Subgingival microbiome of deep and shallow periodontal sites in patients with rheumatoid arthritis: a pilot study

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

33964928

DOI Digital object identifier for electronic documents.

10.1186/s12903-021-01597-x

URI

Authors

Lehenaff R, Tamashiro R, Nascimento MM, Lee K, Jenkins R, Whitlock J, Li EC, Sidhu G, Anderson S, Progulske-Fox A, Bubb MR, Chan EKL, Wang GP

Journal

BMC oral health

Year

2021

Keywords:

16S rRNA sequencing, Microbial dysbiosis, Periodontal disease, Rheumatoid arthritis, Subgingival microbiome

BACKGROUND: Subgingival microbiome in disease-associated subgingival sites is known to be dysbiotic and significantly altered. In patients with rheumatoid arthritis (RA), the extent of dysbiosis in disease- and health-associated subgingival sites is not clear. METHODS: 8 RA and 10 non-RA subjects were recruited for this pilot study. All subjects received full oral examination and underwent collection of subgingival plaque samples from both shallow (periodontal health-associated, probing depth ≤ 3mm) and deep subgingival sites (periodontal disease-associated, probing depth ≥ 4 mm). RA subjects also had rheumatological evaluation. Plaque community profiles were analyzed using 16 S rRNA sequencing. RESULTS: The phylogenetic diversity of microbial communities in both RA and non-RA controls was significantly higher in deep subgingival sites compared to shallow sites (p = 0.022), and the overall subgingival microbiome clustered primarily according to probing depth (i.e. shallow versus deep sites), and not separated by RA status. While a large number of differentially abundant taxa and gene functions was observed between deep and shallow sites as expected in non-RA controls, we found very few differentially abundant taxa and gene functions between deep and shallow sites in RA subjects. In addition, compared to non-RA controls, the UniFrac distances between deep and shallow sites in RA subjects were smaller, suggesting increased similarity between deep and shallow subgingival microbiome in RA. Streptococcus parasanguinis and Actinomyces meyeri were overabundant in RA subjects, while Gemella morbillorum, Kingella denitrificans, Prevotella melaninogenica and Leptotrichia spp. were more abundant in non-RA subjects. CONCLUSIONS: The aggregate subgingival microbiome was not significantly different between individuals with and without rheumatoid arthritis. Although the differences in the overall subgingival microbiome was driven primarily by probing depth, in contrast to the substantial microbiome differences typically seen between deep and shallow sites in non-RA patients, the microbiome of deep and shallow sites in RA patients were more similar to each other. These results suggest that factors associated with RA may modulate the ecology of subgingival microbiome and its relationship to periodontal disease, the basis of which remains unknown but warrants further investigation.

Experiment 1

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Curated date: 2022/11/02

Curator: Tislam

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

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

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 shallow

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 patient -

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 8

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-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).: relative abundances

Statistical test: LEfSe

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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 1

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Curated date: 2022/11/02

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Source: Figure 6

Description: Differentially abundant OTUs in RA and non-RA controls. Differentially abundant OTUs were identified by LEfSe with a minimum LDA threshold of 2. Taxa enriched in non-RA controls are indicated by green bars. Those enriched in RA subjects are indicated by yellow bars. The OTUs associated with RA or non-RA controls shown were observed for both shallow and deep sites. OTU, Operational taxonomic unit

Abundance in Group 1: decreased abundance in Rheumatoid Arthritis

NCBI	Quality Control	Links
Gemella morbillorum
Kingella denitrificans
Leptotrichia
Prevotella melaninogenica

Revision editor(s): Tislam, Aiyshaaaa

Signature 2

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Mark reviewed

Your review change was submitted

Needs review

Curated date: 2022/11/02

Curator: Tislam

Revision editor(s): Tislam, Aiyshaaaa

Source: Figure 6

Description: Differentially abundant OTUs in RA and non-RA controls. Differentially abundant OTUs were identified by LEfSe with a minimum LDA threshold of 2. Taxa enriched in non-RA controls are indicated by green bars. Those enriched in RA subjects are indicated by yellow bars. The OTUs associated with RA or non-RA controls shown were observed for both shallow and deep sites. OTU, Operational taxonomic unit

Abundance in Group 1: increased abundance in Rheumatoid Arthritis

NCBI	Quality Control	Links
Schaalia meyeri
Streptococcus parasanguinis

Revision editor(s): Tislam, Aiyshaaaa