diff --git a/bugsigdb_signatures_genus_metaphlan.gmt b/bugsigdb_signatures_genus_metaphlan.gmt index 91ac9858b..29188a767 100644 --- a/bugsigdb_signatures_genus_metaphlan.gmt +++ b/bugsigdb_signatures_genus_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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__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__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus 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 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 @@ -4859,5 +4859,5 @@ bsdb:1169/2/1_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglyca bsdb:1169/2/2_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium bsdb:1169/3/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia bsdb:1169/3/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium -bsdb:1169/4/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter -bsdb:1169/4/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium +bsdb:1169/4/1_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter +bsdb:1169/4/2_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium diff --git a/bugsigdb_signatures_genus_metaphlan_exact.gmt b/bugsigdb_signatures_genus_metaphlan_exact.gmt index bfa20ff83..88e541e61 100644 --- a/bugsigdb_signatures_genus_metaphlan_exact.gmt +++ b/bugsigdb_signatures_genus_metaphlan_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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__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__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus 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 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 @@ -4053,5 +4053,5 @@ bsdb:1169/2/1_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglyca bsdb:1169/2/2_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium bsdb:1169/3/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia bsdb:1169/3/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium -bsdb:1169/4/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter -bsdb:1169/4/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium +bsdb:1169/4/1_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter +bsdb:1169/4/2_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium diff --git a/bugsigdb_signatures_genus_ncbi.gmt b/bugsigdb_signatures_genus_ncbi.gmt index 0355ee5c2..8929d4758 100644 --- a/bugsigdb_signatures_genus_ncbi.gmt +++ b/bugsigdb_signatures_genus_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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 1654 1716 1301 162289 189330 33024 40544 2759736 1386 bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA 100883 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 207244 2759736 @@ -4859,5 +4859,5 @@ bsdb:1169/2/1_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglyca bsdb:1169/2/2_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA 1263 848 bsdb:1169/3/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA 216851 572511 bsdb:1169/3/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA 816 142587 40544 459786 580596 1263 1392389 35829 29465 216851 -bsdb:1169/4/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA 216851 102106 109326 239759 1632780 -bsdb:1169/4/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA 142587 816 84111 216851 +bsdb:1169/4/1_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_UP NA 216851 102106 109326 239759 1632780 +bsdb:1169/4/2_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA 142587 816 84111 216851 diff --git a/bugsigdb_signatures_genus_ncbi_exact.gmt b/bugsigdb_signatures_genus_ncbi_exact.gmt index 3e277a677..6b0c0f1de 100644 --- a/bugsigdb_signatures_genus_ncbi_exact.gmt +++ b/bugsigdb_signatures_genus_ncbi_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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 1654 1716 1301 162289 189330 33024 40544 1386 bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA 100883 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 207244 @@ -4053,5 +4053,5 @@ bsdb:1169/2/1_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglyca bsdb:1169/2/2_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA 1263 848 bsdb:1169/3/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA 216851 572511 bsdb:1169/3/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA 816 142587 40544 459786 580596 1263 1392389 35829 29465 216851 -bsdb:1169/4/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA 216851 102106 109326 239759 1632780 -bsdb:1169/4/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA 142587 816 84111 216851 +bsdb:1169/4/1_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_UP NA 216851 102106 109326 239759 1632780 +bsdb:1169/4/2_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA 142587 816 84111 216851 diff --git a/bugsigdb_signatures_genus_taxname.gmt b/bugsigdb_signatures_genus_taxname.gmt index 73908eeb4..bdead7760 100644 --- a/bugsigdb_signatures_genus_taxname.gmt +++ b/bugsigdb_signatures_genus_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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 Actinomyces Corynebacterium Streptococcus Peptoniphilus Dorea Phascolarctobacterium Sutterella Lacticaseibacillus Bacillus bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA Coprobacillus bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Anaerostipes Lacticaseibacillus @@ -4859,5 +4859,5 @@ bsdb:1169/2/1_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglyca bsdb:1169/2/2_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA Ruminococcus Fusobacterium bsdb:1169/3/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA Faecalibacterium Blautia bsdb:1169/3/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA Bacteroides Isobaculum Sutterella Oscillibacter Butyricicoccus Ruminococcus Intestinimonas Acetivibrio Veillonella Faecalibacterium -bsdb:1169/4/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA Faecalibacterium Collinsella Anaerovorax Alistipes Phreatobacter -bsdb:1169/4/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA Isobaculum Bacteroides Eggerthella Faecalibacterium +bsdb:1169/4/1_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_UP NA Faecalibacterium Collinsella Anaerovorax Alistipes Phreatobacter +bsdb:1169/4/2_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA Isobaculum Bacteroides Eggerthella Faecalibacterium diff --git a/bugsigdb_signatures_genus_taxname_exact.gmt b/bugsigdb_signatures_genus_taxname_exact.gmt index 353ce74a4..0282af43d 100644 --- a/bugsigdb_signatures_genus_taxname_exact.gmt +++ b/bugsigdb_signatures_genus_taxname_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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 Actinomyces Corynebacterium Streptococcus Peptoniphilus Dorea Phascolarctobacterium Sutterella Bacillus bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA Coprobacillus bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Anaerostipes @@ -4053,5 +4053,5 @@ bsdb:1169/2/1_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglyca bsdb:1169/2/2_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA Ruminococcus Fusobacterium bsdb:1169/3/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA Faecalibacterium Blautia bsdb:1169/3/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA Bacteroides Isobaculum Sutterella Oscillibacter Butyricicoccus Ruminococcus Intestinimonas Acetivibrio Veillonella Faecalibacterium -bsdb:1169/4/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA Faecalibacterium Collinsella Anaerovorax Alistipes Phreatobacter -bsdb:1169/4/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA Isobaculum Bacteroides Eggerthella Faecalibacterium +bsdb:1169/4/1_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_UP NA Faecalibacterium Collinsella Anaerovorax Alistipes Phreatobacter +bsdb:1169/4/2_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA Isobaculum Bacteroides Eggerthella Faecalibacterium diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt index 67926fe0d..6f3914ca3 100644 --- a/bugsigdb_signatures_mixed_metaphlan.gmt +++ b/bugsigdb_signatures_mixed_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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 @@ -5491,5 +5491,5 @@ bsdb:1169/2/1_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglyca bsdb:1169/2/2_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales bsdb:1169/3/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia bsdb:1169/3/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium -bsdb:1169/4/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter -bsdb:1169/4/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium +bsdb:1169/4/1_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter +bsdb:1169/4/2_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt index 639a51688..a6cf73ce2 100644 --- a/bugsigdb_signatures_mixed_ncbi.gmt +++ b/bugsigdb_signatures_mixed_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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 @@ -5491,5 +5491,5 @@ bsdb:1169/2/1_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglyca bsdb:1169/2/2_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA 1263 203492 848 72274 bsdb:1169/3/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA 216851 572511 bsdb:1169/3/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA 816 142587 40544 128827 459786 580596 1263 1392389 35829 29465 216851 -bsdb:1169/4/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA 216851 102106 109326 239759 1632780 -bsdb:1169/4/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA 186803 142587 816 84111 216851 +bsdb:1169/4/1_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_UP NA 216851 102106 109326 239759 1632780 +bsdb:1169/4/2_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA 186803 142587 816 84111 216851 diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt index eba3013df..15950b2b5 100644 --- a/bugsigdb_signatures_mixed_taxname.gmt +++ b/bugsigdb_signatures_mixed_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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 @@ -5491,5 +5491,5 @@ bsdb:1169/2/1_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglyca bsdb:1169/2/2_Gestational-diabetes:Previous-GDM-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA Ruminococcus Fusobacteriaceae Fusobacterium Pseudomonadales bsdb:1169/3/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA Faecalibacterium Blautia bsdb:1169/3/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA Bacteroides Isobaculum Sutterella Erysipelotrichaceae Oscillibacter Butyricicoccus Ruminococcus Intestinimonas Acetivibrio Veillonella Faecalibacterium -bsdb:1169/4/1_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_UP NA Faecalibacterium Collinsella Anaerovorax Alistipes Phreatobacter -bsdb:1169/4/2_Gestational-diabetes:gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Normoglycaemic--pregnancy_DOWN NA Lachnospiraceae Isobaculum Bacteroides Eggerthella Faecalibacterium +bsdb:1169/4/1_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_UP NA Faecalibacterium Collinsella Anaerovorax Alistipes Phreatobacter +bsdb:1169/4/2_Gestational-diabetes:Previous-gestational-diabetes-mellitus-(GDM)-pregnancy_vs_Previous-normoglycaemic--pregnancy_DOWN NA Lachnospiraceae Isobaculum Bacteroides Eggerthella Faecalibacterium diff --git a/file_size.csv b/file_size.csv index 7194fa540..e2cd488ef 100644 --- a/file_size.csv +++ b/file_size.csv @@ -432,3 +432,4 @@ "2024-10-18_16:58_UTC" "4053" "4859" "4053" "4859" "4053" "4859" "5491" "5491" "5491" "2321" "2321" "2321" "2321" "2321" "2321" "3699" "6572" "5939" "1347" "2024-10-18_17:59_UTC" "4057" "4863" "4057" "4863" "4057" "4863" "5495" "5495" "5495" "2321" "2321" "2321" "2321" "2321" "2321" "3700" "6575" "5943" "1347" "2024-10-18_18:58_UTC" "4057" "4863" "4057" "4863" "4057" "4863" "5495" "5495" "5495" "2321" "2321" "2321" "2321" "2321" "2321" "3700" "6575" "5943" "1347" +"2024-10-18_19:58_UTC" "4057" "4863" "4057" "4863" "4057" "4863" "5495" "5495" "5495" "2321" "2321" "2321" "2321" "2321" "2321" "3700" "6575" "5943" "1347" diff --git a/full_dump.csv b/full_dump.csv index 3ac32f5a4..10319b0b0 100644 --- a/full_dump.csv +++ b/full_dump.csv @@ -1,4 +1,4 @@ -# BugSigDB 2024-10-18_17:59_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2024-10-18_19:58_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 @@ -6449,11 +6449,11 @@ 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: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,"Kruskall-Wallis,PERMANOVA",0.05,FALSE,2,NA,"age,ethnic group,sexual preference",NA,decreased,decreased,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 -bsdb:1124/2/1,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 2,"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 CG women","AK, African Kenyan women",The vaginal microbiome compositions of African Kenyan women descent.,120,31,NA,16S,34,Illumina,"Kruskall-Wallis,PERMANOVA",0.05,FALSE,2,NA,"age,ethnic group,sexual preference",NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3,17 October 2024,NA,NA,"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__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens",2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|201174|1760|85007|1653|1716|598660,Complete,NA -bsdb:1124/3/1,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 3,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,"Combination of groups - AA, AC, AK and CG women","AI, Asian Indonesian women",Asian Indonesian women with different vaginal microbiome compositions.,115,36,30 days,16S,34,Illumina,"Kruskall-Wallis,PERMANOVA",0.05,TRUE,2,NA,"age,ethnic group,sexual preference",NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3,17 October 2024,NA,NA,"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,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",2;2|1239|186801;2|1239|91061|1385;2|1239|91061;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300;2|1239|91061|186826;2|1239|1737404|1737405|1570339|165779;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1239|1737404|1582879;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|1300|1301|1328;2|201174|1760|85004|31953|1678|216816;2|1239|91061|186826|1300|1301|1304,Complete,NA -bsdb:1124/4/1,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 4,"Germany,Kenya,Indonesia,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,"Combination of groups - AA, AI, AK and CG women","AC, Afro-Caribbean women",Vaginal microbiome compositions of Afro-Caribbean women descent.,133,18,30 days,16S,34,Illumina,"Kruskall-Wallis,PERMANOVA",0.05,TRUE,2,NA,"age,ethnic group,sexual preference",NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3,17 October 2024,NA,NA,"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).",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|976|200643|171549;2|976|200643;2|976|200643|171549|171552|2974257|28127;2|976|200643|171549|171552|838|28125;2|1239|1737404|1737405|1570339|165779|33037;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|162289|33031,Complete,NA -bsdb:1124/5/1,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 5,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,"Combination of groups - AK, AI, CG and AC women","AA, African American women",African American women with different vaginal microbiome compositions.,123,28,30 days,16S,34,Illumina,"Kruskall-Wallis,PERMANOVA",0.05,TRUE,2,NA,"age,ethnic group,sexual preference",NA,decreased,decreased,NA,NA,NA,Signature 1,Figure 3,17 October 2024,NA,NA,"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__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,2|1239|91061|186826|33958|1578|47770,Complete,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 +bsdb:1124/2/1,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 2,"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 CG women","AK, African Kenyan women",The vaginal microbiome compositions of African Kenyan women descent.,120,31,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,"age,ethnic group,sexual preference",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,17 October 2024,NA,NA,"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__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium pyruviciproducens",2|976|200643|171549|171551;2|976|200643|171549|171551|836;2|201174|1760|85007|1653|1716|598660,Complete,NA +bsdb:1124/3/1,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 3,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,"Combination of groups - AA, AC, AK and CG women","AI, Asian Indonesian women",Asian Indonesian women with different vaginal microbiome compositions.,115,36,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,"age,ethnic group,sexual preference",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,17 October 2024,NA,NA,"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,k__Bacteria|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales,k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|g__Ezakiella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus anginosus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius",2;2|1239|186801;2|1239|91061|1385;2|1239|91061;2|1239|91061|1385|90964;2|1239|91061|1385|90964|1279;2|1239|91061|186826|1300;2|1239|91061|186826;2|1239|1737404|1737405|1570339|165779;2|1239|186801|3082720|186804;2|1239|186801|3082720|186804|1257;2|1239|1737404|1582879;2|1239|91061|186826|33958|1578|1596;2|1239|91061|186826|1300|1301|1328;2|201174|1760|85004|31953|1678|216816;2|1239|91061|186826|1300|1301|1304,Complete,NA +bsdb:1124/4/1,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 4,"Germany,Kenya,Indonesia,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,"Combination of groups - AA, AI, AK and CG women","AC, Afro-Caribbean women",Vaginal microbiome compositions of Afro-Caribbean women descent.,133,18,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,"age,ethnic group,sexual preference",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,17 October 2024,NA,NA,"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).",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Hoylesella|s__Hoylesella buccalis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella bivia,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Anaerococcus|s__Anaerococcus vaginalis,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus|s__Peptoniphilus lacrimalis",2|976|200643|171549|171552;2|976|200643|171549|171552|838;2|976|200643|171549;2|976|200643;2|976|200643|171549|171552|2974257|28127;2|976|200643|171549|171552|838|28125;2|1239|1737404|1737405|1570339|165779|33037;2|1239|1737404|1737405|1570339|162289;2|1239|1737404|1737405|1570339|162289|33031,Complete,NA +bsdb:1124/5/1,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 5,"Germany,Indonesia,Kenya,United States of America",Homo sapiens,Mucosa of vagina,UBERON:0004983,Vaginal microbiome measurement,EFO:0011013,"Combination of groups - AK, AI, CG and AC women","AA, African American women",African American women with different vaginal microbiome compositions.,123,28,NA,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,"age,ethnic group,sexual preference",NA,decreased,NA,NA,NA,NA,Signature 1,Figure 3,17 October 2024,NA,NA,"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__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus crispatus,2|1239|91061|186826|33958|1578|47770,Complete,NA bsdb:1125/1/1,Study 1125,prospective cohort,36246928,10.3389/fendo.2022.942383,NA,"Nizigiyimana P, Xu B, Liu L, Luo L, Liu T, Jiang M, Liu Z, Li C, Luo X , Lei M",Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese,Frontiers in endocrinology,2022,"16S rRNA gene sequencing, Africans, Chinese, bacterial communities, gut microbiota, healthy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Glucose metabolism measurement,EFO:0009367,Han-Chinese citizens,African citizens,African citizens born in Africa with no known recent non-African ancestry.,27,29,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3.8,NA,NA,NA,increased,increased,NA,NA,increased,Signature 