From 7a76538763f98c268007b8be049ee1b8d280dab5 Mon Sep 17 00:00:00 2001 From: GitHub Actions Bot Date: Mon, 21 Oct 2024 05:00:36 +0000 Subject: [PATCH] Hourly export update --- bugsigdb_signatures_mixed_metaphlan.gmt | 4 ++-- bugsigdb_signatures_mixed_ncbi.gmt | 4 ++-- bugsigdb_signatures_mixed_taxname.gmt | 4 ++-- file_size.csv | 1 + full_dump.csv | 8 ++++---- 5 files changed, 11 insertions(+), 10 deletions(-) diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt index 66bb1a665..e6853807b 100644 --- a/bugsigdb_signatures_mixed_metaphlan.gmt +++ b/bugsigdb_signatures_mixed_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-20_22:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-21_04:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus k__Bacteria|p__Cyanobacteriota bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae @@ -5370,7 +5370,7 @@ bsdb:1106/5/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-non bsdb:1106/5/3_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_DOWN NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus k__Bacteria|p__Pseudomonadota k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae bsdb:1106/6/1_Breastfeeding-duration:Non-Exclusive-Breastfeeding-(Non-EBF)_vs_Exclusive-BreastFeeding-(EBF)_UP NA k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella bsdb:1106/7/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales k__Bacteria|p__Bacteroidota|c__Bacteroidia -bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP NA k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae k__Bacteria|p__Bacillota k__Bacteria|p__Bacillota|c__Clostridia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae +bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP NA k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia bsdb:1108/1/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae bsdb:1108/2/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP NA k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae bsdb:1108/2/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN NA k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt index 29ad1b282..e1a30d134 100644 --- a/bugsigdb_signatures_mixed_ncbi.gmt +++ b/bugsigdb_signatures_mixed_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-20_22:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-21_04:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA 91061 1236 1654 1716 1301 162289 189330 33024 40544 2037 2049 506 186826 1300 31977 91347 1653 57037 1386 186817 bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA 100883 1117 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 207244 57037 @@ -5370,7 +5370,7 @@ bsdb:1106/5/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-non bsdb:1106/5/3_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_DOWN NA 244127 33024 583 1224 1279 543 bsdb:1106/6/1_Breastfeeding-duration:Non-Exclusive-Breastfeeding-(Non-EBF)_vs_Exclusive-BreastFeeding-(EBF)_UP NA 904 816 1485 33042 1730 906 29465 bsdb:1106/7/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_UP NA 816 1485 1730 186803 906 31979 186802 200643 -bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP NA 102106 84108 84999 1268 1239 186801 3085636 186803 +bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP NA 102106 84999 1268 84108 bsdb:1108/1/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN NA 1485 31979 bsdb:1108/2/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP NA 1843491 bsdb:1108/2/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN NA 1501226 1485 diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt index 1dcdabe3e..38c4fda79 100644 --- a/bugsigdb_signatures_mixed_taxname.gmt +++ b/bugsigdb_signatures_mixed_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-20_22:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-21_04:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA Bacilli Gammaproteobacteria Actinomyces Corynebacterium Streptococcus Peptoniphilus Dorea Phascolarctobacterium Sutterella Actinomycetales Actinomycetaceae Alcaligenaceae Lactobacillales Streptococcaceae Veillonellaceae Enterobacterales Corynebacteriaceae Lacticaseibacillus zeae Bacillus Bacillaceae bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA Coprobacillus Cyanobacteriota bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Anaerostipes Lacticaseibacillus zeae @@ -5370,7 +5370,7 @@ bsdb:1106/5/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-non bsdb:1106/5/3_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_DOWN NA Anaerotruncus