Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease/Experiment 2
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
- Ulcerative colitis colitis ulcerative,Colitis, Ulcerative,Left-sided ulcerative (chronic) colitis,Left-sided ulcerative colitis,left-sided ulcerative colitis,Other ulcerative colitis,Other ulcerative colitis (disorder),UC - ulcerative colitis,ulcerative colitis,ulcerative colitis (disease),ulcerative colitis (disorder),Ulcerative colitis, unspecified,ULCERATVE COLITIS UNSPCF,Ulcerative colitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NON-IBD controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- UC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The patient who is diagnosed from ulcerative colitis(UC).
- 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
- 43
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
- Welch's 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
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(b)
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 UC
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Blautia | ||
| Citrobacter | ||
| Lactobacillus | ||
| Veillonella | ||
| unclassified Bacillota |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-27
Source: Figure 5(b)
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 UC
| NCBI | Quality Control | Links |
|---|---|---|
| Brachyspira | ||
| Helicobacter | ||
| Odoribacter | ||
| Alistipes | ||
| Gemmiger | ||
| Pseudomonas | ||
| Coprococcus | ||
| Prevotella |
