The subgingival microbiome in patients with established rheumatoid arthritis

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-27

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

29562298

DOI Digital object identifier for electronic documents.

10.1093/rheumatology/key052

URI

Authors

Mikuls TR, Walker C, Qiu F, Yu F, Thiele GM, Alfant B, Li EC, Zhao LY, Wang GP, Datta S, Payne JB

Journal

Rheumatology (Oxford, England)

Year

2018

Keywords:

osteoarthritis, periodontitis, rheumatoid arthritis, subgingival microbiome

OBJECTIVES: To profile and compare the subgingival microbiome of RA patients with OA controls. METHODS: RA (n = 260) and OA (n = 296) patients underwent full-mouth examination and subgingival samples were collected. Bacterial DNA was profiled using 16 S rRNA Illumina sequencing. Following data filtering and normalization, hierarchical clustering analysis was used to group samples. Multivariable regression was used to examine associations of patient factors with membership in the two largest clusters. Differential abundance between RA and OA was examined using voom method and linear modelling with empirical Bayes moderation (Linear Models for Microarray Analysis, limma), accounting for the effects of periodontitis, race, marital status and smoking. RESULTS: Alpha diversity indices were similar in RA and OA after accounting for periodontitis. After filtering, 286 taxa were available for analysis. Samples grouped into one of seven clusters with membership sizes of 324, 223, 3, 2, 2, 1 and 1 patients, respectively. RA-OA status was not associated with cluster membership. Factors associated with cluster 1 (vs 2) membership included periodontitis, smoking, marital status and Caucasian race. Accounting for periodontitis, 10 taxa (3.5% of those examined) were in lower abundance in RA than OA. There were no associations between lower abundance taxa or other select taxa examined with RA autoantibody concentrations. CONCLUSION: Leveraging data from a large case-control study and accounting for multiple factors known to influence oral health status, results from this study failed to identify a subgingival microbial fingerprint that could reliably discriminate RA from OA patients.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-27

Curated date: 2022/11/02

Curator: Tislam

Revision editor(s): WikiWorks, Tislam, Peace Sandy, Victoria

Subjects

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: Subgingival dental plaque Subgingival plaque,Subgingival dental plaque,subgingival dental plaque

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Arthritis arthritic joint disease,arthritides,arthritis,inflammation of skeletal joint,inflammatory disorder of joint,skeletal joint inflammation,Arthritis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Osteoarthritis (OA)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Rheumatoid Arthritis (RA)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with Rheumatoid Arthritis

Group 0 sample size Number of subjects in the control (unexposed) group: 296

Group 1 sample size Number of subjects in the case (exposed) group: 260

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

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).: raw counts

Statistical test: Linear Regression

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: comorbidity, marital status, race, smoking status

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: increased

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

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Curated date: 2022/11/02

Curator: Tislam

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Source: text

Description: Differential expression of OTUs between RA and OA patients based on periodontitis status

Differential expression analysis conducted using two separate linear models: the first fitted with RA vs OA status, periodontitis status and the interaction between these factors (base model); and the second fitted with the same factors as the base model in addition to race, marital status and smoking (fully adjusted model). OTU: operational taxonomic unit; FDR: false discovery rate.

Abundance in Group 1: decreased abundance in Rheumatoid Arthritis (RA)

NCBI	Quality Control	Links
Catonella
Clostridiales bacterium
Lachnospiraceae
Peptostreptococcaceae
Porphyromonas
Prevotella multiformis
Prevotella sp.
Selenomonas
Treponema sp.

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