Phascolarctobacterium Proteus Pseudomonadota Staphylococcus Enterobacteriaceae bsdb:1106/6/1_Breastfeeding-duration:Non-Exclusive-Breastfeeding-(Non-EBF)_vs_Exclusive-BreastFeeding-(EBF)_UP NA Acidaminococcus Bacteroides Clostridium Coprococcus Eubacterium Megasphaera Veillonella bsdb:1106/7/1_Breastfeeding-duration:Reduced-exclusivity-of-beast-feeding-to-none-breastfeeding_vs_Increasing-Exclusive-Breast-Feeding-(EBF)_UP NA Bacteroides Clostridium Eubacterium Lachnospiraceae Megasphaera Clostridiaceae Eubacteriales Bacteroidia -bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP NA Collinsella Slackia Coriobacteriales Micrococcaceae Bacillota Clostridia Lachnospirales Lachnospiraceae +bsdb:1108/1/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP NA Collinsella Coriobacteriales Micrococcaceae Slackia bsdb:1108/1/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN NA Clostridium Clostridiaceae bsdb:1108/2/1_HIV-infection:HIV---infected_vs_HIV---uninfected_UP NA Selenomonadaceae bsdb:1108/2/2_HIV-infection:HIV---infected_vs_HIV---uninfected_DOWN NA Romboutsia Clostridium diff --git a/file_size.csv b/file_size.csv index e3b5573e7..5effef631 100644 --- a/file_size.csv +++ b/file_size.csv @@ -488,3 +488,4 @@ "2024-10-21_02:23_UTC" "4082" "4891" "4082" "4891" "4082" "4891" "5526" "5526" "5526" "2325" "2325" "2325" "2325" "2325" "2325" "3724" "6618" "5981" "1357" "2024-10-21_03:07_UTC" "4082" "4891" "4082" "4891" "4082" "4891" "5526" "5526" "5526" "2325" "2325" "2325" "2325" "2325" "2325" "3724" "6618" "5981" "1357" "2024-10-21_03:58_UTC" "4082" "4891" "4082" "4891" "4082" "4891" "5526" "5526" "5526" "2325" "2325" "2325" "2325" "2325" "2325" "3724" "6618" "5981" "1357" +"2024-10-21_04:58_UTC" "4082" "4891" "4082" "4891" "4082" "4891" "5526" "5526" "5526" "2325" "2325" "2325" "2325" "2325" "2325" "3724" "6618" "5981" "1357" diff --git a/full_dump.csv b/full_dump.csv index d2a0046e8..eb63d0b09 100644 --- a/full_dump.csv +++ b/full_dump.csv @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-20_22:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-21_04:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org BSDB ID,Study,Study design,PMID,DOI,URL,Authors list,Title,Journal,Year,Keywords,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 bsdb:1/1/1,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,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,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+ S4,10 January 2021,Levi Waldron,WikiWorks,"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__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|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|3085636|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 bsdb:1/1/2,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,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,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+ S4,10 January 2021,Levi Waldron,WikiWorks,"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__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Cyanobacteriota",2|1239|526524|526525|2810280|100883;2|1117,Complete,Shaimaa Elsafoury @@ -6382,7 +6382,7 @@ bsdb:1106/6/1,Study 1106,meta-analysis,30301893,10.1038/s41467-018-06473-x,https bsdb:1106/7/1,Study 1106,meta-analysis,30301893,10.1038/s41467-018-06473-x,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec1title,"Ho NT, Li F, Lee-Sarwar KA, Tun HM, Brown BP, Pannaraj PS, Bender JM, Azad MB, Thompson AL, Weiss ST, Azcarate-Peril MA, Litonjua AA, Kozyrskyj AL, Jaspan HB, Aldrovandi GM , Kuhn L",Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations,Nature communications,2018,NA,Experiment 7,United States of America,Homo sapiens,Feces,UBERON:0001988,Breastfeeding duration,EFO:0006864,Increasing Exclusive Breast Feeding (EBF),Reduced exclusivity of beast feeding to none breastfeeding,NA,12,8,NA,16S,12,Roche454,ANOSIM,0.005,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,increased,Signature 1,Table 4,6 October 2024,Shulamite,Shulamite,Meta-analysis of six studies without data from North Carolina study for gut bacterial taxa with differential relative abundances between non-exclusivelybreastfed vs. exclusively breastfed infants ≤6 months of age (sensitivity analysis).,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|976|200643|171549|815|816;2|1239|186801|186802|31979|1485;2|1239|186801|186802|186806|1730;2|1239|186801|3085636|186803;2|1239|909932|1843489|31977|906;2|1239|186801|186802|31979;2|1239|186801|186802;2|976|200643,Complete,NA bsdb:1107/1/2,Study 