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Hourly export update
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4 changes: 2 additions & 2 deletions full_dump.csv
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# BugSigDB 2024-10-22_21:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org
# BugSigDB 2024-10-22_22:58_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
Expand Down Expand Up @@ -6364,7 +6364,7 @@ bsdb:1103/2/1,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou X
bsdb:1103/2/2,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou XR, Zhang P, Zhou Y , Yin Y",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 2,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,control,Moderate-to-severe dry eye,Tear Film Breakup Time less than 2 sec,61,82,Within 3 months excluded,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,decreased,decreased,decreased,unchanged,NA,decreased,Signature 2,Paragraph on page 1990,4 October 2024,NA,NA,Linear Discriminant Analysis Effect Size (Top 5 taxa at the family and genus levels),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|g__Enhydrobacter,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",2|201174|1760|85007|1653;2|1239|91061|186826|33958|1578;2|1224|28211|356|212791;2|1224|28211|356|118882|528;2|1224|1236|2887326|468;2|1224|28211|356|118882;2|201174|1760|85009|31957;2|201174|1760|85007|1653|1716;2|201174|1760|85009|31957|1743,Complete,NA
bsdb:1103/3/1,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou XR, Zhang P, Zhou Y , Yin Y",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 3,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,mild dry eye,Moderate-to-severe dry eye,Tear Film Breakup Time less than 2 sec,56,82,Within 3 months excluded,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 1,Paragraph on page 1990,4 October 2024,Mary Bearkland,Mary Bearkland,Linear Discriminant Analysis Effect Size (top five taxa at the family and genus levels),increased,"k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae,k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Allobaculum,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Beijerinckiaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Chelativorans,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Chelatococcaceae|g__Chelatococcus,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus|s__Cupriavidus basilensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae,k__Bacteria|p__Deinococcota|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus",2|1224|28211|204441|433;2|1239|526524|526525|128827|174708;2|1224|28211|356|45404;2|1224|28211|356|69277|449972;2|1224|28211|356|2036754|28209;2|1224|28216|80840|119060|106589|68895;2|1224|1236|135614|32033;2|1224|28216|80840|75682;2|1297|188787|68933|188786;2|1297|188787|68933|188786|270,Complete,NA
bsdb:1103/3/2,Study 1103,case-control,38111925,10.18240/ijo.2023.12.10,NA,"Zou XR, Zhang P, Zhou Y , Yin Y",Ocular surface microbiota in patients with varying degrees of dry eye severity,International journal of ophthalmology,2023,"dry eye, microbiota, ocular surface, tear film break up time",Experiment 3,China,Homo sapiens,Tear film,UBERON:0022287,Dry eye syndrome,EFO:1000906,mild dry eye,Moderate-to-severe dry eye,Tear Film Breakup Time less than 2 sec,56,82,Within 3 months excluded,16S,34,Illumina,LEfSe,0.05,NA,2,NA,NA,decreased,decreased,decreased,decreased,NA,decreased,Signature 2,Paragraph on page 1990,4 October 2024,Mary Bearkland,Mary Bearkland,Linear Discriminant Analysis Effect Size (top five taxa at the family and genus levels),decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Aphanizomenonaceae|g__Dolichospermum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Nesterenkonia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Planococcaceae|g__Sporosarcina,k__Bacteria|p__Cyanobacteriota|c__Cyanophyceae|o__Nostocales|f__Nostocaceae",2|201174|1760|85006|1268|1663;2|1224|28216|80840|80864;2|1117|3028117|1161|1892259|748770;2|201174|1760|85006|1268;2|201174|1760|85006|1268|57494;2|1224|1236|72274|135621;2|1224|28211|204457;2|1224|28211|204457|41297|13687;2|1239|91061|1385|186818|1569;2|1117|3028117|1161|1162,Complete,NA
