Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis

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Reviewed Marked as Reviewed by Peace Sandy on 2023-12-28

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

36077282

DOI Digital object identifier for electronic documents.

10.3390/ijms23179883

URI

Authors

Chen YJ, Hung WC, Chou YH, Lai CH, Peng P, Jhou PS, Tsai MR, Sheu JJ, Yen JH

Journal

International journal of molecular sciences

Year

2022

Keywords:

anti-citrullinated protein antibody (ACPA), microbial dysbiosis, periodontitis, rheumatoid arthritis, subgingival microbiome

Rheumatoid arthritis (RA) and periodontitis are suggested to be closely linked based on microbial dysbiosis, but limited subgingival bacteria have been proven in the pathogenesis of RA. We enrolled 30 RA patients and 25 controls and divided them into three groups with matched age, gender, and diabetes statuses: group AM (all of the matched participants), group PD (periodontally diseased), and group PH (periodontally healthy). Their subgingival microbial composition was determined by V3-V4 16S rRNA gene sequencing. Significant differences in subgingival microbial clustering between the RA patients and controls were observed in groups AM and PD. Among the taxa enriched in RA, Aminipila butyrica and Peptococcus simiae were the only two species displaying positive correlation to the level of anti-citrullinated protein antibodies (ACPAs) in both of the groups. Surprisingly, the median of relative abundances of A. butyrica and P. simiae were 0% in the controls of group PD. Furthermore, a gene encoding arginine deiminase with the capability to produce citrulline was addressed in the complete genome sequence of A. butyrica. This is the first study to elucidate the important roles of A. butyrica and P. simiae as periodontal bacteria leading to RA possibly through the induction of ACPA production.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2023-12-28

Curated date: 2022/11/02

Curator: Tislam

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

Subjects

Location of subjects

Taiwan

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

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

All Matched (AM) Rheumatoid Arthritis

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

All Matched (AM) Rheumatoid Arthritis Patients

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

21

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

21

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

3 months

Lab analysis

Sequencing type

16S

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

V3-V4

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)

0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

No

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

4

Matched on Factors on which subjects have been matched on in a case-control study

age, diabetes mellitus, sex

Alpha Diversity

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

unchanged

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2023-12-28

Curated date: 2022/11/02

Curator: Tislam

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

Source: Text , Supplementary Figure S1A

Description: he composition of subgingival microbiota between the RA patients and controls in groups AM and PD were estimated by LEfSe with the parameter of the logarithmic LDA score > 2. In group AM, 176 discriminative taxa in total were found (Supplementary Figure S1A). Of the species level with the logarithmic LDA score > 4, Streptococcus

Abundance in Group 1: increased abundance in All Matched (AM) Rheumatoid Arthritis

NCBI	Quality Control	Links
Streptococcus anginosus
Treponema denticola
unclassified Fusobacterium

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

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2023-12-28

Curated date: 2022/11/02

Curator: Tislam

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

Source: Text , Supplementary Figure S1A

Description: he composition of subgingival microbiota between the RA patients and controls in groups AM and PD were estimated by LEfSe with the parameter of the logarithmic LDA score > 2. In group AM, 176 discriminative taxa in total were found (Supplementary Figure S1A). Of the species level with the logarithmic LDA score > 4, Streptococcus

Abundance in Group 1: decreased abundance in All Matched (AM) Rheumatoid Arthritis

NCBI	Quality Control	Links
Haemophilus parainfluenzae
Streptococcus sanguinis

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

Experiment 2

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Reviewed Marked as Reviewed by Peace Sandy on 2023-12-28

Curated date: 2023/12/27

Curator: Peace Sandy

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

Periodontally diseased (PD) Rheumatoid Arthritis

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

Patients with periodontally diseased) Rheumatoid Arthritis

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

12

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

12

Lab analysis

Statistical Analysis

Alpha Diversity

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

unchanged

Chao1 Abundance-based estimator of species richness

decreased

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2023-12-28

Curated date: 2023/12/28

Curator: Peace Sandy

Revision editor(s): Peace Sandy, WikiWorks

Source: Text , Supplementary Figure S1B

Description: In group PD, a total of 129 taxa showed differential abundances between the RA patients and controls (Supplementary Figure S1B). Of the species level with the loga�rithmic LDA score > 4, S. anginosus and three unidentified species of genera Actinomyces, Fusobacterium, and Parvimonas demonstrated a significant increase in the RA patients, while Pseudomonas batumici (P. batumici) was the only enriched species found in the controls (the logarithmic LDA score = 5.42).

Abundance in Group 1: increased abundance in Periodontally diseased (PD) Rheumatoid Arthritis

NCBI	Quality Control	Links
Streptococcus anginosus
Actinomyces
Fusobacterium
Parvimonas

Revision editor(s): Peace Sandy, WikiWorks

Signature 2

EditHistoryDelete

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Reviewed Marked as Reviewed by Peace Sandy on 2023-12-28

Curated date: 2023/12/28

Curator: Peace Sandy

Revision editor(s): Peace Sandy, WikiWorks

Source: Text , Supplementary Figure S1B

Description: In group PD, a total of 129 taxa showed differential abundances between the RA patients and controls (Supplementary Figure S1B). Of the species level with the loga�rithmic LDA score > 4, S. anginosus and three unidentified species of genera Actinomyces, Fusobacterium, and Parvimonas demonstrated a significant increase in the RA patients, while Pseudomonas batumici (P. batumici) was the only enriched species found in the controls (the logarithmic LDA score = 5.42)

Abundance in Group 1: decreased abundance in Periodontally diseased (PD) Rheumatoid Arthritis

NCBI	Quality Control	Links
Pseudomonas batumici

Revision editor(s): Peace Sandy, WikiWorks