930,Complete,NA
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with parkinson's disease,"Diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,4,age,NA,NA,increased,increased,increased,NA,decreased,Signature 7,Figure 2D: Family,19 October 2021,Fcuevas3,Fcuevas3,"Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|1239|91061|186826|81850;2|976|200643|171549,Complete,NA
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,patients with parkinson's disease,"Diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,T-Test,0.05,NA,4,age,NA,NA,increased,increased,increased,NA,decreased,Signature 8,Figure 2E: Genus,19 October 2021,Fcuevas3,Fcuevas3,"Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira",2|1239|186801|186802|216572|1263;2|74201|203494|48461|1647988|239934;2|1239|186801|186802|186806|1730;2|976|200643|171549|2005525|375288;2|1239|186801|186802|186803|33042;2|1239|909932|1843488|909930|33024;2157|28890|183925|2158|2159|2172;2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|186803|28050,Complete,NA
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,"healthy controls without any form of Parkinson's Disease, with Wexner scores < 3 using Wilcoxon rank sum test.",patients with Parkinson's disease with Wexner scores < 3,Patients with Parkinson's disease with Wexner scores < 3.,25,13,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,Mann-Whitney (Wilcoxon),0.01,NA,4,age,NA,NA,NA,decreased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 554,case-control,31354427,10.3389/fnmol.2019.00171,NA,"Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G , Zhang Y",Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China,Frontiers in molecular neuroscience,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,controls without any form of Parkinson's,patients with Parkinson's disease,"Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.",48,51,"No antibiotic use for at least 3 months prior to the study. 

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.",16S,4,Illumina,ANOVA,0.05,NA,4,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplemental Figure 7,18 October 2021,Fcuevas3,Fcuevas3,Two-way ANOVA analysis to assess the impact of gender and PD on gut microbiota taxa identified by LDA scores>4 in LEfSe analysis.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli",2|976|200643|171549;2|1239|91061|186826|81850;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|91061,Complete,NA
Study 555,case-control,33681234,10.3389/fmed.2020.00538,NA,"Liu Z, Wu Y, Luo Y, Wei S, Lu C, Zhou Y, Wang J, Miao T, Lin H, Zhao Y, Liu Q , Liu Y",Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis,Frontiers in medicine,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patient,rheumatoid arthritis patient,20,30,"Potential volunteer enrolees (including patients and or healthy individuals) were excluded from this study if having: (1) ingested antibiotics in the last 6 months,",16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 5,"Figure 3, text",19 October 2021,Tislam,Tislam,Discriminant analysis of LEfSe multistage species difference.,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,2|1239|186801|186802|186803|841,Complete,NA
Study 555,case-control,33681234,10.3389/fmed.2020.00538,NA,"Liu Z, Wu Y, Luo Y, Wei S, Lu C, Zhou Y, Wang J, Miao T, Lin H, Zhao Y, Liu Q , Liu Y",Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis,Frontiers in medicine,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,rheumatoid arthritis,EFO:0000685,healthy controls,rheumatoid arthritis patient,rheumatoid arthritis patient,20,30,"Potential volunteer enrolees (including patients and or healthy individuals) were excluded from this study if having: (1) ingested antibiotics in the last 6 months,",16S,34,Illumina,LEfSe,0.05,TRUE,2,"age,sex",NA,NA,decreased,decreased,decreased,NA,NA,Signature 8,Figure1,20 October 2021,Fatima,Fatima,NA,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Acetitomaculum,2|1239|186801|186802|186803|31980,Complete,NA
Study 558,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O , Brown JR","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Table 2,18 November 2021,Mmarin,Mmarin,Significantly changed gut bacterial operational taxonomic units in subjects receiving oral-i.v.-administered GSK1322322 in prestudy versus end-of-study comparisons,increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium pseudolongum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|201174|1760|85004|31953|1678;2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1694;2|1224|1236|91347|543;2|1239|186801|186802|186803;2|1224|28216|80840|995019|40544,Complete,NA
Study 558,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O , Brown JR","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Roche454,ANOVA,0.05,TRUE,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Table 2,18 November 2021,Mmarin,Mmarin,Significantly changed gut bacterial operational taxonomic units in subjects receiving oral-i.v.-administered GSK1322322 in prestudy versus end-of-study comparisons,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis",2|1239|186801|186802|186803|207244;2|976|200643|171549;2|976|200643|171549|815|816|820;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|572511|40520;2|976|200643|171549|1853231|574697;2|1239|186801|186802;2|1239|186801|186802|216572|216851;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572;2|976|200643|171549|2005525|375288|823,Complete,NA
Study 558,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O , Brown JR","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Roche454,NA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 1,Figure 5,13 January 2022,Mmarin,Mmarin,"Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium dentium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Enterobacteriaceae bacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella parvirubra,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella wadsworthensis",2|201174|1760|85004|31953|1678|1680;2|201174|1760|85004|31953|1678|1689;2|201174|1760|85004|31953|1678|41200;2|1224|1236|91347|543|1849603;2|1224|28216|80840|995019|40544|437898;2|1224|28216|80840|995019|40544|40545,Complete,NA
Study 558,randomized controlled trial,25487798,10.1128/AAC.04506-14,NA,"Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O , Brown JR","Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase",Antimicrobial agents and chemotherapy,2015,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,received oral-i.v.-administered GSK1322322 (prestudy),received oral-i.v.-administered GSK1322322 (end-of-study),received oral-i.v.-administered GSK1322322,38,38,NA,16S,4,Roche454,NA,0.05,NA,NA,NA,NA,NA,NA,decreased,NA,NA,NA,Signature 2,Figure 5,13 January 2022,Mmarin,Mmarin,"Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter laneus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] lactaris,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia hansenii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia hydrogenotrophica,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus",2|976|200643|171549|2005525|375288;2|976|200643|171549|1853231|283168;2|976|200643|171549|171552|838|165179;2|976|200643|171549|815|816|820;2|976|200643|171549|1853231|283168|626933;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186803|2316020|46228;2|1239|186801|186802|186803|572511|1322;2|1239|186801|186802|216572|1263|41978;2|1239|186801|186802|186803;2|1239|186801|186802|186803|572511|53443;2|1239|186801|186802|186803|207244|1872530;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|216572|1263|1161942;2|1239|186801|186802|186803|2316020|33038,Complete,NA
Study 559,randomized controlled trial,33440171,10.1016/j.chom.2020.12.012,NA,"Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD , Wu GD",Role of dietary fiber in the recovery of the human gut microbiome and its metabolome,Cell host & microbe,2021,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,regular fiber omnivore diet,no fiber liquid omnivore diet,omnivores randomized to an enteral liquid nutrition diet devoid of any fiber (but similar in profile to regular food omnivore group),10,10,6 months,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,NA,Signature 1,Figure 2B,11 November 2021,Lorakasselman,"Lorakasselman,Chloe","The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa
that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] gnavus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|186801|186802|186803|2316020|33038;2|1239|186801|186802|186803|2316020|33039,Complete,Chloe
Study 559,randomized controlled trial,33440171,10.1016/j.chom.2020.12.012,NA,"Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD , Wu GD",Role of dietary fiber in the recovery of the human gut microbiome and its metabolome,Cell host & microbe,2021,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,diet,EFO:0002755,regular fiber omnivore diet,no fiber liquid omnivore diet,omnivores randomized to an enteral liquid nutrition diet devoid of any fiber (but similar in profile to regular food omnivore group),10,10,6 months,16S,NA,Illumina,Linear Regression,0.05,TRUE,NA,NA,age,NA,unchanged,NA,NA,NA,NA,Signature 2,Figure 2B,11 November 2021,Lorakasselman,"Lorakasselman,Chloe","The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa
that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale",2|976|200643|171549|815|816|28116;2|1239|186801|186802|216572|216851|853;2|976|200643|171549|2005525|375288|46503;2|976|200643|171549|171552|838|165179;2|1239|91061|186826|1300|1301|1308;2|1239|186801|186802|186803|39491,Complete,Chloe
Study 560,case-control,28449715,10.1186/s13073-017-0428-y,NA,"Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P , Wüllner U",Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients,Genome medicine,2017,Experiment 3,Germany,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy men without Parkinson's Disease.,Men with Parkinson's Disease.,Only early stage PD men who were naïve to L-DOPA therapy as diagnosed according to the UK Brain Bank criteria.,28,30,"The use of antibiotics in the past three months in principle was an exclusion criterion. However, we included three PD patients and three controls despite the intake of antibiotics for one to three days in a period of 28–34 days prior to feces sampling as the omission of those cases from the analyses did not change any result",16S,NA,Illumina,Kruskall-Wallis,0.1,TRUE,NA,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2C,14 November 2021,Fcuevas3,Fcuevas3,Functional differences in PD patients based on the Glucuronate and the Tryptophan pathways.,increased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,2|1239|186801|186802|186806|1730,Complete,NA
Study 561,case-control,31247001,10.1371/journal.pone.0218252,NA,"Mihaila D, Donegan J, Barns S, LaRocca D, Du Q, Zheng D, Vidal M, Neville C, Uhlig R , Middleton FA",The oral microbiome of early stage Parkinson's disease and its relationship with functional measures of motor and non-motor function,PloS one,2019,Experiment 1,United States of America,Homo sapiens,Major salivary gland,UBERON:0001829,Parkinson's disease,MONDO:0005180,Healthy age-sex matched controls without Parkinson's disease.,Participants with early stage Parkinson's Disease.,Subjects included in the Parkinson’s disease (PD) group had been previously diagnosed by a neurologist and met the general diagnostic criteria for early PD.,36,48,None of the participants underwent antibiotic use in the past month prior to sample collection.,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Table 4. Significantly changed microbiota in early stage PD.,29 November 2021,Fcuevas3,Fcuevas3,Significantly changed microbiota in early stage PD.,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Priestia|s__Priestia megaterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Buchnera,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|g__Candidatus Azobacteroides|s__Candidatus Azobacteroides pseudotrichonymphae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium sp. IHB B 17019,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|s__Flavobacteriaceae bacterium 3519-10,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Halobacillus|s__Halobacillus mangrovi,k__Viruses|s__Streptococcus phage PhiSpn_200,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Wenyingzhuangia|s__Wenyingzhuangia fucanilytica",2|1239|91061|1385|186817|2800373|1404;2|1224|1236|91347|1903409|32199;2|976|200643|171549|511434;2|976|200643|171549|511434|511435;2|976|117743|200644|2762318|59732|1721091;2|976|117743|200644|49546|531844;2|1239|91061|1385|186817|45667|402384;10239|890041;2|976|117743|200644|49546|1518147|1790137,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 1,"Italy,Luxembourg,United States of America",Homo sapiens,vagina,UBERON:0000996,healthy,NA,NA,healthy adult vagina 50% up,NA,NA,96,No,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult vagina genus >=50%,NA,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 1,"Italy,Luxembourg,United States of America",Homo sapiens,vagina,UBERON:0000996,healthy,NA,NA,healthy adult vagina 50% up,NA,NA,96,No,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,"Haoyanzh,Lwaldron",healthy adult vagina species >=50%,NA,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,2|1239|91061|186826|33958|1578|47770,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 2,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,skin of body,UBERON:0002097,healthy,NA,none,healthy adult skin 50% up,NA,NA,362,All records NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult skin genus >=50%,NA,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Eukaryota|p__Ciliophora|c__Litostomatea|o__Haptorida|f__Trachelophyllidae|g__Enchelyodon|s__Enchelyodon sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia",2|1239|91061|1385|90964|1279;2|201174|1760|85009|31957|1912216;2759|5878|5988|5989|197900|55195|55196;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|1269;2|1239|1737404|1737405|1570339|150022;2|1224|1236|2887326|468|475;2|201174|1760|85006|1268|32207,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 2,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,skin of body,UBERON:0002097,healthy,NA,none,healthy adult skin 50% up,NA,NA,362,All records NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult skin species in >=50% samples,NA,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pseudogenitalium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium namnetense,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia|s__Finegoldia magna,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia globosa,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Micrococcus|s__Micrococcus luteus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella osloensis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus hominis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis",2|201174|1760|85007|1653|1716|38303;2|201174|1760|85009|31957|1912216|1747;2|201174|1760|85009|31957|1912216|33011;2|201174|1760|85009|31957|1912216|1574624;2|1239|1737404|1737405|1570339|150022|1260;2759|4751|5204|1538075|162474|742845|55193|76773;2759|4751|5204|1538075|162474|742845|55193|76775;2|201174|1760|85006|1268|1269|1270;2|1224|1236|2887326|468|475|34062;2|1239|91061|1385|90964|1279|29388;2|1239|91061|1385|90964|1279|1282;2|1239|91061|1385|90964|1279|1290;2|1239|91061|186826|1300|1301|28037;2|1239|91061|186826|1300|1301|1303,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 3,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,feces,UBERON:0001988,NA,NA,none - 50% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult stool genus in >= 50% samples,NA,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Agathobaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Thiotrichales|f__Thiotrichaceae|g__Thiothrix|s__Thiothrix nivea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Lawsonibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter",2|1239|186801|186802|216572|216851;2|976|200643|171549|815|816;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|2316020;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186806|1730;2|976|200643|171549|815|909656;2|1239|186801|186802|186803|1407607;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|33042;2|201174|84998|84999|84107|102106;2|1239|186801|186802|216572|2048137;2|1239|186801|186802|186803|2569097;2|1239|186801|186802|216572|1263;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|28050;2|1224|1236|72273|135617|1030|1031;2|1239|186801|186802|204475;2|1239|186801|186802|216572|1905344;2|1239|186801|186802|216572|459786;2|1239|186801|186802|31979|1485;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|946234;2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171552|838;2|976|200643|171549|2005519|397864;2|201174|84998|1643822|1643826|644652;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|2172004;2|1224|1236|91347|543|561;2|1224|28221|213115|194924|35832;2|74201|203494|48461|1647988|239934;2|976|200643|171549|1853231|574697;2|1224|28216|80840|995019|577310;2|1239|186801|186802|186804|1505657,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 3,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,feces,UBERON:0001988,NA,NA,none - 50% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult stool species in >=50% samples,NA,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Firmicutes|s__Firmicutes bacterium CAG:83,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides merdae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia|s__Adlercreutzia equolifaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. CAG:241,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bicirculans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella intestinihominis,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter pamelaeae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides xylanisolvens,k__Eukaryota|p__Ciliophora|c__Spirotrichea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. CAG:38,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. CAG:471,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella excrementihominis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas|s__Butyricimonas virosa,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella intestinalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Firmicutes|s__Firmicutes bacterium CAG:110,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter bartlettii,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Zingiberales|f__Cannaceae|g__Canna|s__Canna indica",2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186803|1407607|1150298;2|976|200643|171549|815|816|820;2|1239|186801|186802|186803|39491;2|1239|186801|186802|186803|572511|418240;2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|216572|2048137|1628085;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|189330|39486;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|815|909656|821;2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|186803|841|360807;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802|204475|745368;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|186802|186803|841|301301;2|1239|186801|186802|186803|28050|39485;2|1239|186801|186802|186803|2316020|33039;2|1239|186801|186802|186803|841|301302;2|976|200643|171549|815|816|28116;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|171550|239759|28117;2|1239|186801|186802|186803|33042|116085;2|1239|1262992;2|1239|91061|186826|1300|1301|1304;2|201174|1760|85004|31953|1678|216816;2|976|200643|171549|815|816|818;2|976|200643|171549|171550|239759|214856;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|216572|459786|1897011;2|976|200643|171549|171550|239759|328814;2|1239|186801|186802|186803|841|166486;2|1239|186801|186802|216572|946234|292800;2|1239|186801|186802|216572|1263|40518;2|976|200643|171549|2005525|375288|46503;2|201174|84998|1643822|1643826|447020|446660;2|1239|186801|186802|216572|459786|1262911;2|976|200643|171549|815|816|47678;2|1239|186801|186802|216572|1263|1160721;2|976|200643|171549|2005519|397864|487174;2|201174|84998|1643822|1643826|644652|471189;2|201174|1760|85004|31953|1678|1680;2|976|200643|171549|815|816|371601;2759|5878|33829;2|976|200643|171549|815|909656|357276;2|1239|186801|186802|186806|1730|1262889;2|1224|1236|91347|543|561|562;2|1239|186801|186802|216572|39492;2|1239|91061|186826|1300|1301|1318;2|1224|28221|213115|194924|35832|35833;2|1239|186801|186802|186803|28050|28052;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|1535;2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|186803|841|1262948;2|1224|28216|80840|995019|577310|487175;2|976|200643|171549|1853231|574697|544645;2|201174|84998|84999|84107|102106|147207;2|976|200643|171549|171552|838|165179;2|1239|1263000;2|1239|186801|186802|186804|1505657|261299;2759|33090|35493|3398|4618|4626|4627|4628,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 4,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,NA,NA,none - 50% prevalence threshold,nasal cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,92,Unknown,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult nasal cavity genus in >=50% samples,NA,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia",2|201174|1760|85009|31957|1912216;2|1239|91061|1385|90964|1279;2|201174|1760|85007|1653|1716;2759|4751|5204|1538075|162474|742845|55193,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 4,United States of America,Homo sapiens,nasal cavity,UBERON:0001707,NA,NA,none - 50% prevalence threshold,nasal cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,92,Unknown,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult nasal cavity species in >=50% samples,NA,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium accolens,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282;2|201174|1760|85007|1653|1716|38284;2759|4751|5204|1538075|162474|742845|55193|76775;2|201174|1760|85009|31957|1912216|33011,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 5,"Italy,Philippines,United States of America",Homo sapiens,nasal cavity,UBERON:0001707,NA,NA,none - 50% prevalence threshold,oral cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,659,No (n=16),WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult oral cavity genus in >=50% samples,NA,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Ornithinimicrobiaceae|g__Serinicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus",2|1239|91061|186826|1300|1301;2|201174|1760|85006|1268|32207;2|201174|1760|2037|2049|1654;2|1239|909932|1843489|31977|29465;2|976|200643|171549|171552|838;2|32066|203490|203491|203492|848;2|1239|91061|1385|1378;2|1224|28216|206351|481|482;2|1224|1236|135625|712|724;2|976|200643|171549|171551|836;2|1224|29547|213849|72294|194;2|201174|1760|2037|2049|2529408;2|976|117743|200644|49546|1016;2|32066|203490|203491|1129771|32067;2|201174|1760|85007|1653|1716;2|1224|28216|80840|119060|47670;2|1224|1236|135625|712|416916;2|976|200643|171549|2005525|195950;2|976|200643|171549|171552|1283313;2|1239|91061|186826|186828|117563;2|201174|1760|85006|2805590|265976;2|1239|186801|186802|186803|1164882;2|1239|1737404|1737405|1570339|543311;2|1239|909932|909929|1843491|970;2|203691|203692|136|2845253|157;2|1239|91061|186826|186827|46123;2|1224|28216|206351|481|32257;2|1239|186801|186802|543314|86331;2|1239|186801|186802|186803|1213720;2|1239|526524|526525|128827|123375;2|1224|1236|135615|868|2717;2|1239|909932|1843489|31977|906;2|1224|28216|206351|481|538;2|1239|186801|186802|186804|1257,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 5,"Italy,Philippines,United States of America",Homo sapiens,nasal cavity,UBERON:0001707,NA,NA,none - 50% prevalence threshold,oral cavity from healthy adult,non-disease adult participants from curatedMetagenomicData,0,659,No (n=16),WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult oral cavity species in >=50% samples,NA,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus oralis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces oris,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria flavescens,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria sicca,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter concisus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga leadbetteri,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia wadei,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella dispar,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus haemolyticus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella infantium,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Asparagales|f__Orchidaceae|s__Epidendroideae|g__Lockhartia|s__Lockhartia amoena,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella|s__Tannerella serpentiformis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella atypica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella nigrescens,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter sp. oral taxon 458,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. HMSC035G02,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum saburreum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter|s__Aggregatibacter segnis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oris,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria elongata,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella parvula,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. ICM47,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria subflava,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pallens,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium|s__Oribacterium sinus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella|s__Lancefieldella rimae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus pseudopneumoniae,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga ochracea,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella sp. T11011-6,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella salivae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas endodontalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum|s__Stomatobaculum longum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC034E03,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella sp. oral taxon 473,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. HMSC24B09,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga granulosa,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oulorum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium|s__Mogibacterium diversum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. A12,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera micronuciformis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. HMSC067H01,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella jejuni,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. oral taxon 306,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus quentini,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 879,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] sulci,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella denticola",2|1239|91061|186826|1300|1301|1303;2|1239|909932|1843489|31977|29465|29466;2|1239|91061|186826|1300|1301|28037;2|1224|1236|135625|712|724|729;2|201174|1760|85006|1268|32207|2047;2|1239|91061|1385|1378|1379;2|1239|91061|186826|1300|1301|1305;2|201174|1760|85006|1268|32207|43675;2|1239|91061|1385|1378|84135;2|1239|91061|1385|1378|29391;2|32066|203490|203491|203492|848|851;2|201174|1760|2037|2049|1654|544580;2|1239|91061|186826|1300|1301|68892;2|976|200643|171549|171552|838|28132;2|201174|1760|2037|2049|2529408|1660;2|1224|28216|206351|481|482|484;2|1224|28216|206351|481|482|490;2|1224|29547|213849|72294|194|199;2|976|200643|171549|171551|836|322095;2|32066|203490|203491|203492|848|860;2|1224|28216|80840|119060|47670|47671;2|1239|91061|186826|1300|1301|1318;2|976|117743|200644|49546|1016|327575;2|32066|203490|203491|1129771|32067|157687;2|201174|1760|85006|1268|32207|172042;2|1239|909932|1843489|31977|29465|39778;2|976|117743|200644|49546|1016|1019;2|976|117743|200644|49546|1016|1017;2|1224|1236|135625|712|724|726;2|201174|1760|85007|1653|1716|43768;2|1239|91061|186826|186828|117563|46124;2|1239|909932|1843489|31977|29465|1911679;2759|33090|35493|3398|73496|4747|158332|125137|154688;2|1239|91061|186826|1300|1301|1302;2|1224|29547|213849|72294|194|204;2|976|200643|171549|2005525|195950|712710;2|32066|203490|203491|1129771|32067|712359;2|1239|909932|1843489|31977|29465|39777;2|976|200643|171549|171552|838|28133;2|1239|91061|186826|1300|1301|1304;2|1239|91061|186826|1300|1301|45634;2|1224|1236|135625|712|416916|712148;2|201174|1760|2037|2049|1654|1739406;2|1239|186801|186802|186803|1164882|467210;2|1224|1236|135625|712|416916|739;2|976|200643|171549|171552|838|28135;2|1224|28216|206351|481|482|495;2|1239|1737404|1737405|1570339|543311|33033;2|201174|84998|84999|1643824|2767353|1382;2|201174|1760|2037|2049|1654|936548;2|1224|28216|206351|481|482|28449;2|976|200643|171549|171552|838|60133;2|32066|203490|203491|1129771|32067|712357;2|1239|91061|186826|1300|1301|113107;2|1239|186801|186802|186803|265975|237576;2|201174|84998|84999|1643824|2767353|1383;2|201174|1760|85007|1653|1716|61592;2|1239|91061|186826|1300|1301|257758;2|976|117743|200644|49546|1016|1018;2|1239|909932|1843489|31977|29465|2027459;2|201174|1760|2037|2049|1654|1655;2|201174|1760|2037|2049|1654|55565;2|976|200643|171549|171552|838|228604;2|976|200643|171549|171551|836|28124;2|976|200643|171549|171552|1283313|76122;2|1239|186801|186802|186803|1213720|796942;2|1239|91061|186826|1300|1301|1739309;2|1239|526524|526525|128827|123375|102148;2|976|200643|171549|171552|1283313|712469;2|1239|91061|186826|186827|46123|1581061;2|976|200643|171549|171552|838|470565;2|1224|28216|206351|481|482|488;2|976|117743|200644|49546|1016|45242;2|976|200643|171549|171552|838|28136;2|1239|186801|186802|543314|35517;2|1239|186801|186802|543314|86331|114527;2|1224|1236|135625|712|724|1078480;2|1239|91061|186826|1300|1301|1759399;2|32066|203490|203491|1129771|32067|671213;2|1224|1236|135615|868|2717|2718;2|1239|91061|186826|186827|46123|46125;2|1239|909932|1843489|31977|906|187326;2|1239|91061|186826|1300|1301|1739491;2|976|200643|171549|171552|838|1177574;2|1224|28216|206351|481|538|539;2|976|200643|171549|171552|838|712461;2|1224|1236|135625|712|724|123834;2|32066|203490|203491|1129771|32067|1227267;2|1239|186801|186802|543314|143393;2|1239|186801|186802|186804|1257|341694;2|32066|203490|203491|1129771|32067|40542;2|976|200643|171549|171552|838|28129,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 6,Italy,Homo sapiens,milk,UBERON:0001913,NA,NA,none - 50% prevalence threshold,milk from healthy adult,non-disease adult participants from curatedMetagenomicData,0,8,Unknown,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,8 December 2021,Haoyanzh,Haoyanzh,healthy adult milk genus in >=50% samples,NA,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1239|91061|186826|1300|1301,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 7,"Italy,Luxembourg,United States of America",Homo sapiens,vagina,UBERON:0000996,healthy,NA,NA,healthy adult vagina 70% up,NA,NA,96,No,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult vagina genus in >=70% samples,NA,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,2|1239|91061|186826|33958|1578,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 8,"China,India,Italy,Malaysia,Singapore,United States of America",Homo sapiens,skin of body,UBERON:0002097,healthy,NA,none,healthy adult skin 70% up,NA,NA,362,All records NA,WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult skin species in >=70% samples,NA,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus capitis,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium granulosum",2|201174|1760|85009|31957|1912216|1747;2|1239|91061|1385|90964|1279|1282;2759|4751|5204|1538075|162474|742845|55193|76775;2|1239|91061|1385|90964|1279|29388;2|201174|1760|85009|31957|1912216|33011,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 9,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,feces,UBERON:0001988,NA,NA,none - 70% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult stool genus in >= 70% samples,NA,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Agathobaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Viruses|k__Orthornavirae|p__Pisuviricota|c__Pisoniviricetes|o__Picornavirales|f__Caliciviridae|g__Norovirus|s__Norwalk virus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia",2|1239|186801|186802|216572|216851;2|976|200643|171549|815|816;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|2316020;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186806|1730;2|976|200643|171549|815|909656;2|1239|186801|186802|186803|1407607;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|33042;2|201174|84998|84999|84107|102106;2|1239|186801|186802|216572|2048137;2|1239|186801|186802|186803|2569097;2|1239|186801|186802|216572|1263;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|28050;2|1239|91061|186826|1300|1301;2|1239|186801|186802|204475;10239|2732396|2732408|2732506|464095|11974|142786|11983;2|1239|186801|186802|216572|459786;2|1239|186801|186802|31979|1485;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|946234;2|201174|84998|1643822|1643826|447020,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 9,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,feces,UBERON:0001988,NA,NA,none - 70% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,10.5281/zenodo.5565690,27 January 2022,Haoyanzh,Haoyanzh,healthy adult stool species in >= 70% samples,NA,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__[Eubacterium] rectale,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Agathobaculum|s__Agathobaculum butyriciproducens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea longicatena,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia inulinivorans,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides distasonis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger|s__Gemmiger formicilis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia hominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia faecis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter splanchnicus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes putredinis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Firmicutes|s__Firmicutes bacterium CAG:83,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides thetaiotaomicron,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes finegoldii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ramulus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. 57_20,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes shahii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor|s__Flavonifractor plautii",2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|186803|1407607|1150298;2|976|200643|171549|815|816|820;2|1239|186801|186802|186803|39491;2|1239|186801|186802|186803|572511|418240;2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|216572|2048137|1628085;2|1239|186801|186802|186803|189330|88431;2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|189330|39486;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|815|909656|821;2|1239|186801|186802|186803|572511|40520;2|1239|186801|186802|186803|841|360807;2|976|200643|171549|2005525|375288|823;2|1239|186801|186802|204475|745368;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|186802|186803|841|301301;2|1239|186801|186802|186803|28050|39485;2|1239|186801|186802|186803|2316020|33039;2|1239|186801|186802|186803|841|301302;2|976|200643|171549|815|816|28116;2|976|200643|171549|1853231|283168|28118;2|976|200643|171549|171550|239759|28117;2|1239|186801|186802|186803|33042|116085;2|1239|1262992;2|1239|91061|186826|1300|1301|1304;2|201174|1760|85004|31953|1678|216816;2|976|200643|171549|815|816|818;2|976|200643|171549|171550|239759|214856;2|1239|186801|186802|186806|1730|39490;2|1239|186801|186802|216572|459786|1897011;2|976|200643|171549|171550|239759|328814;2|1239|186801|186802|186803|841|166486;2|1239|186801|186802|216572|946234|292800,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 10,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,feces,UBERON:0001988,NA,NA,none - 0% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,7 February 2022,Haoyanzh,Haoyanzh,healthy stool genus in any adult sample,NA,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Acholeplasmatales|f__Acholeplasmataceae|g__Acholeplasma,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Achromobacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Acidipropionibacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acidocella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinotignum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Aeriscardovia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Aerococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Agathobaculum,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Agitococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Agrococcus,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenes,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Arcobacteraceae|g__Aliarcobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Alkalihalobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Chromatiales|f__Ectothiorhodospiraceae|g__Alkalilimnicola,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Alkanindiges,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Allisonella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Alloiococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Alloscardovia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Allosphingosinicella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Amedibacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Anaerofustis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Anaeroglobus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaeromassilibacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerosporobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerotignum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Aneurinibacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Aquamicrobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Arcanobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Cyanobacteria|o__Oscillatoriales|f__Microcoleaceae|g__Arthrospira,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Aurantimonadaceae|g__Aureimonas,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Xanthobacteraceae|g__Azorhizobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bartonellaceae|g__Bartonella|s__Bartonella sp. na18990nm,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Bavariicoccus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Bordetella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Boseaceae|g__Bosea,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae|g__Brachybacterium,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Bradyrhizobiaceae|g__Bradyrhizobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Paenibacillaceae|g__Brevibacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Brevibacteriaceae|g__Brevibacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Brevundimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Brochothrix,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Brucella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Caldibacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermacoccaceae|g__Calidifontibacter,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Debaryomycetaceae|g__Candida,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Candidatus Methanomethylophilaceae|g__Candidatus Methanomethylophilus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Carnobacterium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Catonella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae|g__Caulobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Cellulosilyticum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Promicromonosporaceae|g__Cellulosimicrobium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Cereibacter,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Cetobacterium,k__Bacteria|p__Chlamydiae|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Citricoccus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Clavibacter,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Companilactobacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Insecta|o__Blattodea|f__Rhinotermitidae|s__Coptotermitinae|g__Coptotermes|s__Coptotermes heimi,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Corticimicrobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Criibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Curtobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Cytobacillus,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Dellaglioa,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Denitrobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermabacteraceae|g__Dermabacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Dermacoccaceae|g__Dermacoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Desemzia,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobulbaceae|g__Desulfobulbus,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfomicrobiaceae|g__Desulfomicrobium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Dietziaceae|g__Dietzia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Edwardsiella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Eggerthia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Elizabethkingia,k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiaceae|g__Elusimicrobium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Empedobacter,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Ensifer,k__Eukaryota|p__Evosea|o__Mastigamoebida|f__Entamoebidae|g__Entamoeba,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Epilithonimonas,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Eremococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Erwinia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Ewingella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Exiguobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Facklamia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Faecalicatena,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalicoccus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalitalea,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Fannyhessea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Filifactor,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Franconibacter,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Fretibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Frischella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Fructilactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Geobacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Orbales|f__Orbaceae|g__Gilliamella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Glutamicibacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Gordoniaceae|g__Gordonia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Haematobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Harryflintia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Helcococcus,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Hornefia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Nevskiales|f__Sinobacteraceae|g__Hydrocarboniphaga,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Hydrogenibacillus,k__Bacteria|p__Proteobacteria|c__Hydrogenophilalia|o__Hydrogenophilales|f__Hydrogenophilaceae|g__Hydrogenophilus,k__Eukaryota|k__Metazoa|p__Arthropoda|c__Collembola|o__Poduromorpha|f__Hypogastruridae|g__Hypogastrura|s__Hypogastrura sp. BOLD:AAI2333,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Ignavigranum,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Ileibacterium,k__Viruses|k__Orthornavirae|p__Negarnaviricota|c__Insthoviricetes|o__Articulavirales|f__Orthomyxoviridae|g__Alphainfluenzavirus|s__Influenza A virus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Intrasporangiaceae|g__Janibacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Janthinobacterium,k__Eukaryota|k__Metazoa|p__Mollusca|c__Gastropoda|f__Acteonidae|g__Japonacteon|s__Japonacteon