1,Figure 3C,3 October 2024,Balogun adekemi,"Balogun adekemi,Folakunmi",Lefse cladogram generated to depict the key and most differentially abundant taxa associated with ethnicity in Chinese and Africans.,increased,k__Bacteria|p__Verrucomicrobiota,2|74201,Complete,Folakunmi bsdb:1125/1/2,Study 1125,prospective cohort,36246928,10.3389/fendo.2022.942383,NA,"Nizigiyimana P, Xu B, Liu L, Luo L, Liu T, Jiang M, Liu Z, Li C, Luo X , Lei M",Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese,Frontiers in endocrinology,2022,"16S rRNA gene sequencing, Africans, Chinese, bacterial communities, gut microbiota, healthy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Glucose metabolism measurement,EFO:0009367,Han-Chinese citizens,African citizens,African citizens born in Africa with no known recent non-African ancestry.,27,29,NA,16S,34,Illumina,LEfSe,0.05,FALSE,3.8,NA,NA,NA,increased,increased,NA,NA,increased,Signature 2,Figure 3C,3 October 2024,Balogun adekemi,"Balogun adekemi,Folakunmi",Lefse cladogram generated to depict the key and most differentially abundant taxa associated with ethnicity in Chinese and Africans.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacteroidota|c__Bacteroidia",2|976|200643|171549|815;2|976|200643|171549;2|976|200643|171549|815|816;2|976|200643,Complete,Folakunmi bsdb:1126/1/1,Study 1126,"cross-sectional observational, not case-control",39198450,10.1038/s41522-024-00542-4,https://pubmed.ncbi.nlm.nih.gov/39198450/,"Licht P, Dominelli N, Kleemann J, Pastore S, Müller ES, Haist M, Hartmann KS, Stege H, Bros M, Meissner M, Grabbe S, Heermann R , Mailänder V",The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival,NPJ biofilms and microbiomes,2024,NA,Experiment 1,Germany,Homo sapiens,Skin epidermis,UBERON:0001003,Cutaneous T-cell lymphoma,EFO:0002913,Healthy control( ΔSA-neutral subgroup),Mycosis fungoides( ΔSA-positive),"Patients with significant dysbiosis on MF lesions exhibiting S. aureus expansion. Antimicrobial peptides (AMPs) were probably less prevalent when the overgrowth occurred, and S. aureus was able to adapt to these peptides to become a more virulent strain on the lesions.",20,20,1 month,PCR,NA,Illumina,ANOVA,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,decreased,Signature 1,"fig 2b, d-g",3 October 2024,Jayybb,"Jayybb,Peace Sandy",Differential abundance analysis of microbial species for N = 65 metagenomic samples.,increased,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus aureus,2|1239|91061|1385|90964|1279|1280,Complete,Peace Sandy @@ -6571,5 +6571,5 @@ bsdb:1169/2/1,Study 1169,"cross-sectional observational, not case-control",29764 bsdb:1169/2/2,Study 1169,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell MKW, Hansen TH, Nielsen T, Allin KH, Rühlemann MC, Damm P, Vestergaard H, Rørbye C, Jørgensen NR, Christiansen OB, Heinsen FA, Franke A, Hansen T, Lauenborg J , Pedersen O",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 2,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Previous normoglycaemic pregnancy,Previous GDM pregnancy,Women with gestational diabetes mellitus (GDM) pregnancy Postpartum (average of nine months) during second visit,82,43,2 months,16S,12,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,FIG 2 (D),18 October 2024,NA,NA,Taxonomic biomarkers of gestational diabetes during postpartum pregnancy identified by linear discriminant analysis (LDA) using LEfSe .,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales",2|1239|186801|186802|216572|1263;2|32066|203490|203491|203492;2|32066|203490|203491|203492|848;2|1224|1236|72274,Complete,NA bsdb:1169/3/1,Study 1169,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell MKW, Hansen TH, Nielsen T, Allin KH, Rühlemann MC, Damm P, Vestergaard H, Rørbye C, Jørgensen NR, Christiansen OB, Heinsen FA, Franke A, Hansen T, Lauenborg J , Pedersen O",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic pregnancy,gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) during third trimester pregnancy within genus-level OTUs,157,50,2 months,16S,12,Illumina,Wald Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,18 October 2024,Rahila,Rahila,Operational taxonomic units differentially abundant in women with and without gestational diabetes during third trimester pregnancy at the genus level,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|1239|186801|186802|216572|216851;2|1239|186801|3085636|186803|572511,Complete,NA bsdb:1169/3/2,Study 1169,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell MKW, Hansen TH, Nielsen T, Allin KH, Rühlemann MC, Damm P, Vestergaard H, Rørbye C, Jørgensen NR, Christiansen OB, Heinsen FA, Franke A, Hansen T, Lauenborg J , Pedersen O",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 3,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic pregnancy,gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) during third trimester pregnancy within genus-level OTUs,157,50,2 months,16S,12,Illumina,Wald Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,18 