The subgingival microbiome in patients with established rheumatoid arthritis

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-27
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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

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

Curated date: 2022/11/02

Curator: Tislam

Revision editor(s): Tislam, Peace Sandy

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 ControlLinks
Catonella
Clostridiales bacterium
Lachnospiraceae
Peptostreptococcaceae
Porphyromonas
Prevotella multiformis
Prevotella sp.
Selenomonas
Treponema sp.

Revision editor(s): Tislam, Peace Sandy