suturalis,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Jeotgalibacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Jeotgalicoccus,k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Jonquetella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Kerstersia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kluyvera,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Intrasporangiaceae|g__Knoellia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Kosakonia,k__Bacteria|p__Chloroflexi|c__Chloroflexia|o__Chloroflexales|f__Roseiflexaceae|g__Kouleothrix,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Kurthia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Kytococcaceae|g__Kytococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lacrimispora,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactiplantibacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Lactonifactor,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Lancefieldella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lapidilactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Latilactobacillus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Lawsonellaceae|g__Lawsonella,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Lawsonia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Lawsonibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Leclercia,k__Eukaryota|p__Euglenozoa|c__Kinetoplastea|o__Trypanosomatida|f__Trypanosomatidae|s__Leishmaniinae|g__Leishmania,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lentilactobacillus,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Levilactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus,k__Bacteria|p__Firmicutes|c__Limnochordia|o__Limnochordales|f__Limnochordaceae|g__Limnochorda,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Limosilactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Liquorilactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Loigolactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Lysinibacillus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Macrococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Mageeibacillus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Mammaliicoccus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Margalitia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Marmoricola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Massilia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Mediterranea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Melaminivora,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Melissococcus,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Metakosakonia,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Archaea|p__Candidatus Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Methylibium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Methylobacteriaceae|g__Methylorubrum,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Microlunatus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Chromobacteriaceae|g__Microvirgula,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Mixta,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Geodermatophilales|f__Geodermatophilaceae|g__Modestobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Moellerella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Monoglobus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Morococcus,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Mucispirillum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Murimonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacteroides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycolicibacterium,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasmopsis,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Myxococcales|f__Nannocystaceae|g__Nannocystis,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Negativicoccus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptosporangiales|f__Nocardiopsaceae|g__Nocardiopsis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Oenococcus,o__Burkholderiales|f__Alcaligenaceae|g__Oligella",2|1239|91061|186826|186827|46123;2|544448|31969|186329|2146|2147;2|1224|28216|80840|506|222;2|1239|909932|1843488|909930|904;2|201174|1760|85009|31957|1912215;2|1224|28211|204441|433|50709;2|1224|28216|80840|80864|12916;2|1224|1236|2887326|468|469;2|201174|1760|2037|2049|76833;2|201174|1760|2037|2049|1654;2|201174|1760|2037|2049|1653174;2|201174|84998|1643822|1643826|447020;2|201174|1760|85004|31953|240233;2|1239|91061|186826|186827|1375;2|1224|1236|135624|84642|642;2|1239|186801|186802|216572|2048137;2|1224|1236|135625|712|416916;2|1224|1236|2887326|468|186829;2|201174|1760|85006|85023|46352;2|74201|203494|48461|1647988|239934;2|1224|28216|80840|506|507;2|1224|29547|213849|2808963|2321111;2|976|200643|171549|171550|239759;2|1239|91061|1385|186817|2675234;2|1224|1236|135613|72276|133193;2|1224|1236|2887326|468|222991;2|1239|909932|1843489|31977|209879;2|1239|91061|186826|186828|1651;2|976|200643|171549|171552|1283313;2|201174|1760|85004|31953|419014;2|1224|28211|204457|41297|2823232;2|1239|526524|526525|128827|2749846;2|1239|186801|186802|186803|2569097;2|1239|1737404|1737405|1570339|165779;2|1239|186801|186802|216572|52784;2|1239|186801|186802|186806|264995;2|1239|909932|1843489|31977|156454;2|1239|186801|186802|216572|1924093;2|1239|186801|186802|186803|653683;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|2039240;2|1239|186801|186802|216572|244127;2|1239|91061|1385|186822|55079;2|1239|91061|1385|186817|150247;2|1224|28211|356|69277|69278;2|201174|1760|85009|31957|2801844;2|201174|1760|2037|2049|28263;2|201174|1760|85006|1268|1663;2|1117|1150|1892252|35823;2759|4751|4890|147545|5042|1131492|5052;2|201174|84998|84999|1643824|1380;2|1224|28211|356|255475|414371;2|1224|28211|356|335928|6;2|1239|91061|1385|186817|1386;2|976|200643|171549|815|816;2|976|200643|171549|2005519|397864;2|1224|28211|356|772|773|94406;2|1239|91061|186826|81852|697279;2|976|117743|200644|2762318|59735;2|201174|1760|85004|31953|1678;2|1224|28221|213115|194924|35832;2|1239|186801|186802|186803|572511;2|1224|28216|80840|506|517;2|1224|28211|356|2831100|85413;2|201174|1760|85006|85020|43668;2|203691|203692|1643686|143786|29521;2|1224|28211|356|41294|374;2|1239|91061|1385|186822|55080;2|201174|1760|85006|85019|1696;2|1224|28211|204458|76892|41275;2|1239|91061|1385|186820|2755;2|1224|28211|356|118882|234;2|1224|28216|80840|119060|32008;2|1239|186801|186802|31979|580596;2|976|200643|171549|1853231|574697;2|1239|186801|186802|186803|830;2|1239|91061|1385|186817|1276290;2|201174|1760|85006|145357|1158982;2759|4751|4890|4891|4892|766764|1535326;2157|2283796|183967|1235850|2517203|1291539;2|1239|526524|526525|128827|1470349;2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717;2|1239|91061|186826|186828|2747;2|1239|526524|526525|2810280|135858;2|1239|186801|186802|186803|43996;2|1224|28211|204458|76892|75;2|1224|1236|91347|543|158483;2|1239|186801|186802|186803|698776;2|201174|1760|85006|85017|157920;2|1224|28211|204455|31989|1653176;2|32066|203490|203491|203492|180162;2|204428|204429|51291|809|810;2|1239|186801|186802|990719|990721;2|976|117743|200644|2762318|59732;2|201174|1760|85006|1268|169133;2|201174|1760|85006|85023|1573;2|508458|649775|649776|649777|508459;2|976|117743|200644|2762318|501783;2|1239|186801|186802|186804|1870884;2|1239|186801|186802|31979|1485;2|201174|84998|84999|84107|102106;2|1224|28216|80840|80864|283;2|1239|91061|186826|33958|2767879;2|1239|526524|526525|2810280|100883;2|976|200643|171549|2005519|1348911;2|1239|186801|186802|186803|33042;2759|33208|6656|50557|85823|36985|72653|36986|282472;2|1224|28216|80840|506|2678534;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186804|1937664;2|1224|1236|91347|543|413496;2|1224|28216|80840|119060|106589;2|201174|1760|85006|85023|2034;2|201174|1760|85009|31957|1912216;2|1239|91061|1385|186817|2675230;2|1297|188787|118964|183710|1298;2|1224|28216|80840|80864|80865;2|1239|91061|186826|33958|2767880;2|201174|84998|1643822|1643826|79603;2|201174|1760|85006|85020|36739;2|201174|1760|85006|145357|57495;2|1239|91061|186826|186828|82800;2|1224|28221|213118|213121|893;2|1224|28221|213115|213116|898;2|1224|28221|213115|194924|872;2|1239|909932|1843489|31977|39948;2|1239|526524|526525|128827|1472649;2|201174|1760|85007|85029|37914;2|1239|91061|186826|186828|29393;2|1239|186801|186802|186803|189330;2|976|200643|171549|2005473|2518495;2|976|200643|171549|2005520|156973;2|1224|1236|91347|1903412|635;2|201174|84998|1643822|1643826|84111;2|1239|526524|526525|2810280|1279384;2|1224|28216|206351|481|538;2|1239|186801|186802|186803|1432051;2|976|117743|200644|2762318|308865;2|74152|641853|641854|641876|423604;2|976|117743|200644|2762318|59734;2|1224|28211|356|212791;2|201174|84998|84999|84107|1472762;2|1224|28211|356|82115|106591;2759|2605435|2682482|33084|5758;2|1224|1236|91347|543|547;2|1239|186801|186802|186803|2719313;2|1239|91061|186826|81852|1350;2|976|117743|200644|2762318|2782229;2|1239|91061|186826|186827|171412;2|1224|1236|91347|1903409|551;2|1239|526524|526525|128827|1505663;2|1239|526524|526525|128827|1647;2|1224|1236|91347|543|561;2|1239|186801|186802|186806|1730;2|1224|1236|91347|1903411|41201;2|1239|91061|1385|33986;2|1239|1737404|1582879;2|1239|91061|186826|186827|66831;2|1239|186801|186802|186803|2005359;2|1239|526524|526525|128827|1573536;2|1239|526524|526525|128827|1573534;2|201174|1760|2037|2049|2767327;2|1239|186801|186802|186804|44259;2|1239|1737404|1737405|1570339|150022;2|976|117743|200644|49546|237;2|1239|186801|186802|216572|946234;2|1224|1236|91347|543|1649295;2|508458|649775|649776|649777|1434006;2|1224|1236|1240482|1240483|1335631;2|1239|91061|186826|33958|2767881;2|1239|186801|186802|186803|1407607;2|32066|203490|203491|203492|848;2|201174|1760|85004|31953|2701;2|1239|91061|1385|1378;2|1239|186801|186802|204475;2|1239|91061|1385|186817|129337;2|1224|1236|1240482|1240483|1193503;2|1239|91061|186826|186827|13075;2|201174|1760|85006|1268|1742989;2|201174|1760|85007|85026|2053;2|201174|84998|1643822|1643826|644652;2|1239|91061|186826|186828|117563;2|1224|28211|204455|31989|366614;2|1224|1236|135625|712|724;2|1224|1236|91347|1903412|568;2|1239|186801|186802|216572|1892380;2|1239|1737404|1737405|1570339|31983;2|1224|29547|213849|72293|209;2|1239|526524|526525|128827|1573535;2|1239|526524|526525|128827|61170;2|1239|186801|186802|543314|2815774;2|1239|186801|186802|31979|1649459;2|1224|1236|1775403|568386|243627;2|1239|91061|1385|186817|1609627;2|1224|2008785|119069|206349|70774;2759|33208|6656|30001|730331|30002|30003|283377;2|1239|91061|186826|186827|89092;2|1239|526524|526525|128827|1937007;10239|2732396|2497569|2497577|2499411|11308|197911|11320;2|1239|186801|186802|186804|1505657;2|1239|186801|186802|1392389;2|201174|1760|85006|85021|53457;2|1224|28216|80840|75682|29580;2759|33208|6447|6448|71511|96461|96462;2|1239|91061|1385|186818|157226;2|1239|91061|1385|90964|227979;2|508458|649775|649776|649777|428711;2|1224|28216|80840|506|257820;2|1224|28216|206351|481|32257;2|1224|1236|91347|543|570;2|1224|1236|91347|543|579;2|201174|1760|85006|85021|136099;2|1224|1236|91347|543|1330547;2|200795|32061|32064|1508635|186475;2|1239|91061|1385|186818|1649;2|201174|1760|85006|2805426|57499;2|1239|186801|186802|186803|1506553;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803|2719231;2|1239|91061|186826|33958|2759736;2|1239|91061|186826|33958|2767842;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1357;2|1239|186801|186802|31979|420345;2|201174|84998|84999|1643824|2767353;2|1239|91061|186826|33958|2767884;2|1239|91061|186826|33958|2767885;2|1224|28216|80840|119060|47670;2|201174|1760|85007|2805586|1847725;2|1224|28221|213115|194924|41707;2|1239|186801|186802|2172004;2|1224|1236|91347|543|83654;2759|33682|5653|2704949|5654|1286322|5658;2|1239|91061|186826|33958|2767893;2|32066|203490|203491|1129771|32067;2|32066|203490|203491|1129771|32067|712363;2|201174|1760|85006|85023|55968;2|1239|91061|186826|33958|1243;2|1239|91061|186826|33958|2767886;2|1239|91061|186826|33958|2767887;2|1239|1676648|1676649|1676650|1676651;2|1239|91061|186826|33958|2742598;2|1239|91061|186826|33958|2767888;2|1239|91061|1385|186820|1637;2|1239|91061|186826|33958|2767889;2|1239|91061|1385|186817|400634;2|1224|1236|135614|32033|68;2|1239|91061|1385|90964|69965;2|1239|186801|186802|216572|1637257;2759|4751|5204|1538075|162474|742845|55193;2|1239|91061|1385|90964|2803850;2|1239|91061|1385|186817|2837505;2|201174|1760|85009|85015|86795;2|1239|186801|186802|186803|248744;2|1224|28216|80840|75682|149698;2|976|200643|171549|815|1926659;2|1239|186801|186802|186803|2316020;2|1239|909932|909929|1843491|158846;2|1239|909932|1843489|31977|906;2|1297|188787|68933|188786|65551;2|1224|28216|80840|80864|1649468;2|1239|91061|186826|81852|33969;2|1224|28211|356|69277|68287;2|1224|1236|91347|543|2055876;2157|28890|183925|2158|2159|2172;2157|2283796|183967|1235850|1577788|1080709;2157|28890|183925|2158|2159|2316;2|1224|28216|80840|316612;2|1224|28211|356|119045|2282523;2|201174|1760|85006|85023|33882;2|201174|1760|85009|31957|29404;2|1224|28216|206351|1499392|57479;2|1239|909932|909929|1843491|52225;2|1224|1236|91347|1903409|2100764;2|201174|1760|2037|2049|2050;2|201174|1760|1643682|85030|88138;2|1224|1236|91347|1903414|158848;2|1239|186801|186802|543314|86331;2|1239|186801|186802|216572|2039302;2|1224|1236|2887326|468|475;2|1224|1236|91347|1903414|581;2|1224|28216|206351|481|212742;2|200930|68337|191393|191394|248038;2|976|200643|171549|2005473|1918540;2|1239|186801|186802|186803|1774128;2|201174|1760|85007|1762|1763;2|201174|1760|85007|1762|670516;2|201174|1760|85007|1762|1866885;2|544448|31969|2085|2092|2093;2|544448|31969|2085|2092|2767358;2|1224|28221|29|224463|53;2|1239|909932|1843489|31977|909928;2|1224|28216|206351|481|482;2|201174|1760|85009|85015|1839;2|201174|1760|85012|83676|2013;2|976|200643|171549|1853231|283168;2|1239|91061|186826|33958|46254;80840|506|90243,Complete,NA
Study 562,meta-analysis,NA,10.5281/zenodo.5565690,NA,NA,NA,NA,NA,Experiment 11,"Australia,Canada,China,Denmark,Finland,France,Germany,India,Ireland,Israel,Italy,Japan,Luxembourg,Netherlands,South Korea,Spain,Switzerland,United Kingdom,United Republic of Tanzania,United States of America",Homo sapiens,feces,UBERON:0001988,NA,NA,none - 30% prevalence threshold,feces from healthy adult,non-disease adult participants from curatedMetagenomicData,0,9623,"no (n=5572), yes (n=276)",WMS,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,10.5281/zenodo.5565690,24 March 2022,Haoyanzh,Haoyanzh,healthy stool genus prevalence >=30%,NA,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Agathobaculum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Lawsonibacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaeromassilibacillus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Tractidigestivibacter,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Turicimonas,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1239|186801|186802|216572|216851;2|976|200643|171549|815|816;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|2316020;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186806|1730;2|976|200643|171549|815|909656;2|1239|186801|186802|186803|1407607;2|976|200643|171549|2005525|375288;2|976|200643|171549|171550|239759;2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|33042;2|201174|84998|84999|84107|102106;2|1239|186801|186802|216572|2048137;2|1239|186801|186802|186803|2569097;2|1239|186801|186802|216572|1263;2|201174|1760|85004|31953|1678;2|1239|186801|186802|186803|28050;2|1239|91061|186826|1300|1301;2|1239|186801|186802|204475;2|1239|186801|186802|216572|1905344;2|1239|186801|186802|216572|459786;2|1239|186801|186802|31979|1485;2|976|200643|171549|1853231|283168;2|1239|186801|186802|216572|946234;2|201174|84998|1643822|1643826|447020;2|976|200643|171549|171552|838;2|976|200643|171549|2005519|397864;2|201174|84998|1643822|1643826|644652;2|1239|909932|1843488|909930|33024;2|1239|186801|186802|2172004;2|1224|1236|91347|543|561;2|1224|28221|213115|194924|35832;2|74201|203494|48461|1647988|239934;2|976|200643|171549|1853231|574697;2|1224|28216|80840|995019|577310;2|1239|186801|186802|186804|1505657;2|1239|91061|186826|33958|1578;2|1239|526524|526525|128827|1505663;2|201174|84998|1643822|1643826|84108;2|1239|186801|186802|186803|2719313;2|976|200643|171549|2005519|1348911;2|201174|84998|1643822|1643826|84111;2|1239|909932|1843489|31977|39948;2|1239|909932|1843489|31977|29465;2|201174|84998|84999|84107|1472762;2|1239|186801|186802|1392389;2|1224|1236|135625|712|724;2|1239|186801|186802|216572|1924093;2|1239|526524|526525|128827|1573535;2157|28890|183925|2158|2159|2172;2|1239|526524|526525|128827|61170;2|976|200643|171549|171552|577309;2|201174|84998|84999|1643824|2847313;2|1239|526524|526525|2810281|191303;2|1224|28216|80840|995019|1918598;2|201174|1760|2037|2049|1654,Complete,NA
Study 564,randomized controlled trial,26237371,10.1097/MPG.0000000000000928,NA,"Corvaglia L, Tonti G, Martini S, Aceti A, Mazzola G, Aloisio I, Di Gioia D , Faldella G",Influence of Intrapartum Antibiotic Prophylaxis for Group B Streptococcus on Gut Microbiota in the First Month of Life,Journal of pediatric gastroenterology and nutrition,2016,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Control group (@7 days),IAP group (@7 days),"infants born to GBS-positive mothers who had received IAP. According to the institutional treatment protocol for GBS prophylaxis (derived from the Centers for Disease Control and Prevention guidelines (13)), intravenous ampicillin was given every 4 hours until delivery (first dose 2 g, following doses 1 g each).",49,35,"The mother had received any antibiotic other than IAP in the 4 weeks before delivery.
Maternal IAP was performed with antibiotics other than ampicillin, such as erythromycin.",16S,NA,NA,Mann-Whitney (Wilcoxon),0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Influence of IAP on Fecal Bacterial Counts (text),19 November 2021,Mmarin,Mmarin,NA,decreased,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,2|201174|1760|85004|31953|1678|41200,Complete,NA
Study 566,NA,27833598,10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,Experiment 1,Italy,Homo sapiens,NA,NA,NA,NA,HLAB27-,HLAB27+,enthesitis-related arthritis (JIA-ERA) patients with HLA-B27 allele,10,9,3 months,16S,56,NA,LEfSe,2,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",30 November 2021,Tislam,Tislam,"Differences in bacterial taxa related to HLA-B27 status. LEfSe analysis shows a statistically significant enrichment of (A) families, and (B,C)
genera, in (A,B) all JIA patients and in (C) JIA-ERA patients, considering the HLA-B27 status. LEfSe results indicate a sequentially significant ranking among groups
(Alpha value = 0.05 for the factorial Kruskal–Wallis test among classes). The threshold for the logarithmic LDA score was 2.0",decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,2|1224|1236|135625|712|724,Complete,NA
Study 566,NA,27833598,10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,Experiment 1,Italy,Homo sapiens,NA,NA,NA,NA,HLAB27-,HLAB27+,enthesitis-related arthritis (JIA-ERA) patients with HLA-B27 allele,10,9,3 months,16S,56,NA,LEfSe,2,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, text",30 November 2021,Tislam,"Tislam,Fatima","Differences in bacterial taxa related to HLA-B27 status. LEfSe analysis shows a statistically significant enrichment of (A) families, and (B,C)
genera, in (A,B) all JIA patients and in (C) JIA-ERA patients, considering the HLA-B27 status. LEfSe results indicate a sequentially significant ranking among groups
(Alpha value = 0.05 for the factorial Kruskal–Wallis test among classes). The threshold for the logarithmic LDA score was 2.0",increased,"k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas",2|1224|28221|213115|194924|35832;2|1239|186801|186802|31979|1485|1506;2|1239|909932|1843489|31977|39948;2|1239|186801|186802|216572|596767;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|459786;2|1239|1737404|1737405|1570339|543311,Complete,NA
Study 566,NA,27833598,10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,Experiment 2,Italy,Homo sapiens,NA,NA,NA,NA,HLAB27-,HLAB27+,JIA patients with HLA-B27 allele,20,9,3 months,16S,56,NA,LEfSe,2,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,"Figure 2, text",30 November 2021,Tislam,Tislam,"Differences in bacterial taxa related to HLA-B27 status. LEfSe analysis shows a statistically significant enrichment of (A) families, and (B,C)
genera, in (A,B) all JIA patients and in (C) JIA-ERA patients, considering the HLA-B27 status. LEfSe results indicate a sequentially significant ranking among groups
(Alpha value = 0.05 for the factorial Kruskal–Wallis test among classes). The threshold for the logarithmic LDA score was 2.0.",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella",2|1224|1236|135625|712|724;2|201174|84998|1643822|1643826|84111,Complete,NA
Study 566,NA,27833598,10.3389/fmicb.2016.01703,NA,"Di Paola M, Cavalieri D, Albanese D, Sordo M, Pindo M, Donati C, Pagnini I, Giani T, Simonini G, Paladini A, Lionetti P, De Filippo C , Cimaz R",Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status,Frontiers in microbiology,2016,Experiment 2,Italy,Homo sapiens,NA,NA,NA,NA,HLAB27-,HLAB27+,JIA patients with HLA-B27 allele,20,9,3 months,16S,56,NA,LEfSe,2,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,"Figure 2, text",30 November 2021,Tislam,Tislam,"Differences in bacterial taxa related to HLA-B27 status. LEfSe analysis shows a statistically significant enrichment of (A) families, and (B,C)
genera, in (A,B) all JIA patients and in (C) JIA-ERA patients, considering the HLA-B27 status. LEfSe results indicate a sequentially significant ranking among groups
(Alpha value = 0.05 for the factorial Kruskal–Wallis test among classes). The threshold for the logarithmic LDA score was 2.0.",increased,"k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Hydrogenoanaerobacterium,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter",2|1224|28221|213115|194924|35832;2|1239|186801|186802|31979|1485|1506;2|1239|186801|186802|216572|596767;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|216572|459786,Complete,NA
Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.,New Parkinson's disease patients: patients suffering with with PD for less than 1 year and before treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.05,FALSE,NA,"age,life style",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Figure 3. Genus level comparison among NPD samples.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,increased,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,Rimsha
Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with suffering with with PD for less than 1 year and before treatment.,New Parkinson's disease patients: patients suffering with with PD for less than 1 year and before treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.05,FALSE,NA,"age,life style",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,FIGURE 3,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|976|200643|171549|171552|577309;2|1239|186801|186802|216572|1263;2|1239|91061|186826|1300|1301,Complete,Rimsha
Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with PD for less than 1 year and 5 days after treatment.,New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 5 days after treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.01,NA,NA,age,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,FIGURE 3.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,increased,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,Rimsha
Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.,New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 14 days after treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.05,NA,NA,age,NA,NA,increased,unchanged,increased,NA,NA,Signature 1,FIGURE 3.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,increased,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,Rimsha
Study 568,case-control,31824239,10.3389/fnins.2019.01184,NA,"Jin M, Li J, Liu F, Lyu N, Wang K, Wang L, Liang S, Tao H, Zhu B , Alkasir R",Analysis of the Gut Microflora in Patients With Parkinson's Disease,Frontiers in neuroscience,2019,Experiment 3,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,healthy controls without any form of Parkinson's Disease,NPD group: patients suffering with PD for less than 1 year and 14 days after treatment.,New Parkinson's disease patients: patients suffering with PD for less than 1 year and samples taken 14 days after treatment.,68,13,The use of any antibiotics or probiotics within 90 days before collection of the samples.,16S,NA,Illumina,Metastats,0.05,NA,NA,age,NA,NA,increased,unchanged,increased,NA,NA,Signature 2,FIGURE 3.,29 November 2021,Fcuevas3,"Fcuevas3,Rimsha",Genus-level comparison among NPD samples collected at different times.,decreased,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,2|1239|186801|186802|216572|1263,Complete,Rimsha
Study 569,case-control,32280686,10.1155/2020/2948282,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114766/,"Liu X, Cheng Y, Shao L , Ling Z",Alterations of the Predominant Fecal Microbiota and Disruption of the Gut Mucosal Barrier in Patients with Early-Stage Colorectal Cancer,BioMed research international,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy controls,colorectal cancer patients,diagnosed with primary early-stage CRC (aged 46-75 years old) between January 2011 and March 2012,45,53,1 month,16S,NA,RT-qPCR,T-Test,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure1,16 February 2022,Fatima,Fatima,Quantitative real-time PCR analysis of the fecal abundant bacteria in patients with colorectal cancer,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum",2|1224|1236|91347|543;2|32066|203490|203491|203492|848|851,Complete,Fatima
Study 569,case-control,32280686,10.1155/2020/2948282,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114766/,"Liu X, Cheng Y, Shao L , Ling Z",Alterations of the Predominant Fecal Microbiota and Disruption of the Gut Mucosal Barrier in Patients with Early-Stage Colorectal Cancer,BioMed research international,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy controls,colorectal cancer patients,diagnosed with primary early-stage CRC (aged 46-75 years old) between January 2011 and March 2012,45,53,1 month,16S,NA,RT-qPCR,T-Test,0.05,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure1,16 February 2022,Fatima,Fatima,Quantitative real-time PCR analysis of the fecal abundant bacteria in patients with colorectal cancer,decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus sp.,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.",2|1239|91061|186826|33958|1578|1591;2|201174|1760|85004|31953|1678|41200;2|1239|186801|186802|31979|1485|1506,Complete,Fatima
Study 570,NA,31100891,10.3390/jcm8050693,NA,"Jeong Y, Kim JW, You HJ, Park SJ, Lee J, Ju JH, Park MS, Jin H, Cho ML, Kwon B, Park SH , Ji GE",Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis,Journal of clinical medicine,2019,Experiment 1,South Korea,Homo sapiens,NA,NA,NA,NA,female healthy control,female with early RA,female early rheumatoid arthritis patients,25,29,"People using antibiotics, probiotics, or prebiotics at the time of sample collection were excluded
from subject selection.",16S,NA,Illumina,LEfSe,0.1,TRUE,3,NA,NA,NA,increased,NA,NA,NA,increased,Signature 1,"Figure 3, text",30 November 2021,Tislam,Tislam,"Featured taxa based on LDA effect size (LEfSe) analysis and random forest predictive
analysis of CT and ER groups. (A) Selected taxa based on LEfSe analysis. (B) Selected taxa based on
random forest analysis of the top 20 abundant genera. (C) Relative abundance of the genus Collinse",decreased,"k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc,k__Bacteria|p__Actinobacteria",2|508458|649775|649776|649777;2|1239|186801|186802|186806|1730;2|201174|84998|84999;2|201174|84998|84999|84107;2|201174|84998;2|1239|526524|526525|128827;2|1239|526524|526525;2|201174|84998|84999|84107|102106;2|1239|91061|186826|33958|1243;2|201174,Complete,NA
Study 570,NA,31100891,10.3390/jcm8050693,NA,"Jeong Y, Kim JW, You HJ, Park SJ, Lee J, Ju JH, Park MS, Jin H, Cho ML, Kwon B, Park SH , Ji GE",Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis,Journal of clinical medicine,2019,Experiment 1,South Korea,Homo sapiens,NA,NA,NA,NA,female healthy control,female with early RA,female early rheumatoid arthritis patients,25,29,"People using antibiotics, probiotics, or prebiotics at the time of sample collection were excluded
from subject selection.",16S,NA,Illumina,LEfSe,0.1,TRUE,3,NA,NA,NA,increased,NA,NA,NA,increased,Signature 2,"Figure 3, text",30 November 2021,Tislam,Tislam,"Featured taxa based on LDA effect size (LEfSe) analysis and random forest predictive
analysis of CT and ER groups. (A) Selected taxa based on LEfSe analysis. (B) Selected taxa based on
random forest analysis of the top 20 abundant genera. (C) Relative abundance of the genus Collinse",increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales",2|976;2|976|200643;2|976|200643|171549,Complete,NA
Study 571,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B, Magne F, Tripathy SK, Venugopal G, Mukherjee D , Balamurugan R",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,Experiment 1,NA,Homo sapiens,feces,UBERON:0001988,"osteoarthritis, knee",EFO:0004616,Normal Vitamin D status,Knee osteroarthritis,Knee osteoarthritis,6,4,excluded if antibiotics for last 12 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,"Figure 2, text",30 November 2021,Tislam,"Tislam,Fatima",A histogram of the log 10 transformed Linear discriminant analysis (LDA) scores was computed for features that showed differential abundance between healthy subjects and KOA patients.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae",2|1239|186801|186802|216572|52784;2|976|200643|171549|171551,Complete,Fatima
Study 571,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B, Magne F, Tripathy SK, Venugopal G, Mukherjee D , Balamurugan R",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,Experiment 1,NA,Homo sapiens,feces,UBERON:0001988,"osteoarthritis, knee",EFO:0004616,Normal Vitamin D status,Knee osteroarthritis,Knee osteoarthritis,6,4,excluded if antibiotics for last 12 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 2, text",30 November 2021,Tislam,"Tislam,Fatima",A histogram of the log 10 transformed Linear discriminant analysis (LDA) scores was computed for features that showed differential abundance between healthy subjects and KOA patients.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shimwellia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae",2|1239|186801|186802|1392389;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186807|2740;2|201174|1760|85009|31957|1743;2|1224|1236|91347|543|1335483;2|201174|84998|84999|84107;2|1239|526524|526525|128827,Complete,Fatima
Study 571,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B, Magne F, Tripathy SK, Venugopal G, Mukherjee D , Balamurugan R",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,Experiment 2,NA,Homo sapiens,feces,UBERON:0001988,"osteoarthritis, knee",EFO:0004616,Vitamin D deficiency,Knee osteroarthritis with vit D deficiency,Knee osteoarthritis,7,7,excluded if antibiotics for last 12 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 1,Figure 3,9 March 2022,Fatima,Fatima,differential abundance between KOA_VDD and VDD patients.,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552|1283313;2|976|200643|171549|1853231|283168;2|1239|186801|186802|186803|265975;2|976|200643|171549|171552|838,Complete,Fatima
Study 571,"cross-sectional observational, not case-control",33924396,10.3390/nu13041272,NA,"Ramasamy B, Magne F, Tripathy SK, Venugopal G, Mukherjee D , Balamurugan R",Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study,Nutrients,2021,Experiment 2,NA,Homo sapiens,feces,UBERON:0001988,"osteoarthritis, knee",EFO:0004616,Vitamin D deficiency,Knee osteroarthritis with vit D deficiency,Knee osteoarthritis,7,7,excluded if antibiotics for last 12 weeks,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,Figure 3,9 March 2022,Fatima,Fatima,differential abundance between KOA_VDD and VDD patients.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Candidatus Saccharibacteria|g__Candidatus Saccharimonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium",2|976|200643|171549|1853231|574697;2|95818|1331051;2|1224|28216|80840|80864|80865;2|201174|84998|1643822|1643826|644652;2|976|200643|171549|2005525|375288;2|1239|909932|1843488|909930|33024;2|976|200643|171549|171551;2|201174|84998|84999|84107;2|1239|186801|186802|1898207,Complete,Fatima
Study 573,"cross-sectional observational, not case-control",32083132,10.1155/2020/7828392,https://pubmed.ncbi.nlm.nih.gov/32083132/,"Liu W, Zhang R, Shu R, Yu J, Li H, Long H, Jin S, Li S, Hu Q, Yao F, Zhou C, Huang Q, Hu X, Chen M, Hu W, Wang Q, Fang S , Wu Q",Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing,BioMed research international,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,NA,NA,Healthy Controls (HC),Colorectal Cancer (CC),Patients who visited the department of gastroenterology of Tianyou hospital of Wuhan from January 2017 to December 2017 and received colonoscopy and histopathological examination were recruited to the study. Patients with colorectal adenocarcinoma were recorded as the colorectal cancer (CC) group.,42,51,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 1,Table 4,9 December 2021,Itslanapark,Itslanapark,Difference analysis at the phylum level between Colorectal Cancer and Healthy Controls. Wilcoxon tests were used to analyze differences in the abundance between the two groups. Significant differences were evaluated by False Discovery Rate.,increased,"k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria,k__Bacteria|p__Spirochaetes,k__Bacteria|p__Synergistetes",2|32066;2|1224;2|203691;2|508458,Complete,Fatima
Study 573,"cross-sectional observational, not case-control",32083132,10.1155/2020/7828392,https://pubmed.ncbi.nlm.nih.gov/32083132/,"Liu W, Zhang R, Shu R, Yu J, Li H, Long H, Jin S, Li S, Hu Q, Yao F, Zhou C, Huang Q, Hu X, Chen M, Hu W, Wang Q, Fang S , Wu Q",Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing,BioMed research international,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,NA,NA,Healthy Controls (HC),Colorectal Cancer (CC),Patients who visited the department of gastroenterology of Tianyou hospital of Wuhan from January 2017 to December 2017 and received colonoscopy and histopathological examination were recruited to the study. Patients with colorectal adenocarcinoma were recorded as the colorectal cancer (CC) group.,42,51,2 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,decreased,NA,NA,decreased,Signature 2,Table 4,10 December 2021,Itslanapark,Itslanapark,Difference analysis at the phylum level between Colorectal Cancer and Healthy Controls. Wilcoxon tests were used to analyze differences in the abundance between the two groups. Significant differences were evaluated by False Discovery Rate.,decreased,k__Bacteria|p__Firmicutes,2|1239,Complete,Fatima
Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,Experiment 1,Russian Federation,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,azithromycin-lactulose treated (day 0),azithromycin-lactulose treated (day 18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,2 December 2021,Mmarin,Mmarin,"AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1224|1236|91347|543|547;2|976|200643|171549|171552|838,Complete,NA
Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,Experiment 1,Russian Federation,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,azithromycin-lactulose treated (day 0),azithromycin-lactulose treated (day 18),"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Table 1,2 December 2021,Mmarin,Mmarin,"AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus",2|1239|186801|186802|186803|207244;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|1239|186801|186802|186803|841;2|1239|186801|186802|216572|1263,Complete,NA
Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,Experiment 2,Russian Federation,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 18),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 December 2021,Mmarin,Mmarin,"Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",decreased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,2|1224|1236|91347|543|547,Complete,NA
Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,Experiment 2,Russian Federation,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 18),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 December 2021,Mmarin,Mmarin,"Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira",2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|186803|28050,Complete,NA
Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,Experiment 3,Russian Federation,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 60),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,3 December 2021,Mmarin,Mmarin,"Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella",2|1224|1236|91347|543|547;2|976|200643|171549|1853231|283168;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838;2|1224|28216|80840|995019|40544,Complete,NA
Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,Experiment 3,Russian Federation,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,azithromycin treated (day 0),azithromycin treated (day 60),"administered 10 mg/kg body weight per day of azithromycin, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 1,3 December 2021,Mmarin,Mmarin,"Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively",increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Adlercreutzia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Alkaliphilus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|84998|1643822|1643826|447020;2|1239|186801|186802|31979|114627;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,Experiment 4,Russian Federation,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,azithromycin treated,azithromycin-lactulose treated,"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,increased,NA,NA,NA,unchanged,Signature 1,Table 1,3 December 2021,Mmarin,Mmarin,"AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively

(day 18)",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Dysgonomonadaceae|g__Dysgonomonas,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelothrix,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera",2|1239|186801|186802|186803|207244;2|1239|186801|186802|186803|572511;2|976|200643|171549|1853231|574697;2|1239|526524|526525|2810280|100883;2|976|200643|171549|2005520|156973;2|1239|526524|526525|128827|1647;2|1239|909932|1843489|31977|906,Complete,NA
Study 574,randomized controlled trial,31583533,10.1007/s12519-019-00315-6,NA,"Nikolaou E, Kamilari E, Savkov D, Sergeev A, Zakharova I, Vogazianos P, Tomazou M, Antoniades A , Shammas C",Intestinal microbiome analysis demonstrates azithromycin post-treatment effects improve when combined with lactulose,World journal of pediatrics : WJP,2020,Experiment 4,Russian Federation,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,azithromycin treated,azithromycin-lactulose treated,"administered a single daily dosage of 10 mg/kg body weight azithromycin in addition with 20 mg/kg body weight lactulose per day, as powder for oral suspension.",42,42,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,NA,age,NA,NA,increased,NA,NA,NA,unchanged,Signature 2,Table 1,3 December 2021,Mmarin,Mmarin,"AZ azithromycin. A and L represent higher mean relative abundance for the azithromycin only and azitrhomycin + lactulose groups, respectively Arrows point up or down indicate an increase or increase compared to the relative abundance at day 0, respectively

(day 60)",increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Sporosarcina",2|1239|909932|1843489|31977|906;2|1239|91061|1385|186818|1569,Complete,NA
Study 575,prospective cohort,33824448,10.1038/s41390-021-01494-7,NA,"Ainonen S, Tejesvi MV, Mahmud MR, Paalanne N, Pokka T, Li W, Nelson KE, Salo J, Renko M, Vänni P, Pirttilä AM , Tapiainen T",Antibiotics at birth and later antibiotic courses: effects on gut microbiota,Pediatric research,2021,Experiment 1,Finland,Homo sapiens,feces,UBERON:0001988,antimicrobial agent,CHEBI:33281,Control group,perinatal antibiotics,"postnatal antibiotics during the first week of life, or to any maternal antibiotics within 1 week before delivery, the IAP group received only IAP (n=27), the postnatal group was exposed to empirical postnatal intravenous antibiotics within 24 h after birth (n=24), and the IAP + postnatal group received both IAP and postnatal intravenous antibiotics (n=22)",27,73,NA,16S,NA,Ion Torrent,T-Test,0.05,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 576,case-control,24316595,10.1093/jnci/djt300,https://pubmed.ncbi.nlm.nih.gov/24316595/,"Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB , Yang L",Human gut microbiome and risk for colorectal cancer,Journal of the National Cancer Institute,2013,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,contemporaneous patients awaiting elective surgery for nononcologic conditions,adenocarcinoma,"newly diagnosed, histologically confirmed adenocarcinoma of the colon or rectum",94,47,1 year,16S,34,NA,"Mann-Whitney (Wilcoxon),T-Test",0.05,TRUE,NA,"body mass index,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,10 December 2021,Itslanapark,Itslanapark,Prevalence and relative abundance of fecal microbial taxa in patients with colorectal cancer and control subjects,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|186801;2|1239|186801|186802;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803,Complete,NA
Study 577,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R, Wang L, Koch T, Curtis V, Yin-DeClue H, Handley SA, Shan L, Holtzman MJ, Castro M , Wang L",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,Experiment 1,United States of America,Homo sapiens,NA,NA,NA,NA,Female,Male,NA,32,15,NA,16S,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,12 December 2021,Joyessa,Joyessa,"Differences of the sputum microbiome by sex in major bacterial phyla and at the community level. A, Relative abundance of the top 5 most abundant bacterial phyla for women and men. Statistical significance was assessed by Wilcoxon rank-sum test. B, Alpha diversity (Shannon index) in women and men. Statistical significance was assessed by Wilcoxon rank-sum test. C, PC analysis plot of Bray-Curtis distances. Statistical significance was assessed by the ANOSIM test. ANOSIM, analysis of similarities; PC, principal component.",decreased,NA,NA,Complete,NA
Study 577,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R, Wang L, Koch T, Curtis V, Yin-DeClue H, Handley SA, Shan L, Holtzman MJ, Castro M , Wang L",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,Experiment 1,United States of America,Homo sapiens,NA,NA,NA,NA,Female,Male,NA,32,15,NA,16S,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,14 December 2021,Joyessa,Joyessa,"Bacterioidetes, Proteobacteria, Fusobacteria.",increased,NA,NA,Complete,NA
Study 577,case-control,32931909,10.1016/j.anai.2020.09.007,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043253/,"Chen R, Wang L, Koch T, Curtis V, Yin-DeClue H, Handley SA, Shan L, Holtzman MJ, Castro M , Wang L",Sex effects in the association between airway microbiome and asthma,"Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology",2020,Experiment 1,United States of America,Homo sapiens,NA,NA,NA,NA,Female,Male,NA,32,15,NA,16S,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 3,Figure 1,14 December 2021,Joyessa,Joyessa,"Firmicutes, Actinobacteria.",decreased,NA,NA,Complete,NA
Study 578,prospective cohort,25766736,10.1093/jac/dkv062,NA,"Vervoort J, Xavier BB, Stewardson A, Coenen S, Godycki-Cwirko M, Adriaenssens N, Kowalczyk A, Lammens C, Harbarth S, Goossens H , Malhotra-Kumar S",Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota,The Journal of antimicrobial chemotherapy,2015,Experiment 1,"Belgium,Poland",Homo sapiens,feces,UBERON:0001988,urinary tract infection,EFO:0003103,Control group,Antibiotic treated,receiving nitrofurantoin treatment (100 mg three times daily for 3–15 days),5,8,2 months,16S,345,Roche454,Linear Regression,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,11 December 2021,Mmarin,Mmarin,"changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43.
Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.",decreased,k__Bacteria|p__Bacteroidetes,2|976,Complete,NA
Study 578,prospective cohort,25766736,10.1093/jac/dkv062,NA,"Vervoort J, Xavier BB, Stewardson A, Coenen S, Godycki-Cwirko M, Adriaenssens N, Kowalczyk A, Lammens C, Harbarth S, Goossens H , Malhotra-Kumar S",Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota,The Journal of antimicrobial chemotherapy,2015,Experiment 2,"Belgium,Poland",Homo sapiens,feces,UBERON:0001988,urinary tract infection,EFO:0003103,Antibiotic treated (day 1),Antibiotic treated (day 5-15),receiving nitrofurantoin treatment (100 mg three times daily for 3–15 days),8,8,2 months,16S,345,Roche454,Linear Regression,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,14 January 2022,Mmarin,Mmarin,"T1, day 1; T2, days 5–15; T3, days 31–43.
Bold type indicates a statistically significant difference (P < 0.05); generalized linear mixed model.",increased,k__Bacteria|p__Actinobacteria,2|201174,Complete,NA
Study 578,prospective cohort,25766736,10.1093/jac/dkv062,NA,"Vervoort J, Xavier BB, Stewardson A, Coenen S, Godycki-Cwirko M, Adriaenssens N, Kowalczyk A, Lammens C, Harbarth S, Goossens H , Malhotra-Kumar S",Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota,The Journal of antimicrobial chemotherapy,2015,Experiment 3,"Belgium,Poland",Homo sapiens,feces,UBERON:0001988,urinary tract infection,EFO:0003103,Control (day 1),Control (day 5-15),did not receve nitrofurantoin treatment,5,5,NA,16S,345,Roche454,Linear Regression,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 1,14 January 2022,Mmarin,Mmarin,"T1, day 1; T2, days 5–15; T3, days 31–43.