bsdb:1104/1/1,Study 1104,laboratory experiment,39293692,https://doi.org/10.1016/j.bbi.2024.09.020,https://pubmed.ncbi.nlm.nih.gov/39293692/,"Masson BA, Kiridena P, Lu D, Kleeman EA, Reisinger SN, Qin W, Davies WJ, Muralitharan RR, Jama HA, Antonacci S, Marques FZ, Gubert C , Hannan AJ",Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice,"Brain, behavior, and immunity",2024,"Antibiotics, Anxiety, Behavior, Depression, Dysbiosis, Gut microbiota, Microbiome, Noncoding RNAs, Paternal epigenetic inheritance",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Seasonal gut microbiome measurement,EFO:0007753,Male Mice that received drinking water without any antibiotics.,Male Mice that were administered a cocktail of non-absorbable antibiotics to deplete their gut microbiota,"This group was defined by the condition where the male mice were exposed to antibiotics, leading to significant depletion of their gut microbiota. This was intended to assess the impact of gut microbiome depletion on their offspring",NA,NA,7 days,16S,4,Illumina,PERMANOVA,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,7 October 2024,Wendy640,"Wendy640,Shulamite","Taxas significantly higher in the control group compared to antibiotic treated
bsdb:1104/1/1,Study 1104,laboratory experiment,39293692,https://doi.org/10.1016/j.bbi.2024.09.020,https://pubmed.ncbi.nlm.nih.gov/39293692/,"Masson BA, Kiridena P, Lu D, Kleeman EA, Reisinger SN, Qin W, Davies WJ, Muralitharan RR, Jama HA, Antonacci S, Marques FZ, Gubert C , Hannan AJ",Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice,"Brain, behavior, and immunity",2024,"Antibiotics, Anxiety, Behavior, Depression, Dysbiosis, Gut microbiota, Microbiome, Noncoding RNAs, Paternal epigenetic inheritance",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,NA,NA,Male Mice that received drinking water without any antibiotics.,Male Mice that were administered a cocktail of non-absorbable antibiotics to deplete their gut microbiota,"This group was defined by the condition where the male mice were exposed to antibiotics, leading to significant depletion of their gut microbiota. This was intended to assess the impact of gut microbiome depletion on their offspring",NA,NA,NA,16S,4,Illumina,PERMANOVA,0.05,TRUE,NA,NA,sex,NA,unchanged,NA,NA,NA,NA,Signature 1,Table 1,7 October 2024,Wendy640,"Wendy640,Shulamite","Taxas significantly higher in the control group compared to antibiotic treated
males after adjusting for cohort effects.",increased,NA,NA,Complete,NA
bsdb:1105/1/1,Study 1105,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S, Chmura O, Wątor J, Panek P , Zapała B",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 1,Poland,Homo sapiens,Mouth,UBERON:0000165,Physical activity,EFO:0003940,Amateurs,Professional football players,Participants in group 1 are professional football players who had oral swabs taken.,12,20,2 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 1,Figure 9a,2 October 2024,Aleru Divine,Aleru Divine,Linear discriminant analysis (LDA) scores of differentially abundant species among amateurs and professional football players.,increased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium matruchotii,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium canifelinum,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia shahii,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas|s__Selenomonas noxia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella tobetsuensis",2|29547|3031852|213849|72294|194|824;2|201174|1760|85007|1653|1716|43768;2|32066|203490|203491|203492|848|285729;2|32066|203490|203491|1129771|32067|157691;2|201174|1760|85006|1268|32207|2047;2|1239|909932|909929|1843491|970|135083;2|1239|91061|186826|1300|1301|1305;2|1239|909932|1843489|31977|29465|29466;2|1239|909932|1843489|31977|29465|1110546,Complete,ChiomaBlessing
bsdb:1105/1/2,Study 1105,prospective cohort,39242653,10.1038/s41598-024-71684-w,https://www.nature.com/articles/s41598-024-71684-w,"Urban S, Chmura O, Wątor J, Panek P , Zapała B",The intensive physical activity causes changes in the composition of gut and oral microbiota,Scientific reports,2024,"Exercises, Microbiome, Professional football player",Experiment 1,Poland,Homo sapiens,Mouth,UBERON:0000165,Physical activity,EFO:0003940,Amateurs,Professional football players,Participants in group 1 are professional football players who had oral swabs taken.,12,20,2 months,16S,34,Illumina,LEfSe,0.05,FALSE,2,"age,body mass index,health",NA,NA,NA,unchanged,NA,NA,unchanged,Signature 2,Figure 9a,2 October 2024,Aleru Divine,Aleru Divine,Linear discriminant analysis (LDA) scores of differentially abundant species among amateurs and professional football players.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella histicola,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella melaninogenica,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus sputorum,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia odontolytica",2|976|200643|171549|171552|838|470565;2|976|200643|171549|171552|838|28132;2|201174|1760|2037|2049|1654|55565;2|1224|1236|135625|712|724|1078480;2|201174|1760|2037|2049|2529408|1660,Complete,ChiomaBlessing
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