1107,prospective cohort,29659737,https://doi.org/10.1093/cid/ciy265,NA,"Wood LF, Brown BP, Lennard K, Karaoz U, Havyarimana E, Passmore JS, Hesseling AC, Edlefsen PT, Kuhn L, Mulder N, Brodie EL, Sodora DL , Jaspan HB",Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 1,South Africa,Homo sapiens,"Mouth mucosa,Blood,Gut wall","UBERON:0003729,UBERON:0000178,UBERON:0000328","HIV mother to child transmission,Susceptibility to HIV infection","EFO:0004595,MONDO:0004951",exclusively breastfed (EBF) infants,nonexclusively breastfed (NEBF) infants,"Nonexclusively breastfed (NEBF) infants: This group includes infants who were breastfed but also received other foods, liquids, or traditional medicines in addition to breast milk",44,55,"No exclusion mentioned in this study. However, it tracked interim antibiotic use during the follow-up visits and reported that antibiotic use was minimal and not significantly different between the exclusively breastfed (EBF) and nonexclusively breastfed (NEBF) groups. Thus, antibiotic use did not significantly affect the study's outcomes",16S,4,Illumina,PERMANOVA,0.05,FALSE,2,NA,"age,sex",NA,NA,NA,NA,NA,NA,Signature 2,"Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants. Clinical Infectious Diseases, 2018",20 October 2024,NA,NA,"this study represents the gut microbial composition changes observed in nonexclusively breastfed (NEBF) infants compared to exclusively breastfed (EBF) infants. The microbial differences were associated with increased peripheral T-cell activation and altered mucosal gene expression, which may impact HIV susceptibility. The study highlights key taxa linked to immune activation and gut health in the context of different feeding practices",increased,NA,NA,Complete,NA bsdb:1107/2/NA,Study 1107,prospective cohort,29659737,https://doi.org/10.1093/cid/ciy265,NA,"Wood LF, Brown BP, Lennard K, Karaoz U, Havyarimana E, Passmore JS, Hesseling AC, Edlefsen PT, Kuhn L, Mulder N, Brodie EL, Sodora DL , Jaspan HB",Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants,Clinical infectious diseases : an official publication of the Infectious Diseases Society of America,2018,NA,Experiment 2,South Africa,Homo sapiens,"Mouth mucosa,Blood,Gut wall","UBERON:0003729,UBERON:0000178,UBERON:0000328","HIV mother to child transmission,Susceptibility to HIV infection","EFO:0004595,MONDO:0004951",exclusively breastfed (EBF) infants,nonexclusively breastfed (NEBF) infants,"Nonexclusively breastfed (NEBF) infants: This group includes infants who were breastfed but also received other foods, liquids, or traditional medicines in addition to breast milk",44,55,"The study did not explicitly exclude infants based on antibiotic use. However, it tracked interim antibiotic use during the follow-up visits and reported that antibiotic use was minimal and not significantly different between the exclusively breastfed (EBF) and nonexclusively breastfed (NEBF) groups. Thus, antibiotic use did not significantly affect the study's outcomes",16S,4,Illumina,PERMANOVA,0.05,FALSE,2,NA,"age,antibiotic,sex",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -bsdb:1108/1/1,Study 1108,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma PT, Chandiwana P, Wyss J, Mazhandu AJ, Jordi SBU, Gutsire R, Katsidzira L, Yilmaz B, Misselwitz B , Duri K",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 weeks postpartum.,48,25,NA,16S,56,Ion Torrent,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,"Figure 6A, Table 3",2 October 2024,Paavni Goyal,Paavni Goyal,Certain bacterial taxa were found to have increased abundance in HIV-infected women.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Bacillota,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|201174|84998|84999|84107|102106;2|201174|84998|1643822|1643826|84108;2|201174|84998|84999;2|201174|1760|85006|1268;2|1239;2|1239|186801;2|1239|186801|3085636;2|1239|186801|3085636|186803,Complete,NA +bsdb:1108/1/1,Study 1108,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma PT, Chandiwana P, Wyss J, Mazhandu AJ, Jordi SBU, Gutsire R, Katsidzira L, Yilmaz B, Misselwitz B , Duri K",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 weeks postpartum.,48,25,NA,16S,56,Ion Torrent,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 6A,2 October 2024,Paavni Goyal,"Paavni Goyal,KateRasheed",Certain bacterial taxa were found to have increased abundance in HIV-infected women.,increased,"k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia",2|201174|84998|84999|84107|102106;2|201174|84998|84999;2|201174|1760|85006|1268;2|201174|84998|1643822|1643826|84108,Complete,NA bsdb:1108/1/2,Study 1108,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma PT, Chandiwana P, Wyss J, Mazhandu AJ, Jordi SBU, Gutsire R, Katsidzira L, Yilmaz B, Misselwitz B , Duri K",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 1,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 weeks postpartum.,48,25,NA,16S,56,Ion Torrent,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,"Figure 6A, Table 3",2 October 2024,Paavni Goyal,Paavni Goyal,Significant decrease in the HIV-infected group at 6weeks postpartum.