Bold type indicates a statistically significant difference (P < 0.05); generalized linear mixed model.",increased,k__Bacteria|p__Bacteroidetes,2|976,Complete,NA
Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,Experiment 1,United States of America,Homo sapiens,NA,NA,NA,NA,HIV+,HIV-,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1 D,15 December 2021,Joyessa,Joyessa,"Linear discriminant analysis effect size demonstrates genera that were significantly increased in individuals with PWH (red) or HIV-uninfected individuals (blue) in saliva. ***P , 0.005. LDA = linear discriminant analysis; NMDS = nonmetric multidimensional scaling.",decreased,"k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",2|1224|29547|213849|72294|194;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|482;2|1239|186801|186802|186803|265975;2|976|200643|171549|171552|838;2|976|200643|171549|2005525|195950;2|1224|28216|206351|481,Complete,NA
Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,Experiment 1,United States of America,Homo sapiens,NA,NA,NA,NA,HIV+,HIV-,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 1 D,16 December 2021,Joyessa,Joyessa,"Linear discriminant analysis effect size demonstrates genera that were significantly increased in individuals with PWH (red) or HIV-uninfected individuals (blue) in saliva. ***P , 0.005. LDA = linear discriminant analysis; NMDS = nonmetric multidimensional scaling.",increased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|201174|1760|85006|1268|32207;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,Experiment 2,United States of America,Homo sapiens,NA,NA,NA,NA,current_smoker,non_smoker,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,2E,15 December 2021,Joyessa,Joyessa,"Differential bacterial abundance in oral samples by smoking status is depicted using linear discriminant analysis effect size. *P , 0.05. LDA = linear discriminant analysis; NMDS = nonmetric multidimensional scaling.",increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella,k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Johnsonella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|976|200643|171549|171552|1283313;2|976|117743|200644|2762318|59735;2|1224|29547|213849|72294|194;2|32066|203490|203491|203492|848;2|1239|186801|186802|186803|43994;2|1224|28216|206351|481|482;2|976|200643|171549|171552|838,Complete,NA
Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,Experiment 2,United States of America,Homo sapiens,NA,NA,NA,NA,current_smoker,non_smoker,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,2E,16 December 2021,Joyessa,Joyessa,"Differential bacterial abundance in oral samples by smoking status is depicted using linear discriminant analysis effect size. *P , 0.05. LDA = linear discriminant analysis; NMDS = nonmetric multidimensional scaling.",decreased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|201174|84998|84999|1643824|1380;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,Experiment 3,United States of America,Homo sapiens,NA,NA,NA,NA,normal_DLCO,low_DLCO,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3 I,16 December 2021,Joyessa,Joyessa,"is depicted using linear discriminant analysis effect size. *P , 0.05. LDA = linear discriminant analysis; NMDS = nonmetric multidimensional scaling.",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|1239|91061|186826|33958|1578;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA
Study 580,"cross-sectional observational, not case-control",31682463,10.1164/rccm.201905-1016OC,https://pubmed.ncbi.nlm.nih.gov/31682463/,"Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B , Morris A",Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function,American journal of respiratory and critical care medicine,2020,Experiment 3,United States of America,Homo sapiens,NA,NA,NA,NA,normal_DLCO,low_DLCO,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 3I,16 December 2021,Joyessa,Joyessa,"is depicted using linear discriminant analysis effect size. *P , 0.05. LDA = linear discriminant analysis; NMDS = nonmetric multidimensional scaling.",decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Stomatobaculum",2|976|200643|171549|171552|1283313;2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|1239|186801|186802|186803|1164882;2|1239|1737404|1737405|1570339|543311;2|976|200643|171549|171552|838;2|1239|186801|186802|186803|1213720,Complete,NA
Study 581,"cross-sectional observational, not case-control",30291996,10.1016/j.eplepsyres.2018.09.013,NA,"Peng A, Qiu X, Lai W, Li W, Zhang L, Zhu X, He S, Duan J , Chen L",Altered composition of the gut microbiome in patients with drug-resistant epilepsy,Epilepsy research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,epilepsy,EFO:0000474,Drug sensitive epilepsy,Drug resistant epilepsy,Drug resistant epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE),49,42,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 2,16 December 2021,Fatima,Fatima,Lefse analysis showing microbiome differences in patients with drug sensitive epilepsy and  drug sensitive epilepsy,decreased,"k__Bacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella",2;2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976;2|976|200643;2|976|200643|171549|2005519|397864,Complete,Lwaldron
Study 581,"cross-sectional observational, not case-control",30291996,10.1016/j.eplepsyres.2018.09.013,NA,"Peng A, Qiu X, Lai W, Li W, Zhang L, Zhu X, He S, Duan J , Chen L",Altered composition of the gut microbiome in patients with drug-resistant epilepsy,Epilepsy research,2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,epilepsy,EFO:0000474,Drug sensitive epilepsy,Drug resistant epilepsy,Drug resistant epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE),49,42,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Figure 2,16 December 2021,Fatima,Fatima,Lefse analysis showing microbiome differences among drug resistance and drug sensitive epilepsy,increased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Negativicutes,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Archaea,k__Archaea|p__Euryarchaeota,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Delftia,k__Bacteria|p__Candidatus Saccharibacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemania,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales",2|1239|526524;2|1224|1236|2887326|468;2|1239;2|1239|186801|186802|186803;2|1239|909932;2|1239|909932|909929;2|1239|186801|186802|186803|841;2|1239|909932|1843488|909930|33024;2|1239|909932|1843488|909930;2157|28890|183925;2157|28890|183925|2158|2159;2157|28890|183925|2158|2159|2172;2157|28890|183925|2158;2|32066;2|32066|203490;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490|203491|203492|848;2|1239|186801|186802|186803|33042;2|1224|28216|206351;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2157;2157|28890;2|74201|203494|48461;2|74201;2|74201|203494|48461|1647988|239934;2|74201|203494|48461|203557;2|74201|203494;2|1239|186801|186802|204475;2|1239|186801|186802|216572|1263;2|976|200643|171549|171552|577309;2|1239|526524|526525|2810280|100883;2|1224|28216|80840|80864|80865;2|95818;2|1239|186801|186802|186803|189330;2|1239|526524|526525|128827|61170;2|1239|526524|526525|128827;2|201174|84998|84999|1643824|1380;2|1239|526524|526525,Complete,Fatima
Study 581,"cross-sectional observational, not case-control",30291996,10.1016/j.eplepsyres.2018.09.013,NA,"Peng A, Qiu X, Lai W, Li W, Zhang L, Zhu X, He S, Duan J , Chen L",Altered composition of the gut microbiome in patients with drug-resistant epilepsy,Epilepsy research,2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,epilepsy,EFO:0000474,Healthy controls,Drug resistant epilepsy,Drug sensitive epilepsy patients were defined according to the 2015 International League Against Epilepsy (ILAE),65,49,3 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 584,case-control,26288821,10.1016/j.ebiom.2015.04.010,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535156/,"Goedert JJ, Gong Y, Hua X, Zhong H, He Y, Peng P, Yu G, Wang W, Ravel J, Shi J , Zheng Y",Fecal Microbiota Characteristics of Patients with Colorectal Adenoma Detected by Screening: A Population-based Study,EBioMedicine,2015,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,precancerous colorectal adenoma,NA,normal participants,cra patients,patients with precancerous colorectal adenoma,24,20,none,16S,34,Illumina,"Linear Regression,Mann-Whitney (Wilcoxon)",0.03,FALSE,NA,sex,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,2 January 2022,Itslanapark,Itslanapark,differential relative abundance at the taxa and genera level between CRA patients and controls,increased,"k__Bacteria|p__Proteobacteria,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Legionellales|f__Legionellaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Halomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Erwiniaceae|g__Pantoea,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Morganella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Trabulsiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia",2|1224;2|1224|1236|72274|135621;2|1224|1236|118969|444;2|1224|1236|135619|28256;2|1224|1236|91347|543;2|1224|1236|91347|1903411|613;2|1224|1236|91347|543|620;2|1224|1236|91347|543|590;2|1224|1236|91347|1903409|53335;2|1224|1236|91347|1903414|581;2|1224|1236|91347|543|158851;2|1224|1236|91347|543|561,Complete,NA
Study 586,case-control,29375539,10.3389/fmicb.2017.02699,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770402/,"Russo E, Bacci G, Chiellini C, Fagorzi C, Niccolai E, Taddei A, Ricci F, Ringressi MN, Borrelli R, Melli F, Miloeva M, Bechi P, Mengoni A, Fani R , Amedei A",Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study,Frontiers in microbiology,2017,Experiment 1,Italy,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,Healthy Controls,CRC Patients,Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections,10,10,3 months,16S,34,Illumina,"ANOSIM,T-Test",NA,NA,NA,NA,NA,NA,increased,increased,decreased,NA,NA,Signature 1,"Figure 1, Discussion Text",12 January 2022,Itslanapark,Itslanapark,"Linear discriminant analysis performed with the “lefse“ pipeline to identify distinctive taxa of saliva, feces, and biopsy was used to reveal body site-specific microbial distributions.",increased,"k__Bacteria|p__Firmicutes,k__Bacteria|p__Fusobacteria",2|1239;2|32066,Complete,NA
Study 586,case-control,29375539,10.3389/fmicb.2017.02699,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770402/,"Russo E, Bacci G, Chiellini C, Fagorzi C, Niccolai E, Taddei A, Ricci F, Ringressi MN, Borrelli R, Melli F, Miloeva M, Bechi P, Mengoni A, Fani R , Amedei A",Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study,Frontiers in microbiology,2017,Experiment 2,Italy,Homo sapiens,saliva,UBERON:0001836,colorectal cancer,EFO:0005842,Healthy Controls,CRC Patients,Italian patients aged 71-95 with colorectal adenocarcinoma confirmed by histological analysis undergoing surgical resections.,10,10,3 months,16S,34,Illumina,ANOSIM,NA,NA,NA,NA,NA,NA,decreased,decreased,NA,decreased,NA,Signature 1,"Figure 1, Results Text",25 January 2022,Itslanapark,Itslanapark,"Linear discriminant analysis performed with the “lefse“ pipeline to identify distinctive taxa of saliva, feces, and biopsy was used to reveal body site-specific microbial distributions.",increased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria,k__Bacteria|p__Firmicutes,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Candidatus Saccharibacteria",2|201174;2|1224|28216;2|1239;2|976|117743;2|32066;2|976|200643|171549|171552;2|95818,Complete,NA
Study 587,"cross-sectional observational, not case-control",31794002,10.1093/ntr/ntz220,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364824/pdf/ntz220.pdf,"Nolan-Kenney R, Wu F, Hu J, Yang L, Kelly D, Li H, Jasmine F, Kibriya MG, Parvez F, Shaheen I, Sarwar G, Ahmed A, Eunus M, Islam T, Pei Z, Ahsan H , Chen Y",The Association Between Smoking and Gut Microbiome in Bangladesh,Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco,2020,Experiment 1,Bangladesh,Homo sapiens,pair of lungs,UBERON:0000170,"nicotine dependence,smoking behavior","EFO:0003768,EFO:0004318",Non smoker,Current Smoker,The relative abundance of bacterial taxa along the Erysipelotrichi-to-Catenibacterium lineage was significantly higher in current smokers compared to never-smokers.,151,62,1 month.,16S,34,Illumina,"Beta Binomial Regression,Chi-Square,Logistic Regression",0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,Table 3,4 January 2022,Joyessa,Joyessa,The relative abundances of 14 taxa were nominally significantly associated with smoking status when comparing current smokers and never-smokers.,increased,NA,NA,Complete,NA
Study 587,"cross-sectional observational, not case-control",31794002,10.1093/ntr/ntz220,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364824/pdf/ntz220.pdf,"Nolan-Kenney R, Wu F, Hu J, Yang L, Kelly D, Li H, Jasmine F, Kibriya MG, Parvez F, Shaheen I, Sarwar G, Ahmed A, Eunus M, Islam T, Pei Z, Ahsan H , Chen Y",The Association Between Smoking and Gut Microbiome in Bangladesh,Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco,2020,Experiment 1,Bangladesh,Homo sapiens,pair of lungs,UBERON:0000170,"nicotine dependence,smoking behavior","EFO:0003768,EFO:0004318",Non smoker,Current Smoker,The relative abundance of bacterial taxa along the Erysipelotrichi-to-Catenibacterium lineage was significantly higher in current smokers compared to never-smokers.,151,62,1 month.,16S,34,Illumina,"Beta Binomial Regression,Chi-Square,Logistic Regression",0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Table 4,6 January 2022,Joyessa,Joyessa,"This table summarizes the odds ratio data of the presence or absence of specific bacterial taxa between current smokers and never smokers. According to this investigation, only Class Alphaproteobacteria is significantly enriched in the former group compared to the latter.",increased,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,2|1224|28211,Complete,NA
Study 587,"cross-sectional observational, not case-control",31794002,10.1093/ntr/ntz220,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7364824/pdf/ntz220.pdf,"Nolan-Kenney R, Wu F, Hu J, Yang L, Kelly D, Li H, Jasmine F, Kibriya MG, Parvez F, Shaheen I, Sarwar G, Ahmed A, Eunus M, Islam T, Pei Z, Ahsan H , Chen Y",The Association Between Smoking and Gut Microbiome in Bangladesh,Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco,2020,Experiment 1,Bangladesh,Homo sapiens,pair of lungs,UBERON:0000170,"nicotine dependence,smoking behavior","EFO:0003768,EFO:0004318",Non smoker,Current Smoker,The relative abundance of bacterial taxa along the Erysipelotrichi-to-Catenibacterium lineage was significantly higher in current smokers compared to never-smokers.,151,62,1 month.,16S,34,Illumina,"Beta Binomial Regression,Chi-Square,Logistic Regression",0.05,TRUE,NA,"age,body mass index,sex",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 3,Table 5,6 January 2022,Joyessa,Joyessa,This table summarizes the odds ratio of mean relative abundances or presence or absence of bacterial taxa associated with one increase in packs of cigarette/bidi smoke.,increased,NA,NA,Complete,NA
Study 588,case-control,34442626,10.3390/microorganisms9081548,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8401100/,"Fang CY, Chen JS, Hsu BM, Hussain B, Rathod J , Lee KH",Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers,Microorganisms,2021,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy subjects,colorectal cancer patients,persons aged 25–95 years old with cancerous large intestine tumor symptoms,17,21,1 month,16S,34,Illumina,NA,0.05,TRUE,2,NA,NA,NA,increased,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 589,case-control,23940645,10.1371/journal.pone.0070803,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3735522/,"Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL , Ryan EP",Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults,PloS one,2013,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy control,CRC patients,recently diagnosed colon cancer patients prior to surgery for colonic resection,11,10,2 months,16S,4,Roche454,NA,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 3,6 January 2022,Itslanapark,Itslanapark,Bacterial species significantly over-represented in CRC stool samples.,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium",2|74201|203494|48461|1647988|239934|239935;2|1239|909932|1843488|909930|33024,Complete,NA
Study 589,case-control,23940645,10.1371/journal.pone.0070803,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3735522/,"Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL , Ryan EP",Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults,PloS one,2013,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,healthy control,CRC patients,recently diagnosed colon cancer patients prior to surgery for colonic resection,11,10,2 months,16S,4,Roche454,NA,0.01,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table 2,6 January 2022,Itslanapark,Itslanapark,Bacterial species that were significantly more abundant in the stool of healthy individuals compared to CRC patients,decreased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides finegoldii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides intestinalis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia|s__Blautia obeum,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister invisus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea|s__Dorea formicigenerans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnobacterium|s__Lachnobacterium bovis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas|s__Megamonas hypermegale,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella copri,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella oris,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Pseudoflavonifractor|s__Pseudoflavonifractor capillosus",2|976|200643|171549|815|816|338188;2|976|200643|171549|815|816|329854;2|1239|186801|186802|186803|572511|40520;2|1239|909932|1843489|31977|39948|218538;2|1239|909932|1843489|31977|39948|39950;2|1239|186801|186802|186803|189330|39486;2|1239|186801|186802|186803|140625|140626;2|1239|186801|186802|186803|28050|28052;2|1239|909932|909929|1843491|158846|158847;2|976|200643|171549|171552|838|165179;2|976|200643|171549|171552|838|28135;2|1239|186801|186802|216572|1017280|106588,Complete,NA
Study 590,case-control,31078141,10.1186/s40168-019-0687-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511141/pdf/40168_2019_Article_687.pdf,"Rocafort M, Noguera-Julian M, Rivera J, Pastor L, Guillén Y, Langhorst J, Parera M, Mandomando I, Carrillo J, Urrea V, Rodríguez C, Casadellà M, Calle ML, Clotet B, Blanco J, Naniche D , Paredes R",Evolution of the gut microbiome following acute HIV-1 infection,Microbiome,2019,Experiment 1,United States of America,Homo sapiens,HIV,NA,infection,EFO:0000544,HIV-1-negative,HIV-1 infection,"Increased fecal shedding of eukaryotic viruses, transitory loss of bacterial taxonomic richness, and long-term declines in microbial gene richness are all linked to HIV-1 infection. Only chronically HIV-1-infected people develop an HIV-1-associated microbiota profile.",54,49,18 months.,16S,34,NA,Fisher's Exact Test,0.05,TRUE,NA,age,HIV infection,NA,increased,unchanged,unchanged,NA,increased,Signature 1,Figure 2,8 January 2022,Joyessa,Joyessa,"Between-group differences in bacterial genera. The median (IQR) abundance of bacterial genera is shown in box plots. The closest taxonomic level identification is used to identify bacterial genera labeled ""unclassified."" Only bacterial genera with a statistically significant difference in abundance across groups (Kruskal–Wallis p value 0.05) are displayed. Asterisks indicate statistically significant post hoc pairwise differences (FDR 0.05, Tukey post hoc pairwise tests corrected for multiple comparisons). For cross-sectional comparisons with CHI ART and CHI noART, only the first microbiome measurement obtained RHI 6, RHI > 6, and NEG was used.",decreased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|74201|203494|48461|1647988|239934;2|201174|1760|85004|31953|1678;2|1239|186801|186802|31979|1485,Complete,NA
Study 590,case-control,31078141,10.1186/s40168-019-0687-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511141/pdf/40168_2019_Article_687.pdf,"Rocafort M, Noguera-Julian M, Rivera J, Pastor L, Guillén Y, Langhorst J, Parera M, Mandomando I, Carrillo J, Urrea V, Rodríguez C, Casadellà M, Calle ML, Clotet B, Blanco J, Naniche D , Paredes R",Evolution of the gut microbiome following acute HIV-1 infection,Microbiome,2019,Experiment 1,United States of America,Homo sapiens,HIV,NA,infection,EFO:0000544,HIV-1-negative,HIV-1 infection,"Increased fecal shedding of eukaryotic viruses, transitory loss of bacterial taxonomic richness, and long-term declines in microbial gene richness are all linked to HIV-1 infection. Only chronically HIV-1-infected people develop an HIV-1-associated microbiota profile.",54,49,18 months.,16S,34,NA,Fisher's Exact Test,0.05,TRUE,NA,age,HIV infection,NA,increased,unchanged,unchanged,NA,increased,Signature 2,Figure 4,8 January 2022,Joyessa,Joyessa,"In Mozambicans, the gut microbial gene richness followed a bimodal distribution as well. High gene counts (HGCs) and low gene counts (LGCs) were assigned to samples with gene counts above and below 444.219 genes, respectively. Only 37 percent (7/19) of HIV-negative samples were LGC (Fisher's test p value 0.003), but 63 percent (22/35) of RHI samples were LGC. At the first timepoint, 10/13 (76.9%) RHI vs 4/8 (50%) HIV-negative participants were already LGC (Fisher's test p value 0.172). In all follow-up timepoints, eight of thirteen (61.5 percent) RHI subjects displayed low gene count levels, whereas none of the HIV-negative persons did. Furthermore, throughout follow-up, 5/8 HIV-negative sub-jects (62.5%) showed increases in gene richness.",increased,NA,NA,Complete,NA