October 2024,Rahila,Rahila,Operational taxonomic units differentially abundant in women with and without gestational diabetes during third trimester pregnancy at the genus level,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Intestinimonas,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Acetivibrio,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|976|200643|171549|815|816;2|1239|91061|186826|186828|142587;2|1224|28216|80840|995019|40544;2|1239|526524|526525|128827;2|1239|186801|186802|216572|459786;2|1239|186801|186802|3085642|580596;2|1239|186801|186802|216572|1263;2|1239|186801|186802|1392389;2|1239|186801|186802|216572|35829;2|1239|909932|1843489|31977|29465;2|1239|186801|186802|216572|216851,Complete,NA -bsdb:1169/4/1,Study 1169,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell MKW, Hansen TH, Nielsen T, Allin KH, Rühlemann MC, Damm P, Vestergaard H, Rørbye C, Jørgensen NR, Christiansen OB, Heinsen FA, Franke A, Hansen T, Lauenborg J , Pedersen O",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic pregnancy,gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) postpartum pregnancy within genus-level OTUs,79,43,2 months,16S,12,Illumina,Wald Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Table S5,18 October 2024,NA,NA,Operational taxonomic units differentially abundant in women with and without gestational diabetes at postpartum pregnancy at the genus level,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter",2|1239|186801|186802|216572|216851;2|201174|84998|84999|84107|102106;2|1239|186801|3082720|3030910|109326;2|976|200643|171549|171550|239759;2|1224|28211|356|2843305|1632780,Complete,NA -bsdb:1169/4/2,Study 1169,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell MKW, Hansen TH, Nielsen T, Allin KH, Rühlemann MC, Damm P, Vestergaard H, Rørbye C, Jørgensen NR, Christiansen OB, Heinsen FA, Franke A, Hansen T, Lauenborg J , Pedersen O",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Normoglycaemic pregnancy,gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) postpartum pregnancy within genus-level OTUs,79,43,2 months,16S,12,Illumina,Wald Test,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Table S5,18 October 2024,NA,NA,Operational taxonomic units differentially abundant in women with and without gestational diabetes at postpartum pregnancy at the genus level,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|3085636|186803;2|1239|91061|186826|186828|142587;2|976|200643|171549|815|816;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|216572|216851,Complete,NA +bsdb:1169/4/1,Study 1169,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell MKW, Hansen TH, Nielsen T, Allin KH, Rühlemann MC, Damm P, Vestergaard H, Rørbye C, Jørgensen NR, Christiansen OB, Heinsen FA, Franke A, Hansen T, Lauenborg J , Pedersen O",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Previous normoglycaemic pregnancy,Previous gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) average of 8.8 months postpartum pregnancy within genus-level OTUs,79,43,2 months,16S,12,Illumina,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 1,Table S5,18 October 2024,NA,NA,Operational taxonomic units differentially abundant in women with and without gestational diabetes at postpartum pregnancy at the genus level,increased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Anaerovorax,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phreatobacteraceae|g__Phreatobacter",2|1239|186801|186802|216572|216851;2|201174|84998|84999|84107|102106;2|1239|186801|3082720|3030910|109326;2|976|200643|171549|171550|239759;2|1224|28211|356|2843305|1632780,Complete,NA +bsdb:1169/4/2,Study 1169,"cross-sectional observational, not case-control",29764499,10.1186/s40168-018-0472-x,NA,"Crusell MKW, Hansen TH, Nielsen T, Allin KH, Rühlemann MC, Damm P, Vestergaard H, Rørbye C, Jørgensen NR, Christiansen OB, Heinsen FA, Franke A, Hansen T, Lauenborg J , Pedersen O",Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum,Microbiome,2018,"Bacterial species, Body mass index, Gestational diabetes, Gestational hyperglycaemia, Glycaemic traits, Gut microbiota, Pregnancy",Experiment 4,Denmark,Homo sapiens,Feces,UBERON:0001988,Gestational diabetes,EFO:0004593,Previous normoglycaemic pregnancy,Previous gestational diabetes mellitus (GDM) pregnancy,Women with gestational diabetes mellitus (GDM) average of 8.8 months postpartum pregnancy within genus-level OTUs,79,43,2 months,16S,12,Illumina,Wald Test,0.05,TRUE,NA,NA,NA,unchanged,unchanged,NA,NA,NA,unchanged,Signature 2,Table S5,18 October 2024,NA,NA,Operational taxonomic units differentially abundant in women with and without gestational diabetes at postpartum pregnancy at the genus level,decreased,"k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Isobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium",2|1239|186801|3085636|186803;2|1239|91061|186826|186828|142587;2|976|200643|171549|815|816;2|201174|84998|1643822|1643826|84111;2|1239|186801|186802|216572|216851,Complete,NA