A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Subjects
- Location of subjects
- Canada
- 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
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with immune-mediated inflammatory disease (IMID)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 8 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Kruskall-Wallis
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): WikiWorks, Fatima, Merit, ChiomaBlessing
Source: Table 2
Description: Abundant taxa in Crohn's disease patients microbiota relative to healthy controls (HC)
Abundance in Group 1: increased abundance in crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bacillota | ||
| Blautia | ||
| Carnobacteriaceae | ||
| Eggerthella | ||
| Faecalicoccus | ||
| Gemella | ||
| Intestinibacter | ||
| Rothia | ||
| Streptococcaceae | ||
| Streptococcus | ||
| unclassified Lachnospiraceae |
Revision editor(s): WikiWorks, Fatima, Merit, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): Fatima, WikiWorks, ChiomaBlessing
Source: Table 2
Description: Abundant taxa in Crohn's disease patients microbiota relative to healthy controls (HC)
Abundance in Group 1: decreased abundance in crohn's disease
Revision editor(s): Fatima, WikiWorks, ChiomaBlessing
