A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?/Experiment 4
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
- Rheumatoid arthritis Arthritis or polyarthritis, rheumatic,arthritis or polyarthritis, rheumatic,Arthritis, Rheumatoid,arthritis, rheumatoid,atrophic Arthritis,atrophic arthritis,autoimmune arthritis,Chronic rheumatic arthritis,Proliferative arthritis,RA,RA - Rheumatoid arthritis,RhA - Rheumatoid arthritis,Rheumatic gout,rheumatoid arthritis,Rheumatoid arthritis (disorder),Rheumatoid arthritis NOS,Rheumatoid arthritis NOS (disorder),rheumatoid arthritis, susceptibility to,Rheumatoid disease,Rheumatoid arthritis
- 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
- arthiritis
- 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
- 21
- 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 Rheumatoid arthritis patients microbiota relative to healthy controls (HC)
Abundance in Group 1: increased abundance in arthiritis
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bacillota | ||
| Eggerthella | ||
| Faecalicoccus | ||
| Gemella | ||
| Rothia | ||
| Streptococcaceae | ||
| Streptococcus | ||
| unclassified Lachnospiraceae |
Revision editor(s): WikiWorks, Fatima, Merit, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/05/17
Source: Table 2
Description: Abundant taxa in Rheumatoid arthritis patients microbiota relative to healthy controls (HC)
Abundance in Group 1: decreased abundance in arthiritis
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerofustis | ||
| Butyricicoccus | ||
| Clostridium | ||
| Faecalibacterium | ||
| Fusicatenibacter | ||
| Gemmiger | ||
| Lachnospira | ||
| Romboutsia | ||
| Roseburia | ||
| Sporobacter | ||
| Subdoligranulum |
Revision editor(s): WikiWorks, ChiomaBlessing