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae",2|1239|186801|186802|31979|1485;2|1239|186801|186802|31979,Complete,NA bsdb:1108/2/1,Study 1108,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma PT, Chandiwana P, Wyss J, Mazhandu AJ, Jordi SBU, Gutsire R, Katsidzira L, Yilmaz B, Misselwitz B , Duri K",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 2,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 months postpartum.,42,23,NA,16S,56,Ion Torrent,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 1,Figure 6b,20 October 2024,Aleru Divine,Aleru Divine,Differentially abundant taxa significantly associated with HIV infection status at 6 months postpartum.,increased,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae,2|1239|909932|909929|1843491,Complete,NA bsdb:1108/2/2,Study 1108,time series / longitudinal observational,38045684,10.3389/fimmu.2023.1280262,NA,"Munjoma PT, Chandiwana P, Wyss J, Mazhandu AJ, Jordi SBU, Gutsire R, Katsidzira L, Yilmaz B, Misselwitz B , Duri K",Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance,Frontiers in immunology,2023,"HIV, fecal calprotectin, gut microbiota, lactating women, microbial translocation, resource limited setting, systemic inflammation",Experiment 2,Zimbabwe,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,HIV - uninfected,HIV - infected,The HIV-infected group consists of HIV-infected lactating women who were followed up at 6 months postpartum.,42,23,NA,16S,56,Ion Torrent,MaAsLin2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,unchanged,NA,NA,Signature 2,Figure 6b,20 October 2024,NA,NA,Differentially abundant taxa significantly associated with HIV infection status at 6 months postpartum.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|1239|186801|3082720|186804|1501226;2|1239|186801|186802|31979|1485,Complete,NA @@ -6454,8 +6454,8 @@ medications within 48 h before selection; BMI > 30; having a history of inflammatory bowel disease (IBD); having active inflammation affecting the gastro intestines.",16S,34,Illumina,LEfSe,3,TRUE,0.05,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 6,"Additional file 4, figure S4 d",11 October 2024,NA,NA,Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and healthy controls (Control) group.,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerobutyricum|s__Anaerobutyricum hallii,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__Christensenellaceae bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ventriosum,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 10-1,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium NK4A136,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__Ruminococcaceae bacterium UCG-005,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus albus",2|1239|186801|3085636|186803|1766253|39491;2|976|200643|171549|171550|239759;2|1239|186801|3085636|186803|2569097|39488;2|1239|186801|3085636|186803|207244;2|976|200643|171549|2005519|397864;2|201174|1760|85004|31953|1678;2|1239|186801|3085636|186803|572511;2|1239|186801|3082768|990719|2054177;2|1239|186801|3085636|186803|33042|116085;2|1239|186801|3085636|186803|189330;2|1239|526524|526525|128827;2|1239|186801|186802|186806|1730|290054;2|1239|186801|186802|186806|1730|42322;2|1239|186801|186802|186806|1730|39496;2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|1407607;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1235800;2|1239|186801|3085636|186803|877420;2|976|200643|171549|171552|577309;2|976|200643|171549|171552|838|28125;2|1239|186801|3085636|186803|841;2|1239|186801|186802|216572|3068309;2|1239|186801|186802|216572|1263|1264,Complete,NA bsdb:1118/3/1,Study 1118,case-control,33407128,https://doi.org/10.1186/s12866-020-02074-1,NA,"Xie Y, Sun J, Wei L, Jiang H, Hu C, Yang J, Huang Y, Ruan B , Zhu B",Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals,BMC microbiology,2021,"Gut microbiota, HAART, HIV-1, Immune activation, Immunological