Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Subjects
- Location of subjects
- Japan
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-IBD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Crohn's disease activity index <150
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(a)
Description: Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.
Abundance in Group 1: increased abundance in CD
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Cetobacterium | ||
| Clostridium | ||
| Enterococcus | ||
| Escherichia | ||
| Lachnoanaerobaculum | ||
| Mediterraneibacter gnavus | ||
| unclassified Bacteroidota |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(a)
Description: Comparative analyses of the taxonomic composition of the microbial community at the genus level. Representative genera with significant differences between groups are presented.
Abundance in Group 1: decreased abundance in CD
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Coprococcus | ||
| Faecalibacterium | ||
| Gemmiger | ||
| Lachnospiraceae | ||
| Oscillospiraceae | ||
| Prevotella | ||
| Roseburia | ||
| Ruminococcus bromii | ||
| Pseudomonas |
