Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis

Study information

EditHistoryDelete

Flag for review

Your review change was submittedAdd a new Experiment

• Quality control
  • Retracted paper
  • Contamination issues suspected
  • Batch effect issues suspected
  • Uncontrolled confounding suspected
  • Results are suspect (various reasons)
  • Apply tags

    Tags applied

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-1

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

22576262

DOI Digital object identifier for electronic documents.

10.1002/art.34539

URI

Authors

Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L, Attur M, Pillinger MH, Weissmann G, Littman DR, Pamer EG, Bretz WA, Abramson SB

Journal

Arthritis and rheumatism

Year

2012

OBJECTIVE: To profile the abundance and diversity of subgingival oral microbiota in patients with never-treated, new-onset rheumatoid arthritis (RA). METHODS: Periodontal disease (PD) status, clinical activity, and sociodemographic factors were determined in patients with new-onset RA, patients with chronic RA, and healthy subjects. Multiplexed-454 pyrosequencing was used to compare the composition of subgingival microbiota and establish correlations between the presence/abundance of bacteria and disease phenotypes. Anti-Porphyromonas gingivalis antibody testing was performed to assess prior exposure to the bacterial pathogen P gingivalis. RESULTS: The more advanced forms of periodontitis were already present at disease onset in patients with new-onset RA. The subgingival microbiota observed in patients with new-onset RA was distinct from that found in healthy controls. In most cases, however, these microbial differences could be attributed to the severity of PD and were not inherent to RA. The presence and abundance of P gingivalis were also directly associated with the severity of PD and were not unique to RA. The presence of P gingivalis was not correlated with anti-citrullinated protein antibody (ACPA) titers. Overall exposure to P gingivalis was similar between patients with new-onset RA and controls, observed in 78% of patients and 83% of controls. The presence and abundance of Anaeroglobus geminatus correlated with the presence of ACPAs/rheumatoid factor. Prevotella and Leptotrichia species were the only characteristic taxa observed in patients with new-onset RA irrespective of PD status. CONCLUSION: Patients with new-onset RA exhibited a high prevalence of PD at disease onset, despite their young age and paucity of smoking history. The subgingival microbiota profile in patients with new-onset RA was similar to that in patients with chronic RA and healthy subjects whose PD was of comparable severity. Although colonization with P gingivalis correlated with the severity of PD, overall exposure to P gingivalis was similar among the groups. The role of A geminatus and Prevotella/Leptotrichia species in this process merits further study.

Experiment 2

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-1

Curated date: 2024/02/01

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

Subjects

Location of subjects

United States of America

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

CRA - [Chronic Established Rheumatoid Arthritis]

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

NORA - [New-Onset Rheumatoid Arthritis] Patient

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

Patients with NORA - [New-Onset Rheumatoid Arthritis]

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

34

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

31

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

V1-V2

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

Statistical test

T-Test

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

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

age, ethnic group, sex

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

increased

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-1

Curated date: 2024/02/01

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Table 2

Description: Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit (OTU).

Abundance in Group 1: increased abundance in NORA - [New-Onset Rheumatoid Arthritis] Patient

NCBI	Quality Control	Links
Porphyromonas
Selenomonas
Prevotella
Treponema
Tannerella

Revision editor(s): Peace Sandy

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-1

Curated date: 2024/02/01

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Table 2

Description: Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit (OTU).

Abundance in Group 1: decreased abundance in NORA - [New-Onset Rheumatoid Arthritis] Patient

NCBI	Quality Control	Links
Veillonellaceae
Mitsuokella
Prevotella

Revision editor(s): Peace Sandy

Experiment 3

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-1

Curated date: 2024/02/01

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

Subjects

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 [RA] - Rheumatoid Arthritis Patients

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

All [RA] - Rheumatoid Arthritis Patients, which includes NORA [new-onset RA] and CRA [Chronic-established RA]

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

18

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

65

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

increased

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

increased

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-1

Curated date: 2024/02/01

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Table 2

Description: Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit (OTU).

Abundance in Group 1: increased abundance in All [RA] - Rheumatoid Arthritis Patients

NCBI	Quality Control	Links
Anaeroglobus
Prevotella
Selenomonas

Revision editor(s): Peace Sandy

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-1

Curated date: 2024/02/01

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Table 2

Description: Oral microbiota differ significantly among patients with new-onset rheumatoid arthritis (NORA), patients with chronic rheumatoid arthritis (CRA), and healthy control participants, and between individuals with healthy gingiva versus periodontal diseases (PD), at the level of both genus and species/operational taxonomic unit (OTU).

Abundance in Group 1: decreased abundance in All [RA] - Rheumatoid Arthritis Patients

NCBI	Quality Control	Links
Corynebacterium
Leptotrichia
Capnocytophaga

Revision editor(s): Peace Sandy