non-responders, Immunological responders",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,immunological non-responders (INR) HIV infected individual,Immunological Responder (IR) HIV infected individual,Immunological Responder HIV infected individual (IR) was defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All HIV-positive subjects were on two nucleoside reverse transcriptase inhibitors (NRTIs) + nonnucleoside reverse transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz (EFV) or Lopinavir/ritonavir (LPV/r).,30,28,6 months.,16S,34,Illumina,LEfSe,3,TRUE,0.05,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 1,"Additional file 4, figure S4 f",11 October 2024,NA,NA,Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and Immunological Responder (IR) HIV infected individual.,increased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Dielma,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.",2|1239|526524|526525|128827|123375;2|1239|526524|526525|128827|1472649;2|1239|186801|3085636|186803|572511;2|1224|1236|91347|543|1940338,Complete,NA bsdb:1118/3/2,Study 1118,case-control,33407128,https://doi.org/10.1186/s12866-020-02074-1,NA,"Xie Y, Sun J, Wei L, Jiang H, Hu C, Yang J, Huang Y, Ruan B , Zhu B",Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals,BMC microbiology,2021,"Gut microbiota, HAART, HIV-1, Immune activation, Immunological non-responders, Immunological responders",Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,immunological non-responders (INR) HIV infected individual,Immunological Responder (IR) HIV infected individual,Immunological Responder HIV infected individual (IR) was defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All HIV-positive subjects were on two nucleoside reverse transcriptase inhibitors (NRTIs) + nonnucleoside reverse transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz (EFV) or Lopinavir/ritonavir (LPV/r).,30,28,6 months.,16S,34,Illumina,LEfSe,3,TRUE,0.05,"age,body mass index",NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,"Additional file 4, figure S4 f",11 October 2024,NA,NA,Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and Immunological Responder (IR) HIV infected,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminiclostridium|s__Ruminiclostridium sp.",2|1239|186801|3085636|186803|207244;2|1239|186801|186802|186806|1730|42322;2|976|200643|171549|171552|1283313;2|1239|186801|186802|186806|1730;2|1239|186801|186802|216572|1508657|2053608,Complete,NA -bsdb:1121/1/1,Study 1121,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu DD, Darby M, Havyarimana E, Brown BP, Horsnell W , Jaspan HB",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 1,South Africa,Mus musculus,Feces,UBERON:0001988,Intestinal helminthiasis,MONDO:0024271,Pregnant NvM (Naive mothers),Pregnant NbM (Mothers with Nippostrongylus brasiliensis),NbM comprises of female BALB/c adult mice who were infected with 500L3 Nippostrongylus brasiliensis (N brasiliensis).,NA,NA,NA,16S,6,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 1D, S1",20 October 2024,KateRasheed,KateRasheed,Differential abundant bacteria at different taxonomy level,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1239|91061|186826|186827;2|1224|28216|80840|506;2|1239|91061|1385;2|1224|28216|80840;2|1239|91061|186826|81852;2|976|117747|200666|84566;2|976|117747|200666;2|1239|91061|1385|90964,Complete,NA -bsdb:1121/1/2,Study 1121,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu DD, Darby M, Havyarimana E, Brown BP, Horsnell W , Jaspan HB",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 1,South Africa,Mus musculus,Feces,UBERON:0001988,Intestinal helminthiasis,MONDO:0024271,Pregnant NvM (Naive mothers),Pregnant NbM (Mothers with Nippostrongylus brasiliensis),NbM comprises of female BALB/c adult mice who were infected with 500L3 Nippostrongylus brasiliensis (N brasiliensis).,NA,NA,NA,16S,6,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 1D, S1",20 October 2024,KateRasheed,KateRasheed,Differential abundant bacteria at different taxonomy level,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|815;2|1239|526524|526525|128827;2|1224|1236|135625|712;2|976|200643|171549|171552,Complete,NA +bsdb:1121/1/1,Study 1121,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu DD, Darby M, Havyarimana E, Brown BP, Horsnell W , Jaspan HB",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 1,South Africa,Mus musculus,Feces,UBERON:0001988,Intestinal helminthiasis,MONDO:0024271,Pregnant NvM (Naive mothers),Pregnant NbM (Mothers with