Study 590,case-control,31078141,10.1186/s40168-019-0687-5,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511141/pdf/40168_2019_Article_687.pdf,"Rocafort M, Noguera-Julian M, Rivera J, Pastor L, Guillén Y, Langhorst J, Parera M, Mandomando I, Carrillo J, Urrea V, Rodríguez C, Casadellà M, Calle ML, Clotet B, Blanco J, Naniche D , Paredes R",Evolution of the gut microbiome following acute HIV-1 infection,Microbiome,2019,Experiment 1,United States of America,Homo sapiens,HIV,NA,infection,EFO:0000544,HIV-1-negative,HIV-1 infection,"Increased fecal shedding of eukaryotic viruses, transitory loss of bacterial taxonomic richness, and long-term declines in microbial gene richness are all linked to HIV-1 infection. Only chronically HIV-1-infected people develop an HIV-1-associated microbiota profile.",54,49,18 months.,16S,34,NA,Fisher's Exact Test,0.05,TRUE,NA,age,HIV infection,NA,increased,unchanged,unchanged,NA,increased,Signature 3,Figure 5,8 January 2022,Joyessa,Joyessa,"Subdoligranulum, methanogenic archaea, multiple butyrate makers from the Ruminococcus, Dorea, and Eubacterium genera, and Butyrivibrio crossotus were all found to be positively connected with higher gene richness. In this study, Prevotella copri was negatively linked with gene richness, which is consistent with the microbiome composition in this Prevotella-rich African population. In the RHI group, the unique taxonomy was an unidentified species from the genus Dorea that was negatively linked with gene richness. Several microbial species linked to gene richness were found to be decreased in RHI when compared to HIV-negative people in a longitudinal study.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio crossotus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus champanellensis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp.",2|1239|186801|186802|186803|830|45851;2|201174|84998|84999|84107|102106|74426;2|1239|186801|186802|186803|189330;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|1263;2|1239|186801|186802|216572|1263|1161942;2|1239|186801|186802|216572|292632|2053618,Complete,NA
Study 592,"cross-sectional observational, not case-control",34378948,10.1128/Spectrum.00708-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8552706/pdf/spectrum.00708-21.pdf,"Ishizaka A, Koga M, Mizutani T, Parbie PK, Prawisuda D, Yusa N, Sedohara A, Kikuchi T, Ikeuchi K, Adachi E, Koibuchi T, Furukawa Y, Tojo A, Imoto S, Suzuki Y, Tsutsumi T, Kiyono H, Matano T , Yotsuyanagi H",Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation,Microbiology spectrum,2021,Experiment 1,Japan,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",HIV infection,EFO:0000764,Healthy control,HIV Patients,NA,61,109,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,3,"age,sex","age,sex",NA,decreased,NA,NA,NA,increased,Signature 1,Figure 2,9 January 2022,Joyessa,Joyessa,"Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria made up the bulk of OTUs. The relative abundance of Actinobacteria in the high-CD4 group was significantly higher than in uninfected controls (P = 0.0031). The top 20 bacterial genera from each group are represented in the Venn diagram. All 20 taxa were shared by HIV patients with high and low CD4 counts, including 13 that were shared by the uninfected control group. Despite the restoration of alpha diversity, the microbiome profile of HIV patients with high CD4 counts appeared different from that of uninfected controls, given that the top abundant taxa remained unchanged for both CD4 categories.A permutational multivariate analysis of variance test of beta-diversity based on weighted UniFrac distance found that bacterial communities were significantly different between the high-CD4 HIV group and uninfected controls (Q = 0.006), supporting this theory. Principal-coordinate analysis based on weighted UniFrac results corroborated the intragroup dissimilarity between the two groups. The difference between the low-CD4 HIV group and uninfected controls, on the other hand, was not statistically significant, which could be attributed to the low-CD4 category's small sample size (n = 10).",increased,k__Bacteria|p__Actinobacteria,2|201174,Complete,NA
Study 592,"cross-sectional observational, not case-control",34378948,10.1128/Spectrum.00708-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8552706/pdf/spectrum.00708-21.pdf,"Ishizaka A, Koga M, Mizutani T, Parbie PK, Prawisuda D, Yusa N, Sedohara A, Kikuchi T, Ikeuchi K, Adachi E, Koibuchi T, Furukawa Y, Tojo A, Imoto S, Suzuki Y, Tsutsumi T, Kiyono H, Matano T , Yotsuyanagi H",Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation,Microbiology spectrum,2021,Experiment 1,Japan,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",HIV infection,EFO:0000764,Healthy control,HIV Patients,NA,61,109,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,3,"age,sex","age,sex",NA,decreased,NA,NA,NA,increased,Signature 2,Figure 3,9 January 2022,Joyessa,Joyessa,"With a log10-transformed LDA score of 3.0, 33 bacterial taxa were discovered to identify HIV patients. The majority of the enhanced bacterial communities in HIV patients belonged to the Negativicutes, Coriobacteriia, or Bacilli classes, whereas the decreased taxa were mostly Clostridia. Actinobacteria were more prevalent at the phylum level in HIV patients than in uninfected controls. From order to genus levels, the genera Collinsella and Slackia, which belong to the class Coriobacteriia in this phylum, were abundant in patients. Dialister and Megamonas, both of the Negativicutes class, were enriched from order to genus levels in HIV patients, as were Acidaminococcaceae from order to family levels.Catenibacterium and Holdemanella were enriched in patients from order to ge-nus levels in the Bacilli class. A depletion of Ruminococcaceae from order to family levels, as well as Anaerostipes from order to genus levels, in the Clostridia class. Finally, HIV patients had higher Prevotella abundance and Bacteroides depletion from family to genus levels (P 0.001 and P = 0.022, respectively).",decreased,k__Bacteria|p__Firmicutes|c__Clostridia,2|1239|186801,Complete,NA
Study 592,"cross-sectional observational, not case-control",34378948,10.1128/Spectrum.00708-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8552706/pdf/spectrum.00708-21.pdf,"Ishizaka A, Koga M, Mizutani T, Parbie PK, Prawisuda D, Yusa N, Sedohara A, Kikuchi T, Ikeuchi K, Adachi E, Koibuchi T, Furukawa Y, Tojo A, Imoto S, Suzuki Y, Tsutsumi T, Kiyono H, Matano T , Yotsuyanagi H",Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation,Microbiology spectrum,2021,Experiment 1,Japan,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",HIV infection,EFO:0000764,Healthy control,HIV Patients,NA,61,109,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,3,"age,sex","age,sex",NA,decreased,NA,NA,NA,increased,Signature 3,Figure 3,9 January 2022,Joyessa,Joyessa,"Differences in taxonomic composition between the feces of HIV patients and healthy controls. Between healthy controls (HC) and HIV patients with CD4 levels greater than 500 cells/ml, the difference in abundance of bacterial taxa was measured using the linear discriminant analysis effect size (LEfSe). Only taxa with a.3.0 LDA score are displayed. The data in panel A are represented by a taxonomic cladogram. Negativicutes, Coriobacteriia, Bacilli, and Clostridia have different relative abundances. Prevotella and Bacteroides genera relative abundance. ****, P = 0.0001; **, P = 0.01.",increased,"k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Firmicutes|c__Negativicutes",2|1239|91061;2|201174|84998;2|1239|909932,Complete,NA
Study 592,"cross-sectional observational, not case-control",34378948,10.1128/Spectrum.00708-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8552706/pdf/spectrum.00708-21.pdf,"Ishizaka A, Koga M, Mizutani T, Parbie PK, Prawisuda D, Yusa N, Sedohara A, Kikuchi T, Ikeuchi K, Adachi E, Koibuchi T, Furukawa Y, Tojo A, Imoto S, Suzuki Y, Tsutsumi T, Kiyono H, Matano T , Yotsuyanagi H",Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation,Microbiology spectrum,2021,Experiment 1,Japan,Homo sapiens,"digestive system,digestive tract,lower digestive tract","UBERON:0001007,UBERON:0001555,UBERON:0004907",HIV infection,EFO:0000764,Healthy control,HIV Patients,NA,61,109,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,NA,3,"age,sex","age,sex",NA,decreased,NA,NA,NA,increased,Signature 4,Figure 5,10 January 2022,Joyessa,Joyessa,"There is a link between patient age and the abundance of the Coriobacteriia class, as well as the Coriobacteriaceae and Eggerthellaceae families in this class. This was in line with a prior study in cynomolgus macaques that found age-related enrichment of these bacterial taxa during normal, healthy aging (26). However, there was no association between the abundance of these taxa and the patient's age among HIV patients. When we separated the patients into two groups according on whether they were older or younger than 50 years old, we found that both groups had higher abundances of these taxa than uninfected controls. There is a link between patient age and bacterial taxa belonging to the Coriobacteriia class. Correlations between age and Coriobacteria relative abundance in HIV patients and healthy controls.",increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|p__Actinobacteria|c__Coriobacteriia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae",2|201174|84998|84999|84107;2|201174|84998;2|201174|84998|1643822|1643826,Complete,NA
Study 594,"cross-sectional observational, not case-control",28328799,10.1097/MD.0000000000005821,https://pubmed.ncbi.nlm.nih.gov/28328799/,"Noguera-Julian M, Guillén Y, Peterson J, Reznik D, Harris EV, Joseph SJ, Rivera J, Kannanganat S, Amara R, Nguyen ML, Mutembo S, Paredes R, Read TD , Marconi VC",Oral microbiome in HIV-associated periodontitis,Medicine,2017,Experiment 1,United States of America,Homo sapiens,HIV,NA,periodontitis,EFO:0000649,HIV–,HIV+,"This was a cross-sectional study that included HIV+ and HIV– people with varied levels of PD. HIV+ patients were recruited at Grady Memorial Hospital's Oral Health Center of Infectious Disease Program in Atlanta, GA. Prior to study admission, HIV-1 infection was verified by ELISA and confirmed by Western blot.",10,40,NA,16S,4,Illumina,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Wald Test",0.05,TRUE,NA,NA,NA,NA,increased,increased,unchanged,NA,increased,Signature 1,Figure 3,10 January 2022,Joyessa,Joyessa,"HIV infection was also linked to variations in the relative abundance of several bacterial species. In HIV+ individuals' samples, Neisseria and taxa of the unclassified Neisseriaceae family were 4-fold more prevalent. Classified differential abundant genera between HIV+andHIV–samples. Fold Log2 On the X-axis, change is plotted. Color codes were used by Phylais. The mean count for a specific genus throughout the entire data set is shown by the point size. Human immunodeficiency virus (HIV) is a virus that causes infection in humans.",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|91061|186826|186827|46123;2|1224|1236|135625|712|416916;2|1239|909932|909929|1843491|82202;2|1224|28216|206351|481|32257;2|32066|203490|203491|1129771|32067;2|1224|28216|206351|481|482;2|201174|1760|85006|1268|32207;2|1239|909932|909929|1843491|970;2|976|200643|171549|2005525|195950;2|203691|203692|136|2845253|157,Complete,NA
Study 594,"cross-sectional observational, not case-control",28328799,10.1097/MD.0000000000005821,https://pubmed.ncbi.nlm.nih.gov/28328799/,"Noguera-Julian M, Guillén Y, Peterson J, Reznik D, Harris EV, Joseph SJ, Rivera J, Kannanganat S, Amara R, Nguyen ML, Mutembo S, Paredes R, Read TD , Marconi VC",Oral microbiome in HIV-associated periodontitis,Medicine,2017,Experiment 1,United States of America,Homo sapiens,HIV,NA,periodontitis,EFO:0000649,HIV–,HIV+,"This was a cross-sectional study that included HIV+ and HIV– people with varied levels of PD. HIV+ patients were recruited at Grady Memorial Hospital's Oral Health Center of Infectious Disease Program in Atlanta, GA. Prior to study admission, HIV-1 infection was verified by ELISA and confirmed by Western blot.",10,40,NA,16S,4,Illumina,"Kruskall-Wallis,Mann-Whitney (Wilcoxon),Wald Test",0.05,TRUE,NA,NA,NA,NA,increased,increased,unchanged,NA,increased,Signature 2,Table 1,10 January 2022,Joyessa,Joyessa,"HIV infection was also linked to variations in the relative abundance of several bacterial species. In HIV+ participants' samples, Neisseria and taxa of the unclassified Neisseriaceae family were 4-fold more frequent (log 2 FC = 1.84, P 0.001). Only the Treponema genus, which is typically connected to PD, was shown to be overabundant in S-PD when compared to N-PD, when HIV infection was not taken into account, in both cheek (log 2 FC = 1.83, Padj 0.005) and saliva (log 2 FC = 2.6, Padj 0.001) samples, albeit in very low abundance.",decreased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia,k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema",2|1239|91061|186826|186827|46123;2|1224|28216|206351|481|482;2|1224|28216|206351|481;2|1224|1236|135625|712;2|201174|1760|85006|1268|32207;2|203691|203692|136|2845253|157,Complete,NA
Study 595,case-control,25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I , Bork P",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,colorectal carcinoma,EFO:1001951,tumor-free controls,CRC patients,patients referred for colonoscopy that had cancerous tumors,53,61,none,16S,34,Illumina,"Fisher's Exact Test,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.01,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure S2,19 January 2022,Itslanapark,Itslanapark,significant differences in the abundance of specific taxa,increased,"k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Proteobacteria",2|976;2|32066;2|1224,Complete,NA
Study 595,case-control,25432777,10.15252/msb.20145645,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606/,"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I , Bork P",Potential of fecal microbiota for early-stage detection of colorectal cancer,Molecular systems biology,2014,Experiment 1,France,Homo sapiens,feces,UBERON:0001988,colorectal carcinoma,EFO:1001951,tumor-free controls,CRC patients,patients referred for colonoscopy that had cancerous tumors,53,61,none,16S,34,Illumina,"Fisher's Exact Test,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.01,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 3,Supplementary Figure S2,19 January 2022,Itslanapark,Itslanapark,significant differences in the abundance of specific taxa,decreased,"k__Bacteria|p__Actinobacteria,k__Bacteria|p__Firmicutes",2|201174;2|1239,Complete,NA
Study 596,case-control,25058515,10.1371/journal.ppat.1004262,https://pubmed.ncbi.nlm.nih.gov/25058515/,"Liu CM, Osborne BJ, Hungate BA, Shahabi K, Huibner S, Lester R, Dwan MG, Kovacs C, Contente-Cuomo TL, Benko E, Aziz M, Price LB , Kaul R",The semen microbiome and its relationship with local immunology and viral load in HIV infection,PLoS pathogens,2014,Experiment 1,United States of America,Homo sapiens,Semen,UBERON:0001968,HIV infection,EFO:0000764,HIV-uninfected men,HIV-infected men,"Semen bacterial burden was associated with seven pro-inflammatory semen cytokines in HIV-infected men, including IL-6 (p = 0.024), TNF-a (p = 0.009), and IL-1b (p = 0.002). Semen VL was linked to IL-1b in particular (r2 = 0.18, p = 0.02). The bacterial load in the sperm was likewise connected to the HIV VL in the sperm (r2 = 0.15, p = 0.02). HIV infection changes the interaction between semen bacteria and pro-inflammatory cytokines, and both are linked to semen VL, implying that the semen microbiome may play a role in HIV transmission.",22,27,6 months.,16S,3456,NA,ANOVA,0.05,TRUE,NA,age,age,NA,increased,NA,NA,NA,increased,Signature 1,Table 2,11 January 2022,Joyessa,Joyessa,"Streptococcus, Corynebacterium, and Staphylococcus were among the most common and proportionally abundant semen bacteria among HIV-uninfected MSM. Prevotella, Porphyromonas, Finegoldia, Micrococcus, and Actinomyces were among the bacteria that were proportionately abundant and made up 1–3% of the semen microbiota. While Ureaplasma was only found in four males, it made up a significant component of their semen microbiome. Regardless of HIV status, Streptococcus was the most common bacterium in sperm. Prior to starting antiretroviral therapy, the prevalence and proportional abundances of the 40 most common semen germs in uninfected men and HIV-infected males.",decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia",2|201174|1760|85004|31953|1678;2|1224|28211|356|212791;2|201174|1760|85010|2070|1847,Complete,NA
Study 596,case-control,25058515,10.1371/journal.ppat.1004262,https://pubmed.ncbi.nlm.nih.gov/25058515/,"Liu CM, Osborne BJ, Hungate BA, Shahabi K, Huibner S, Lester R, Dwan MG, Kovacs C, Contente-Cuomo TL, Benko E, Aziz M, Price LB , Kaul R",The semen microbiome and its relationship with local immunology and viral load in HIV infection,PLoS pathogens,2014,Experiment 1,United States of America,Homo sapiens,Semen,UBERON:0001968,HIV infection,EFO:0000764,HIV-uninfected men,HIV-infected men,"Semen bacterial burden was associated with seven pro-inflammatory semen cytokines in HIV-infected men, including IL-6 (p = 0.024), TNF-a (p = 0.009), and IL-1b (p = 0.002). Semen VL was linked to IL-1b in particular (r2 = 0.18, p = 0.02). The bacterial load in the sperm was likewise connected to the HIV VL in the sperm (r2 = 0.15, p = 0.02). HIV infection changes the interaction between semen bacteria and pro-inflammatory cytokines, and both are linked to semen VL, implying that the semen microbiome may play a role in HIV transmission.",22,27,6 months.,16S,3456,NA,ANOVA,0.05,TRUE,NA,age,age,NA,increased,NA,NA,NA,increased,Signature 2,Figure 1,11 January 2022,Joyessa,Joyessa,"Streptococcus, Corynebacterium, and Staphylococcus were among the most common and proportionally abundant semen bacteria among HIV-uninfected MSM. Prevotella, Porphyromonas, Finegoldia, Micrococcus, and Actinomyces were among the bacteria that were proportionately abundant and made up 1–3% of the semen microbiota. Even though Ureaplasma was only found in four males, it made up a significant component of the semen microbiome. In HIV-positive men, the proportionate abundance of Mycoplasma reduced over time. Richness refers to how far the plot extends along the x-axis, whereas evenness refers to how steep the slope is. A high y-intercept indicates extreme dominance. The HIV uninfected has a richer and more even relationship than the ART-naive, but the relationship converges on the HIV uninfected after 6 months of ART.",increased,"k__Bacteria|p__Tenericutes|c__Mollicutes|o__Mycoplasmatales|f__Mycoplasmataceae|g__Mycoplasma,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|544448|31969|2085|2092|2093;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|168808;2|1239|91061|186826|1300|1301,Complete,NA
Study 598,case-control,28743816,10.1128/mBio.00996-17,https://pubmed.ncbi.nlm.nih.gov/28743816/,"Liu CM, Prodger JL, Tobian AAR, Abraham AG, Kigozi G, Hungate BA, Aziz M, Nalugoda F, Sariya S, Serwadda D, Kaul R, Gray RH , Price LB",Penile Anaerobic Dysbiosis as a Risk Factor for HIV Infection,mBio,2017,Experiment 1,United States of America,Homo sapiens,Genitals,NA,HIV infection,EFO:0000764,HIV seronegative,HIV seroconverted,"The current case-control analysis exclusively included trial participants who were randomized to the delayed circumcision arm of the trial and remained uncircumcised for the course of the trial. Participants who seroconverted over the 2-year study period were classified as cases, whereas those who remained HIV-free throughout that time were classified as controls. Three controls were chosen at random for each case.",136,46,24 months.,16S,34,Illumina,Fisher's Exact Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,12 January 2022,Joyessa,Joyessa,"In a case-control study, there was a link between the absolute abundances of anaerobic bacteria and the chance of HIV seroconversion. At the start of the trial, each 10-fold increase in the absolute abundance of anaerobic bacteria Prevotella, Dialister, Finegoldia, Peptoniphilus, and Peptostreptococcus (measured in log10-transformed number of 16S rRNA gene copies per swab) doubled the risk of HIV infection. After controlling for age, marital status, the number of adulterous sexual partners, condom use, and genital discharge symptoms, the likelihood of seroconversion increased even more. The adjusted odds ratio (i.e., the mean adjusted odds of HIV seroconversion per 10-fold increase in absolute abundance of bacteria) and 95 percent confidence interval (in parentheses) for each genus are shown under each genus.",increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|1239|186801|186802|186804|1257;2|976|200643|171549|171552|838,Complete,NA
Study 598,case-control,28743816,10.1128/mBio.00996-17,https://pubmed.ncbi.nlm.nih.gov/28743816/,"Liu CM, Prodger JL, Tobian AAR, Abraham AG, Kigozi G, Hungate BA, Aziz M, Nalugoda F, Sariya S, Serwadda D, Kaul R, Gray RH , Price LB",Penile Anaerobic Dysbiosis as a Risk Factor for HIV Infection,mBio,2017,Experiment 1,United States of America,Homo sapiens,Genitals,NA,HIV infection,EFO:0000764,HIV seronegative,HIV seroconverted,"The current case-control analysis exclusively included trial participants who were randomized to the delayed circumcision arm of the trial and remained uncircumcised for the course of the trial. Participants who seroconverted over the 2-year study period were classified as cases, whereas those who remained HIV-free throughout that time were classified as controls. Three controls were chosen at random for each case.",136,46,24 months.,16S,34,Illumina,Fisher's Exact Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2,12 January 2022,Joyessa,Joyessa,"Prevotella (slope after the breakpoint [c] used in the piecewise spline model [slopepost-c] 0.56; c 8 log10 copies of 16S rRNA gene per swab; r2 0.14).In a case-control study, there was a link between the absolute abundance of penile anaerobes and the concentration of IL-8. Anaerobe abundance (measured in 16S rRNA gene copies per swab (log10)) and IL-8 concentration (measured in picograms per milliliter (log10)) had a similar association.",increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Finegoldia,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|39948;2|1239|1737404|1737405|1570339|150022;2|1239|1737404|1737405|1570339|162289;2|1239|186801|186802|186804|1257;2|976|200643|171549|171552|838,Complete,NA
