Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/9

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31100891

DOI Digital object identifier for electronic documents.

10.3390/jcm8050693

URI

Authors

Jeong Y, Kim JW, You HJ, Park SJ, Lee J, Ju JH, Park MS, Jin H, Cho ML, Kwon B, Park SH, Ji GE

Journal

Journal of clinical medicine

Year

2019

Keywords:

Collinsella, autoimmune disease, dysbiosis, gut microbiome, microbial diversity, rheumatoid arthritis

Rheumatoid arthritis (RA) is an autoimmune disease characterized by synovial inflammation of the joints and extra-articular manifestations. Recent studies have shown that microorganisms affect RA pathogenesis. However, few studies have examined the microbial distribution of early RA patients, particularly female patients. In the present study, we investigated the gut microbiome profile and microbial functions in early RA female patients, including preclinical and clinically apparent RA cases. Changes in microbiological diversity, composition, and function in each group were analyzed using quantitative insights into microbial ecology (QIIME) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). The results revealed the dysbiosis due to decreased diversity in the early RA patients compared with healthy subjects. There were significant differences in the microbial distribution of various taxa from phylum to genus levels between healthy subjects and early RA patients. Phylum Bacteroidetes was enriched in early RA patients, while Actinobacteria, including the genus Collinsella, was enriched in healthy subjects. Functional analysis based on clusters of orthologous groups revealed that the genes related to the biosynthesis of menaquinone, known to be derived from gram-positive bacteria, were enriched in healthy subjects, while iron transport-related genes were enriched in early RA patients. Genes related to the biosynthesis of lipopolysaccharide, the gram-negative bacterial endotoxin, were enriched in clinically apparent RA patients. The obvious differences in microbial diversity, taxa, and associated functions of the gut microbiota between healthy subjects and early RA patients highlight the involvement of the gut microbiome in the early stages of RA.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/9

Curated date: 2021/11/30

Curator: Tislam

Revision editor(s): Tislam, Claregrieve1, Peace Sandy

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

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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/9

Curated date: 2021/11/30

Curator: Tislam

Revision editor(s): Tislam, Claregrieve1

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