Nippostrongylus brasiliensis),NbM comprises of female BALB/c adult mice who were infected with 500L3 Nippostrongylus brasiliensis (N brasiliensis).,4,4,NA,16S,6,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Figure 1D, S1",20 October 2024,KateRasheed,KateRasheed,Differential abundant bacteria at different taxonomy level,increased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales|f__Sphingobacteriaceae,k__Bacteria|p__Bacteroidota|c__Sphingobacteriia|o__Sphingobacteriales,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae",2|1239|91061|186826|186827;2|1224|28216|80840|506;2|1239|91061|1385;2|1224|28216|80840;2|1239|91061|186826|81852;2|976|117747|200666|84566;2|976|117747|200666;2|1239|91061|1385|90964,Complete,NA +bsdb:1121/1/2,Study 1121,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu DD, Darby M, Havyarimana E, Brown BP, Horsnell W , Jaspan HB",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 1,South Africa,Mus musculus,Feces,UBERON:0001988,Intestinal helminthiasis,MONDO:0024271,Pregnant NvM (Naive mothers),Pregnant NbM (Mothers with Nippostrongylus brasiliensis),NbM comprises of female BALB/c adult mice who were infected with 500L3 Nippostrongylus brasiliensis (N brasiliensis).,4,4,NA,16S,6,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,"Figure 1D, S1",20 October 2024,KateRasheed,KateRasheed,Differential abundant bacteria at different taxonomy level,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|976|200643|171549|815;2|1239|526524|526525|128827;2|1224|1236|135625|712;2|976|200643|171549|171552,Complete,NA bsdb:1121/2/NA,Study 1121,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu DD, Darby M, Havyarimana E, Brown BP, Horsnell W , Jaspan HB",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 2,South Africa,Mus musculus,"Stomach,Breast","UBERON:0000945,UBERON:0000310","Helminthiasis, animal",MONDO:0025082,NvM (Naive Mothers),NbM (Nippostrongylus brasiliensis Mothers),NbM - (Nippostrongylus brasiliensis Mothers) refers to the group of maternal mice that were previously infected with 500L3 larvae of Nippostrongylus brasiliensis. The infection was treated and cleared with ivermectin.,NA,NA,NA,16S,6,NA,"PERMANOVA,DESeq2",0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA bsdb:1121/3/NA,Study 1121,laboratory experiment,32277499,10.1111/pim.12721,NA,"Nyangahu DD, Darby M, Havyarimana E, Brown BP, Horsnell W , Jaspan HB",Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model,Parasite immunology,2020,"Nippostrongylus brasiliensis, CD4 T lymphocytes, Cell, animal model, parasite, tools and techniques",Experiment 3,South Africa,Mus musculus,"Breast,Milk","UBERON:0000310,UBERON:0001913","Helminthiasis, animal",MONDO:0025082,NvM (Naive Mothers),NbM (Nippostrongylus brasiliensis Mothers),NbM - (Nippostrongylus brasiliensis Mothers) refers to the group of maternal mice that were previously infected with 500L3 larvae of Nippostrongylus brasiliensis. The infection was treated and cleared with ivermectin,NA,NA,NA,16S,6,Illumina,"PERMANOVA,DESeq2",0.05,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA bsdb:1124/1/1,Study 1124,"cross-sectional observational, not case-control",36518275,https://doi.org/10.7717/peerj.14449,NA,"Roachford OSE, Alleyne AT , Nelson KE","Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries",PeerJ,2022,"Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome",Experiment 1,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,"Combination of groups - AA, AC, AI and AK women","Main group - CG, Caucasian German women",Caucasian German women with varying vaginal microbiome compositions.,113,38,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,"age,ethnic group,sexual preference",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,3 October 2024,Chrisawoke,Chrisawoke,"Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).",increased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium breve,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella|s__Gardnerella vaginalis,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemelliphila|s__Gemelliphila asaccharolytica,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella amnii,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella montpellierensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|201174|1760|85004|31953|1678|1685;2|201174|1760|85004|31953|2701|2702;2|1239|91061|1385|539738|1378;2|1239|91061|1385|539738|3076174|502393;2|976|200643|171549|171552|838|419005;2|1239|909932|1843489|31977|29465|187328;2|976|200643,Complete,NA