Study 598,case-control,28743816,10.1128/mBio.00996-17,https://pubmed.ncbi.nlm.nih.gov/28743816/,"Liu CM, Prodger JL, Tobian AAR, Abraham AG, Kigozi G, Hungate BA, Aziz M, Nalugoda F, Sariya S, Serwadda D, Kaul R, Gray RH , Price LB",Penile Anaerobic Dysbiosis as a Risk Factor for HIV Infection,mBio,2017,Experiment 2,United States of America,Homo sapiens,Genitals,NA,HIV infection,EFO:0000764,HIV seronegative,HIV seroconverted,NA,136,46,24 months.,16S,34,Illumina,Fisher's Exact Test,0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table 2,12 January 2022,Joyessa,Joyessa,"The likelihood of finding any inflammatory cytokines (interleukin 1 [IL-1], interleukin 8 [IL-8], macrophage chemoattractant 1 [MCP-1], monokine induced by interferon gamma [MIG], macrophage inflammatory protein 3 [MIP-3], RANTES [regulated on activation, normal T cell expressed and secreted], and granulocyte-macrophage colony-stimulating factor.",increased,"k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|909932|1843489|31977|39948;2|1239|186801|186802|186804|1257;2|976|200643|171549|171552|838,Complete,NA
Study 599,case-control,23249810,10.1128/mBio.00370-12,https://pubmed.ncbi.nlm.nih.gov/23249810/,"Ravel J, Gajer P, Fu L, Mauck CK, Koenig SS, Sakamoto J, Motsinger-Reif AA, Doncel GF , Zeichner SL",Twice-daily application of HIV microbicides alter the vaginal microbiota,mBio,2012,Experiment 1,United States of America,Homo sapiens,vagina,UBERON:0000996,Human immunodeficiency virus,NCBITAXON:12721,Healthy females who recieved universal placebo,Healthy females who recieved two vaginal HIV microbicidal gels,Healthy females were treated with two gels twice daily over 13.5 days.,10,25,NA,16S,56,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,14 January 2022,Joyessa,Joyessa,"Complete interconnection Five primary bacterial community state categories were discovered using hierarchical clustering approaches (CSTs). Different Lactobacillus species dominated three CSTs: L. crispatus (CST I), L. iners (CST III), and L. gasseri (CST IV) (CST II). Higher proportions and types of anaerobic bacteria such as Atopobium, Prevotella, Megaspherae, Sneathia, and Mobiluncus, as well as Gardnerella (the latter in proportions ranging from 0.2 percent to 9.9 percent) were found in vaginal bacterial communities from samples that clustered in CST IV-B, whereas CST IV-A Schematicoftheclinicalstudydesign. Green recommends using the gel items twice a day. Idealizedmensesareindicatedinred. At visits 2, 3, 4, 5, and 6, vaginal swabs were taken.",increased,"k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae|g__Mobiluncus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Sneathia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|201174|84998|84999|1643824|1380;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|201174|1760|85004|31953|2701;2|201174|1760|2037|2049|2050;2|976|200643|171549|171552|838;2|32066|203490|203491|1129771|168808;2|1239|91061|186826|1300|1301,Complete,NA
Study 600,case-control,29501802,10.1016/j.bbi.2018.02.016,NA,"Qian Y, Yang X, Xu S, Wu C, Song Y, Qin N, Chen SD , Xiao Q",Alteration of the fecal microbiota in Chinese patients with Parkinson's disease,"Brain, behavior, and immunity",2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,All PD patients eligible for this study were diagnosed with PD according to the UK Brain Bank criteria. Patients with IBS were excluded.,45,45,Participants taking antibiotics or probiotic supplements within the three months prior to sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 1,Figure 3A.,15 January 2022,Fcuevas3,Fcuevas3,Taxonomic differences of fecal microbiota in PD and healthy groups,increased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Firmicutes,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella,k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Nitrososphaera,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Bacteroidetes|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|g__Aquabacterium,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Archaea|p__Thaumarchaeota,k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae",2|1224|1236|2887326|468|469;2|976|200643|171549|171550|239759;2|1239|186801|186802|31979|580596;2|1239|186801|186802|31979|1485;2|1224|28221|213115|194924|872;2|1239;2|1224|1236|91347|543|570;2157|651137|1643678|1033996|1033997|497726;2|976|200643|171549|171552|577309;2|1224|28211|204457|41297|13687;2|976|1853228|1853229|563835;2|1239|526524|526525|128827;2|1239|526524;2|1224|28211|356|82115;2|976|117747;2|1224|28221|213115|194924|872;2|976|117747|200666;2|1224|28216|80840;2|1224|28216|80840|92793;2|1224|1236|135614;2|1224|28211|204457|41297;2|1224|28211|204457;2|1224|1236|135614|32033;2|1224|1236|2887326|468;2157|651137;2157|651137|1643678|1033996|1033997;2|976|200643|171549|171550,Complete,NA
Study 600,case-control,29501802,10.1016/j.bbi.2018.02.016,NA,"Qian Y, Yang X, Xu S, Wu C, Song Y, Qin N, Chen SD , Xiao Q",Alteration of the fecal microbiota in Chinese patients with Parkinson's disease,"Brain, behavior, and immunity",2018,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,All PD patients eligible for this study were diagnosed with PD according to the UK Brain Bank criteria. Patients with IBS were excluded.,45,45,Participants taking antibiotics or probiotic supplements within the three months prior to sample collection.,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,increased,increased,increased,NA,NA,Signature 2,Figure 3A.,22 January 2022,Fcuevas3,Fcuevas3,Taxonomic differences of fecal microbiota in PD and healthy groups.,decreased,"k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia,k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium",2|201174|1760|2037;2|1239|91061|186826|81850;2|1239|91061|186826|33958|1578;2|976|117743|200644;2|976|117743;2|976|1853228|1853229|563835|504481,Complete,NA
Study 600,case-control,29501802,10.1016/j.bbi.2018.02.016,NA,"Qian Y, Yang X, Xu S, Wu C, Song Y, Qin N, Chen SD , Xiao Q",Alteration of the fecal microbiota in Chinese patients with Parkinson's disease,"Brain, behavior, and immunity",2018,Experiment 2,China,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with Parkinson's Disease,All PD patients eligible for this study were diagnosed with PD according to the UK Brain Bank criteria. Patients with IBS and serious chronic illnesses were excluded.,45,45,Participants taking antibiotics or probiotic supplements within the three months prior to sample collection.,16S,34,Illumina,Negative Binomial Regression,0.05,FALSE,NA,NA,age,NA,increased,increased,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 603,"case-control,meta-analysis",33947803,10.1128/mSystems.00112-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269207/,"Jiang P, Wu S, Luo Q, Zhao XM , Chen WH",Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models,mSystems,2021,Experiment 1,NA,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,non disease controls,CRC patients,patients diagnosed with colorectal cancer,632,354,NA,16S,NA,NA,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,24 January 2022,Itslanapark,Itslanapark,microbial markers and their trends in controls and crc patients,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 5_1_63FAA,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus comes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",2|1239|186801|186802|186803|2569097|39488;2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|186803|658089;2|1239|186801|186802|186803|33042|410072;2|1239|186801|186802|186803|841|166486,Complete,NA
Study 603,"case-control,meta-analysis",33947803,10.1128/mSystems.00112-21,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269207/,"Jiang P, Wu S, Luo Q, Zhao XM , Chen WH",Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models,mSystems,2021,Experiment 1,NA,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,non disease controls,CRC patients,patients diagnosed with colorectal cancer,632,354,NA,16S,NA,NA,"Chi-Square,Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,NA,"age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 1,25 January 2022,Itslanapark,Itslanapark,microbial markers and their trends in controls and crc patients,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes onderdonkii,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella|s__Alloprevotella tannerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides salyersiae,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila wadsworthia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster asparagiformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster bolteae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster citroniae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella|s__Gemella morbillorum,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella|s__Hungatella hathewayi,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus stomatis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas asaccharolytica,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas somerae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella intermedia,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelatoclostridium|s__[Clostridium] innocuum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium|s__[Clostridium] symbiosum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 3_1_57FAA_CT1,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 7_1_58FAA,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus anaerobius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum|s__Subdoligranulum sp. 4_3_54A2FAA,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium|s__Solobacterium moorei,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera sp.,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio desulfuricans",2|976|200643|171549|171550|239759|328813;2|976|200643|171549|171552|1283313|76122;2|976|200643|171549|815|816|817;2|976|200643|171549|815|816|291644;2|1224|28221|213115|194924|35832|35833;2|1239|186801|186802|186803|2719313|333367;2|1239|186801|186802|186803|2719313|208479;2|1239|186801|186802|186803|2719313|358743;2|1239|91061|1385|1378|29391;2|1239|91061|186826|186828|117563|46124;2|1239|186801|186802|31979|1649459|154046;2|1239|1737404|1737405|1570339|543311|33033;2|1239|1737404|1737405|1570339|543311|1944660;2|1239|186801|186802|186804|1257|341694;2|976|200643|171549|171551|836|28123;2|976|200643|171549|171551|836|322095;2|976|200643|171549|171551|836|281920;2|976|200643|171549|171552|838|28131;2|201174|84998|1643822|1643826|84108|2049041;2|1239|91061|186826|1300|1301|1328;2|1239|526524|526525|128827|1505663|1522;2|1239|186801|186802|186803|1506553|1512;2|1239|186801|186802|186803|2316020|33039;2|1239|186801|186802|186803|658086;2|1239|186801|186802|186803|658087;2|1239|186801|186802|186804|1257|1261;2|1239|186801|186802|186804|1257|1262;2|1239|186801|186802|216572|244127|169435;2|1239|186801|186802|216572|244127|1872531;2|1239|186801|186802|216572|292632|665956;2|1239|526524|526525|128827|123375|102148;2|1239|909932|1843489|31977|906|2023260;2|32066|203490|203491|203492|848|851;2|1224|28221|213115|194924|872|876,Complete,NA
Study 604,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA, Molho E, Zabetian CP, Standaert DG , Payami H",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls free of neurological disease,Participants with Parkinson's Disease,Dataset 1. PD was diagnosed by a movement disorder specialist using UK Brain Bank criteria.,136,212,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2.,22 January 2022,Fcuevas3,Fcuevas3,Differential abundances of 15 PD-associated genera replicated in two datasets.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|201174|1760|85007|1653|1716;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578,Complete,NA
Study 604,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA, Molho E, Zabetian CP, Standaert DG , Payami H",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls free of neurological disease,Participants with Parkinson's Disease,Dataset 1. PD was diagnosed by a movement disorder specialist using UK Brain Bank criteria.,136,212,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2.,22 January 2022,Fcuevas3,Fcuevas3,Differential abundances of 15 PD-associated genera replicated in two datasets.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|1766253;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|841;2|1239|186801|186802|31979|580596;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803;2|1239|186801|186802|216572|119852,Complete,NA
Study 604,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA, Molho E, Zabetian CP, Standaert DG , Payami H",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,Experiment 1,United States of America,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls free of neurological disease,Participants with Parkinson's Disease,Dataset 1. PD was diagnosed by a movement disorder specialist using UK Brain Bank criteria.,136,212,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 3,Figure 2.,22 January 2022,Fcuevas3,Fcuevas3,Differential abundances of 15 PD-associated genera replicated in two datasets.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillospira",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|1766253;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803|841;2|1239|186801|186802|31979|580596;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|28050;2|1239|186801|186802|186803;2|1239|186801|186802|216572|119852,Complete,NA
Study 604,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA, Molho E, Zabetian CP, Standaert DG , Payami H",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control free of neurological disease.,Participants with Parkinson's Disease,Dataset 2. PD was diagnosed by a movement disorder specialist using UK Brain Bank criteria,184,323,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 1,Figure 2.,22 January 2022,Fcuevas3,Fcuevas3,Differential abundances of 15 PD-associated genera replicated in two datasets.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus",2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|201174|1760|85007|1653|1716;2|1239|186801|186802|186803|572511;2|1239|186801|186802|186803;2|201174|1760|85004|31953|1678;2|1239|91061|186826|33958|1578,Complete,NA
Study 604,case-control,32566740,10.1038/s41531-020-0112-6,NA,"Wallen ZD, Appah M, Dean MN, Sesler CL, Factor SA, Molho E, Zabetian CP, Standaert DG , Payami H",Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens,NPJ Parkinson's disease,2020,Experiment 2,United States of America,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy control free of neurological disease.,Participants with Parkinson's Disease,Dataset 2. PD was diagnosed by a movement disorder specialist using UK Brain Bank criteria,184,323,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,Figure 2.,22 January 2022,Fcuevas3,Fcuevas3,Differential abundances of 15 PD-associated genera replicated in two datasets.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira",2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|1766253;2|1239|186801|186802|186803|841;2|1239|186801|186802|31979|580596;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|28050,Complete,NA
Study 605,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin CH, Chen CC, Chiang HL, Liou JM, Chang CM, Lu TP, Chuang EY, Tai YC, Cheng C, Lin HY , Wu MS",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls without Parkinson's disease,Participants with Parkinson's Disease,PD was diagnosed according to the United Kingdom PD Society Brain Bank clinical diagnostic criteria.,77,80,Individuals currently taking antibiotics or probiotic supplements within 3 months of sample collection,16S,34,Illumina,LEfSe,0.05,NA,2,"age,sex","age,diet,sex",NA,increased,NA,NA,NA,increased,Signature 1,Figure 3A,22 January 2022,Fcuevas3,Fcuevas3,Taxonomic differences of fecal microbiota in PD and control groups,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Firmicutes|c__Erysipelotrichia,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Tenericutes,k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Mucispirillum,k__Bacteria|p__Deferribacteres|c__Deferribacteres,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Tenericutes|c__Mollicutes,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales",2|976|200643|171549|171551;2|976|200643|171549|2005525|375288;2|74201;2|74201|203494|48461|203557;2|74201|203494|48461|1647988|239934;2|74201|203494|48461;2|976|200643|171549|1853231;2|976|200643|171549|171550;2|976|200643|171549|1853231|574697;2|200930|68337|191393|191394;2|1224|28211;2|1239|909932|1843489|31977|29465;2|1239|526524;2|1239|526524|526525;2|1239|526524|526525|128827;2|976|200643|171549|1853231|283168;2|544448;2|200930|68337|191393|191394|248038;2|200930|68337;2|1224|28221|213115|194924|35832;2|1239|91061|186826|81852;2|1239|91061|186826|81850;2|1239|91061|186826|81852|1350;2|1239|91061|186826|33958|1578;2|544448|31969;2|1224|28211|356,Complete,NA
Study 605,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin CH, Chen CC, Chiang HL, Liou JM, Chang CM, Lu TP, Chuang EY, Tai YC, Cheng C, Lin HY , Wu MS",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,Experiment 1,Japan,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls without Parkinson's disease,Participants with Parkinson's Disease,PD was diagnosed according to the United Kingdom PD Society Brain Bank clinical diagnostic criteria.,77,80,Individuals currently taking antibiotics or probiotic supplements within 3 months of sample collection,16S,34,Illumina,LEfSe,0.05,NA,2,"age,sex","age,diet,sex",NA,increased,NA,NA,NA,increased,Signature 2,Figure 2A.,22 January 2022,Fcuevas3,Fcuevas3,Taxonomic differences of fecal microbiota in PD and control groups,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella",2|1239|186801|186802|216572|216851;2|976|200643|171549|171552;2|976|200643|171549|171552|838,Complete,NA
Study 605,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin CH, Chen CC, Chiang HL, Liou JM, Chang CM, Lu TP, Chuang EY, Tai YC, Cheng C, Lin HY , Wu MS",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,Experiment 2,Japan,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Participants with Parkinson's Disease with non-tremor subtypes,Participants with Parkinson's Disease with tremor subtypes,Participants with Parkinson's Disease with tremor subtypes.,33,47,Individuals currently taking antibiotics or probiotic supplements within 3 months of sample collection,16S,34,Illumina,LEfSe,0.05,NA,2,"age,sex","age,diet,sex",NA,increased,NA,NA,NA,increased,Signature 1,Figure 2A.,22 January 2022,Fcuevas3,Fcuevas3,Taxonomic differences of fecal microbiota in non tremor and tremor groups.,increased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__Clostridiales Family XIII bacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales",2|1239|186801;2|1239|186801|186802|543314|2137877;2|1239;2|74201;2|74201|203494|48461|203557;2|74201|203494|48461|1647988|239934;2|74201|203494;2|74201|203494|48461,Complete,NA
Study 605,case-control,31248424,10.1186/s12974-019-1528-y,NA,"Lin CH, Chen CC, Chiang HL, Liou JM, Chang CM, Lu TP, Chuang EY, Tai YC, Cheng C, Lin HY , Wu MS",Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson's disease,Journal of neuroinflammation,2019,Experiment 2,Japan,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Participants with Parkinson's Disease with non-tremor subtypes,Participants with Parkinson's Disease with tremor subtypes,Participants with Parkinson's Disease with tremor subtypes.,33,47,Individuals currently taking antibiotics or probiotic supplements within 3 months of sample collection,16S,34,Illumina,LEfSe,0.05,NA,2,"age,sex","age,diet,sex",NA,increased,NA,NA,NA,increased,Signature 2,Figure 2A.,22 January 2022,Fcuevas3,Fcuevas3,Taxonomic differences of fecal microbiota in PD and control groups,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|g__Mogibacterium,k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flavobacterium,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes",2|1239|186801|186802|543314|86331;2|976|117743|200644|49546|237;2|1224|28221|213115|194924|872;2|201174|1760|85009|31957|1743;2|1224|28216|80840|119060|106589;2|1224|28216|80840|995019|40544;2|1224|28216|80840|506;2|976|200643;2|976|200643|171549;2|976,Complete,NA
Study 606,case-control,31440136,10.3389/fnins.2019.00839,NA,"Gorecki AM, Preskey L, Bakeberg MC, Kenna JE, Gildenhuys C, MacDougall G, Dunlop SA, Mastaglia FL, Akkari PA, Koengten F , Anderton RS",Altered Gut Microbiome in Parkinson's Disease and the Influence of Lipopolysaccharide in a Human α-Synuclein Over-Expressing Mouse Model,Frontiers in neuroscience,2019,Experiment 1,Australia,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with idiopathic Parkinson's Disease and mild symptoms.,"All patients were confirmed to have idiopathic Parkinson’s disease by a movement disorders neurologist, in accordance with the United Kingdom Brain Bank criteria and mild symptoms.",7,7,No history of antibiotic or non-steroidal anti-inflammatory drug use in the previous 3 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1.,22 January 2022,Fcuevas3,Fcuevas3,"Mean class abundance in people with Parkinson’s disease and healthy controls, specifically control vs. mild PD.",increased,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria,2|1224|1236,Complete,NA
