An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis/Experiment 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8

Curated date: 2021/08/16

Curator: Tislam

Revision editor(s): WikiWorks, Rimsha, Claregrieve1, Tislam, Victoria

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: rheumatoid arthritis patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: rheumatoid arthritis patients

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Any patient or control on antibiotics, consuming probiotics, or having a known history of inflammatory bowel disease or other autoimmune diseases like diabetes and multiple sclerosis were excluded.

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8

Curated date: 2021/08/16

Curator: Tislam

Revision editor(s): Rimsha, Claregrieve1, Tislam, Merit

Source: Figure 3, text

Description: Differential microbial abundance between healthy controls and RA patients

Abundance in Group 1: increased abundance in rheumatoid arthritis patients

NCBI	Quality Control	Links
Actinomyces
Actinomycetaceae
Actinomycetales
Actinomycetota
Bacilli
Coriobacteriaceae
Coriobacteriales
Coriobacteriia
Eggerthella
Erwinia
Eubacteriaceae
Eubacterium
Lactobacillales
Streptococcaceae
Streptococcus
Turicibacter
Turicibacteraceae
unclassified Actinomycetota