Dysbiotic Subgingival Microbial Communities in Periodontally Healthy Patients With Rheumatoid Arthritis

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

29513935

DOI Digital object identifier for electronic documents.

10.1002/art.40485

URI Uniform resource identifier for web resources.

Authors

Lopez-Oliva I, Paropkari AD, Saraswat S, Serban S, Yonel Z, Sharma P, de Pablo P, Raza K, Filer A, Chapple I, Dietrich T, Grant MM, Kumar PS

Journal

Arthritis & rheumatology (Hoboken, N.J.)

Year

2018

OBJECTIVE: Studies that demonstrate an association between rheumatoid arthritis (RA) and dysbiotic oral microbiomes are often confounded by the presence of extensive periodontitis in these individuals. This study was undertaken to investigate the role of RA in modulating the periodontal microbiome by comparing periodontally healthy individuals with RA to those without RA. METHODS: Subgingival plaque was collected from periodontally healthy individuals (22 with RA and 19 without RA), and the 16S gene was sequenced on an Illumina MiSeq platform. Bacterial biodiversity and co-occurrence patterns were examined using the QIIME and PhyloToAST pipelines. RESULTS: The subgingival microbiomes differed significantly between patients with RA and controls based on both community membership and the abundance of lineages, with 41.9% of the community differing in abundance and 19% in membership. In contrast to the sparse and predominantly congeneric co-occurrence networks seen in controls, RA patients revealed a highly connected grid containing a large intergeneric hub anchored by known periodontal pathogens. Predictive metagenomic analysis (PICRUSt) demonstrated that arachidonic acid and ester lipid metabolism pathways might partly explain the robustness of this clustering. As expected from a periodontally healthy cohort, Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans were not significantly different between groups; however, Cryptobacterium curtum, another organism capable of producing large amounts of citrulline, emerged as a robust discriminant of the microbiome in individuals with RA. CONCLUSION: Our data demonstrate that the oral microbiome in RA is enriched for inflammophilic and citrulline-producing organisms, which may play a role in the production of autoantigenic citrullinated peptides in RA.

Experiment 1

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Curated date: 2022/11/10

Curator: Tislam

Revision editor(s): Tislam, WikiWorks

Subjects

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

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
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Rheumatoid Arthritis
Group 0 sample size Number of subjects in the control (unexposed) group: 64
Group 1 sample size Number of subjects in the case (exposed) group: 35
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): N/A

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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

Statistical Analysis

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): .05
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

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

Signature 1

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Curated date: 2022/11/10

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Source: Text, Figure 3

Description: Most highly differentially abundant bacteria in buccal swab samples from patients with RA and non-RA control individuals by the LEfSE (linear discriminant analysis effect size) analysis. The graph demonstrates log10-fold change for the most highly enriched bacterial (A) genera and (B) species in RA (dark gray bars) and non-RA controls (light gray bars). All bacterial species and genera listed showed an adjusted p-value < 0.05. RA, rheumatoid arthritis; HMT, human oral taxon.

Abundance in Group 1: decreased abundance in Rheumatoid Arthritis

NCBI	Links
Fusobacterium periodonticum
Granulicatella elegans
Leptotrichia sp.
Porphyromonas endodontalis
Prevotella melaninogenica
Prevotella sp.
Treponema sp.
Veillonella parvula
uncultured Bacteroidetes bacterium

Revision editor(s): Tislam, Aiyshaaaa

Signature 2

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2022/11/10

Curator: Tislam

Revision editor(s): Tislam

Source: Text, Figure 3

Description: Most highly differentially abundant bacteria in buccal swab samples from patients with RA and non-RA control individuals by the LEfSE (linear discriminant analysis effect size) analysis. The graph demonstrates log10-fold change for the most highly enriched bacterial (A) genera and (B) species in RA (dark gray bars) and non-RA controls (light gray bars). All bacterial species and genera listed showed an adjusted p-value < 0.05. RA, rheumatoid arthritis; HMT, human oral taxon.

Abundance in Group 1: increased abundance in Rheumatoid Arthritis

NCBI	Links
Streptococcus salivarius
Rothia mucilaginosa
Prevotella sp.
Leptotrichia sp.
Selenomonas flueggei

Revision editor(s): Tislam