Study 606,case-control,31440136,10.3389/fnins.2019.00839,NA,"Gorecki AM, Preskey L, Bakeberg MC, Kenna JE, Gildenhuys C, MacDougall G, Dunlop SA, Mastaglia FL, Akkari PA, Koengten F , Anderton RS",Altered Gut Microbiome in Parkinson's Disease and the Influence of Lipopolysaccharide in a Human α-Synuclein Over-Expressing Mouse Model,Frontiers in neuroscience,2019,Experiment 2,Australia,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Participants with mild PD,Participants with severe PD,"All patients were confirmed to have idiopathic Parkinson’s disease by a movement disorders neurologist, in accordance with the United Kingdom Brain Bank criteria and severe symptoms.",7,7,No history of antibiotic or non-steroidal anti-inflammatory drug use in the previous 3 months.,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1.,22 January 2022,Fcuevas3,Fcuevas3,Mean class abundance in people with mild and severe Parkinson’s disease.,increased,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,2|74201|203494,Complete,NA
Study 607,case-control,32517799,10.1186/s12915-020-00775-7,NA,"Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R , Thiele I",Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions,BMC biology,2020,Experiment 1,Luxembourg,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with typical PD,"PD patients were defined as typical PD, according to the inclusion criteria by the United Kingdom Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.",162,147,"Excluded control persons who took dopaminergic medications (n = 5; intake for a different than anti-PD indication) and individuals who reported to have taken antibiotics in the last 6 months (controls: n = 20, PD: n = 13).",16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,age,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 2.,22 January 2022,Fcuevas3,Fcuevas3,Boxplots of seven significantly changed species in PD vs. controls (FDR < 0.05).,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella|s__Christensenella minuta,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus bromii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|74201|203494|48461|1647988|239934|239935;2|1239|186801|186802|216572|244127|169435;2|1239|186801|186802|990719|990721|626937;2|1239|186801|186802|216572|1263|40518;2|1239|186801|186802|186803|2316020|33039,Complete,NA
Study 607,case-control,32517799,10.1186/s12915-020-00775-7,NA,"Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R , Thiele I",Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions,BMC biology,2020,Experiment 1,Luxembourg,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with typical PD,"PD patients were defined as typical PD, according to the inclusion criteria by the United Kingdom Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.",162,147,"Excluded control persons who took dopaminergic medications (n = 5; intake for a different than anti-PD indication) and individuals who reported to have taken antibiotics in the last 6 months (controls: n = 20, PD: n = 13).",16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,age,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 2.,22 January 2022,Fcuevas3,Fcuevas3,Boxplots of seven significantly changed species in PD vs. controls (FDR < 0.05).,decreased,"k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter|s__Turicibacter sanguinis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia|s__Roseburia intestinalis",2|1239|526524|526525|2810281|191303|154288;2|1239|186801|186802|186803|841|166486,Complete,NA
Study 607,case-control,32517799,10.1186/s12915-020-00775-7,NA,"Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R , Thiele I",Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions,BMC biology,2020,Experiment 2,Luxembourg,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with typical PD,"PD patients were defined as typical PD, according to the inclusion criteria by the United Kingdom Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.",162,147,"Excluded control persons who took dopaminergic medications (n = 5; intake for a different than anti-PD indication) and individuals who reported to have taken antibiotics in the last 6 months (controls: n = 20, PD: n = 13).",16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,age,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 3.,22 January 2022,Fcuevas3,Fcuevas3,Boxplots of eight significantly changed genera in PD vs. controls (FDR < 0.05).,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Christensenellaceae|g__Christensenella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1239|186801|186802|990719|990721;2|1239|186801|186802|216572|244127;2|1239|91061|186826|33958|1578;2|1224|28221|213115|194924|35832;2|74201|203494|48461|1647988|239934;2|1239|91061|186826|1300|1301,Complete,NA
Study 607,case-control,32517799,10.1186/s12915-020-00775-7,NA,"Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R , Thiele I",Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions,BMC biology,2020,Experiment 2,Luxembourg,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Healthy controls,Participants with typical PD,"PD patients were defined as typical PD, according to the inclusion criteria by the United Kingdom Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.",162,147,"Excluded control persons who took dopaminergic medications (n = 5; intake for a different than anti-PD indication) and individuals who reported to have taken antibiotics in the last 6 months (controls: n = 20, PD: n = 13).",16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,age,NA,unchanged,NA,NA,NA,increased,Signature 2,Figure 3.,22 January 2022,Fcuevas3,Fcuevas3,Boxplots of eight significantly changed genera in PD vs. controls (FDR < 0.05),decreased,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Turicibacteraceae|g__Turicibacter,2|1239|526524|526525|2810281|191303,Complete,NA
Study 607,case-control,32517799,10.1186/s12915-020-00775-7,NA,"Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R , Thiele I",Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions,BMC biology,2020,Experiment 3,Luxembourg,Homo sapiens,feces,UBERON:0001988,Parkinson's disease,MONDO:0005180,Female patients with PD,Male patients with PD,Female/male patients with PD according to United Kingdom Parkinson’s Disease Society Brain Bank Clinical Diagnostic Criteria.,57,105,"Excluded control persons who took dopaminergic medications (n = 5; intake for a different than anti-PD indication) and individuals who reported to have taken antibiotics in the last 6 months (controls: n = 20, PD: n = 13).",16S,34,Illumina,Linear Regression,0.05,NA,NA,NA,age,NA,unchanged,NA,NA,NA,increased,Signature 1,Figure 4,22 January 2022,Fcuevas3,Fcuevas3,Genus alterations in PDs in the context of basic covariates and clinical variables.,increased,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,2|976|200643|171549|171552|577309,Complete,NA
Study 609,case-control,33362375,10.3748/wjg.v26.i45.7173,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723673/,"Sun XZ, Zhao DY, Zhou YC, Wang QQ, Qin G , Yao SK",Alteration of fecal tryptophan metabolism correlates with shifted microbiota and may be involved in pathogenesis of colorectal cancer,World journal of gastroenterology,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,Healthy Controls (HC),CRC,Patients with colorectal neoplastic lesions where tumors were removed and pathologically diagnosed with adenomatous polyp or colorectal adenocarcinoma; ages of participants ranged from 18-80.,38,79,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,Signature 1,Figure 4C,31 January 2022,Itslanapark,"Itslanapark,Chloe",Linear discriminant analysis effect size analysis of fecal bacterial of colorectal cancer patients and HCs was used to represent which taxa were increased in CRC patients and which were enriched in healthy controls. Taxa enriched in HCs are indicated with a negative LDA score and taxa enriched in the CRC group are indicated with a positive LDA score.,increased,"k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia,k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Firmicutes|c__Bacilli,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidetes,k__Bacteria|p__Bacteroidetes|c__Bacteroidia,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella,k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Verrucomicrobia,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae,k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales",2|74201|203494|48461|1647988|239934;2|1224|28211;2|1239|186801|186802|186803|207244;2|1239|91061;2|976|200643|171549;2|976;2|976|200643;2|201174|1760|85007|1653;2|201174|1760|85007|1653|1716;2|201174|84998|1643822|1643826|84111;2|1224|1236|91347;2|1224|1236|91347|543;2|1239|91061|186826|81852;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|1940338;2|1239|91061|186826;2|1239|91061|186826|33958|1578;2|1239|909932|1843489|31977|906;2|976|200643|171549|2005525|375288;2|1224|28216|80840|995019|577310;2|1239|1737404|1737405|1570339|543311;2|1239|186801|186802|186804|1257;2|976|200643|171549|171551|836;2|1239|909932|909929|1843491|970;2|1224|28216|80840|995019|40544;2|74201;2|74201|203494|48461|203557;2|74201|203494;2|74201|203494|48461,Complete,Chloe
Study 609,case-control,33362375,10.3748/wjg.v26.i45.7173,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723673/,"Sun XZ, Zhao DY, Zhou YC, Wang QQ, Qin G , Yao SK",Alteration of fecal tryptophan metabolism correlates with shifted microbiota and may be involved in pathogenesis of colorectal cancer,World journal of gastroenterology,2020,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,Healthy Controls (HC),CRC,Patients with colorectal neoplastic lesions where tumors were removed and pathologically diagnosed with adenomatous polyp or colorectal adenocarcinoma; ages of participants ranged from 18-80.,38,79,4 weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,sex",NA,NA,NA,unchanged,NA,NA,NA,Signature 2,Figure 4c,10 February 2022,Itslanapark,"Itslanapark,Fatima,Chloe",Linear discriminant analysis effect size analysis of fecal bacterial of colorectal cancer patients and HCs was used to represent which taxa were increased in CRC patients and which were enriched in healthy controls. Taxa enriched in HCs are indicated with a negative LDA score and taxa enriched in the CRC group are indicated with a positive LDA score.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerofilum,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Asaccharobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Butyricicoccus,k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Fusobacteria,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales,k__Bacteria|p__Fusobacteria|c__Fusobacteriia,k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|g__Gemmiger,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Tyzzerella",2|1239|186801|186802|216572|52784;2|201174|84998|1643822|1643826|553372;2|1239|186801|186802|186803|572511;2|1239|186801|186802|31979|580596;2|1239|186801;2|1239|186801|186802|1898207;2|201174|84998|84999|84107|102106;2|1239|186801|186802|216572|216851;2|1239;2|1239|186801|186802|186803|1407607;2|32066;2|32066|203490|203491|203492;2|32066|203490|203491;2|32066|203490;2|32066|203490|203491|203492|848;2|1239|186801|186802|204475;2|1239|186801|186802|186803;2|1239|186801|186802|186804|1501226;2|1239|186801|186802|186803|841;2|1239|186801|186802|186803|1506577,Complete,Chloe
Study 612,"case-control,meta-analysis",27171425,10.1371/journal.pone.0155362,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4865240/,"Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P , Sinha R",Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing,PloS one,2016,Experiment 1,"France,United States of America",Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,control subjects,CRC cases,pre treatment colorectal cancer cases,140,105,NA,16S,NA,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"body mass index,sex","age,body mass index,sex",NA,NA,NA,NA,NA,NA,Signature 1,Table 3,3 February 2022,Itslanapark,Itslanapark,Comparison of significant relative abundance of taxa detected in 16S rRNA gene sequencing data with whole-genome shotgun sequencing data.,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae",2|1239|186801;2|1239|186801|186802|186803|33042;2|1239|186801|186802|186803,Complete,NA
Study 614,case-control,31611994,10.3892/ol.2019.10841,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781660/,"Sheng Q, Du H, Cheng X, Cheng X, Tang Y, Pan L, Wang Q , Lin J",Characteristics of fecal gut microbiota in patients with colorectal cancer at different stages and different sites,Oncology letters,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,Healthy Controls,CRC,"The CRC patients were selected according to the criteria of no other health complications, no family history of CRC or recurrence of CRC, and no radiotherapy and chemotherapy prior to surgical resection. Patients were then classified according to postoperative clinical data using the tumor-node-metastasis (TNM) staging system for malignant tumors.",30,67,3 months,16S,34,Illumina,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 1,Figure 5,21 February 2022,Itslanapark,Itslanapark,Comparison of relative abundance of genera in fecal samples of patients with CRC and healthy controls.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoanaerobaculum",2|976|200643|171549|171552|838;2|201174|84998|84999|84107|102106;2|976|200643|171549|1853231|283168;2|1239|186801|186802|186804|1257;2|1239|186801|186802|186803|1164882,Complete,Rimsha
Study 614,case-control,31611994,10.3892/ol.2019.10841,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781660/,"Sheng Q, Du H, Cheng X, Cheng X, Tang Y, Pan L, Wang Q , Lin J",Characteristics of fecal gut microbiota in patients with colorectal cancer at different stages and different sites,Oncology letters,2019,Experiment 1,China,Homo sapiens,feces,UBERON:0001988,colorectal cancer,EFO:0005842,Healthy Controls,CRC,"The CRC patients were selected according to the criteria of no other health complications, no family history of CRC or recurrence of CRC, and no radiotherapy and chemotherapy prior to surgical resection. Patients were then classified according to postoperative clinical data using the tumor-node-metastasis (TNM) staging system for malignant tumors.",30,67,3 months,16S,34,Illumina,"Kruskall-Wallis,Mann-Whitney (Wilcoxon)",0.05,FALSE,NA,"age,sex",NA,NA,increased,unchanged,increased,NA,NA,Signature 2,Figure 5,21 February 2022,Itslanapark,Itslanapark,Comparison of relative abundance of genera in fecal samples of patients with CRC and healthy controls.,decreased,"k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter",2|1224|1236|91347|543|413496;2|1224|1236|91347|543|1940338;2|1239|186801|186802|216572|44748,Complete,Rimsha
Study 617,prospective cohort,28112736,10.1038/nm.4272,NA,"Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD , Aagaard KM",Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery,Nature medicine,2017,Experiment 1,United States of America,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,NA,105,52,NA,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,Experiment 1,Austria,Homo sapiens,NA,NA,NA,NA,"Control, mild, and moderate dementia",Severe dementia,MMSE 0-9: The Mini-Mental State Examination [19] and the clock drawing test [20] were used to quantify cognitive function. We classified cognitive dysfunction according to the German S3-guideline on Dementia 2016 as MMSE 0–9: severe; MMSE 10–19: moderate; MMSE 20–26: mild; MMSE 27–30: no dementia [21].,NA,NA,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4A,28 March 2022,Lwaldron,Lwaldron,4a Features selected by Linear discriminant analysis Effect Size (LEfSe) to discriminate between dementia different stages of cognitive dysfunction and controls. Right-hand bar showing biomarkers of severe dementia.,increased,"k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides uniformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Eisenbergiella,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Hungatella,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Sellimonas,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Sellimonas|s__Sellimonas sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Syntrophococcus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Clostridium] leptum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] nodatum,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus thermophilus,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaeromassilibacillus|s__Anaeromassilibacillus sp. Marseille-P3371,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Oscillospiraceae bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium sp. UBA1819",2|976|200643|171549|815|816|2778071;2|976|200643|171549|815|816|820;2|1239|186801|186802|186803|2719313|1531;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|216572|244127;2|1239|186801|186802|186803|1432051;2|1224|1236|91347|543;2|1239|186801|186802|31979|1649459;2|1239|186801|186802|216572|459786;2|1239|186801|186802|216572|1905344|1550024;2|1239|186801|186802|186803|1769710;2|1239|186801|186802|186803|1769710|2021466;2|1239|91061|186826|1300|1301|1304;2|1239|186801|186802|186803|84036;2|1239|186801|186802|216572|1535;2|1239|186801|186802|543314|35518;2|1239|186801|186802|186803|2316020|33039;2|1239|91061|186826|1300|1301|1308;2|201174|1760|2037|2049;2|1224|1236|91347;2|201174|1760|2037;2|1239|186801|186802|216572|1924093|1944639;2|1239|186801|186802|216572|2485925;2|1239|186801|186802|216572|216851|1946507,Complete,Lwaldron
Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,Experiment 2,Austria,Homo sapiens,feces,UBERON:0001988,Dementia,MONDO:0001627,Controls without cognitive impairments,Patients with dementia,"Participants with any level of dementia (mild, moderate, severe).",18,23,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,3a,15 March 2022,Maryemzaki,"Maryemzaki,Lwaldron",Differentially abundant taxa between any level of dementia vs controls,increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes hadrus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Enterocloster|s__Enterocloster clostridioformis,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola dorei,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1239|186801|186802|186803|207244|649756;2|1239|186801|186802|1898207;2|1239|186801|186802|186803|2719313|1531;2|1239|186801|186802|186803|1506553;2|976|200643|171549|815|909656|357276;2|1239|186801|186802|186803|2316020|33039,Complete,Lwaldron
Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,Experiment 2,Austria,Homo sapiens,feces,UBERON:0001988,Dementia,MONDO:0001627,Controls without cognitive impairments,Patients with dementia,"Participants with any level of dementia (mild, moderate, severe).",18,23,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 2,Figure 3a,15 March 2022,Maryemzaki,"Maryemzaki,Lwaldron",Differentially abundant taxa between any level of dementia vs controls,decreased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter sp.,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MC_35,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__uncultured Erysipelotrichaceae bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1239|186801|186802|186803|1766253;2|1239|186801|186802|186803|1766253|2021311;2|1239|186801|186802|186803|1755642;2|1239|186801|186802|186803|877420;2|1239|526524|526525|128827|331630;2|1239|186801|186802|186803|297314;2|1239|186801|186802|216572|707003,Complete,Lwaldron
Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,Experiment 3,Austria,Homo sapiens,NA,NA,NA,NA,"control, mild, and severe dementia",moderate dementia,MMSE 10-19: The Mini-Mental State Examination [19] and the clock drawing test [20] were used to quantify cognitive function. We classified cognitive dysfunction according to the German S3-guideline on Dementia 2016 as MMSE 0–9: severe; MMSE 10–19: moderate; MMSE 20–26: mild; MMSE 27–30: no dementia [21].,NA,NA,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4A (moderate),28 March 2022,Lwaldron,Lwaldron,"Moderate vs control, mild, and severe dementia",increased,"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus amylovorus,k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides sp.,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae,k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Firmicutes|c__Bacilli",2|1239|91061|186826|33958|1578|1604;2|201174|84998|84999|84107|102106|74426;2|976|200643|171549|815|816|29523;2|1239|91061|186826|33958|1578;2|1239|186801|186802|216572|1508657;2|1239|91061|186826|81850;2|1239|91061|186826|33958;2|1239|91061|186826;2|1239|91061,Complete,Lwaldron
Study 618,case-control,32690030,10.1186/s12877-020-01644-2,NA,"Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R , Horvath A","Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study",BMC geriatrics,2020,Experiment 4,Austria,Homo sapiens,NA,NA,NA,NA,"control, moderate, and severe dementia",mild dementia,MMSE 20-26: The Mini-Mental State Examination [19] and the clock drawing test [20] were used to quantify cognitive function. We classified cognitive dysfunction according to the German S3-guideline on Dementia 2016 as MMSE 0–9: severe; MMSE 10–19: moderate; MMSE 20–26: mild; MMSE 27–30: no dementia [21].,NA,NA,4 weeks,16S,12,Illumina,LEfSe,0.05,FALSE,NA,"age,sex",NA,NA,NA,unchanged,unchanged,NA,NA,Signature 1,Figure 4A (mild),28 March 2022,Lwaldron,Lwaldron,"These are ""biomarkers"" of mild dementia that are lower abundance in controls, moderate, and severe dementia.",increased,"k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium|s__Faecalibacterium prausnitzii,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens",2|1239|186801|186802|216572|216851|853;2|1239|186801|186802|216572|216851;2|1239|186801|186802|186803|1407607;2|1239|186801|186802|186803|28050|39485,Complete,Lwaldron
Study 619,"cross-sectional observational, not case-control",20566857,10.1073/pnas.1002601107,https://pubmed.ncbi.nlm.nih.gov/20566857/,"Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N , Knight R",Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns,Proceedings of the National Academy of Sciences of the United States of America,2010,Experiment 1,NA,Homo sapiens,meconium,UBERON:0007109,cesarean section,EFO:0009636,vaginal delivery,C-section,NA,NA,NA,NA,16S,2,Roche454,ANOSIM,0.001,FALSE,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA