Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/9
Subjects
- Location of subjects
- South Korea
- 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
- female healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- female with early RA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- female early rheumatoid arthritis patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- People using antibiotics, probiotics, or prebiotics at the time of sample collection were excluded from subject selection.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/9
Source: Figure 3, text
Description: Differential microbial abundance between RA patients and controls
Abundance in Group 1: decreased abundance in female with early RA
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Collinsella | ||
| Coriobacteriaceae | ||
| Coriobacteriales | ||
| Coriobacteriia | ||
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Eubacterium | ||
| Leuconostoc | ||
| Synergistaceae | ||
| Erysipelotrichia |
Revision editor(s): Tislam, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/9
Source: Figure 3, text
Description: Differential microbial abundance between RA patients and controls
Abundance in Group 1: increased abundance in female with early RA
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroidia | ||
| Bacteroidota |
Revision editor(s): Tislam, Claregrieve1
