Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Esberg A, Johansson L, Johansson I, Dahlqvist SR
Journal
Microorganisms
Year
2021
Keywords:
16S rDNA sequencing, oral microbiota, periodontitis, rheumatoid arthritis
Rheumatoid arthritis (RA) is the most common autoimmune inflammatory disease, and single periodontitis-associated bacteria have been suggested in disease manifestation. Here, the oral microbiota was characterized in relation to the early onset of RA (eRA) taking periodontal status into consideration. 16S rRNA gene amplicon sequencing of saliva bacterial DNA from 61 eRA patients without disease-modifying anti-rheumatic drugs and 59 matched controls was performed. Taxonomic classification at 98.5% was conducted against the Human Oral Microbiome Database, microbiota functions were predicted using PICRUSt, and periodontal status linked from the Swedish quality register for clinically assessed caries and periodontitis. The participants were classified into three distinct microbiota-based cluster groups with cluster allocation differences by eRA status. Independently of periodontal status, eRA patients had enriched levels of Prevotella pleuritidis, Treponema denticola, Porphyromonas endodontalis and Filifactor alocis species and in the Porphyromonas and Fusobacterium genera and functions linked to ornithine metabolism, glucosylceramidase, beta-lactamase resistance, biphenyl degradation, fatty acid metabolism and 17-beta-estradiol-17-dehydrogenase metabolism. The results support a deviating oral microbiota composition already in eRA patients compared with healthy controls and highlight a panel of oral bacteria that may be useful in eRA risk assessment in both periodontally healthy and diseased persons.

Experiment 1


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31

Curated date: 2022/11/02

Curator: Tislam

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

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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
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
Early Rheumatoid Arthritis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with Early Rheumatoid Arthritis
Group 0 sample size Number of subjects in the control (unexposed) group
59
Group 1 sample size Number of subjects in the case (exposed) group
61
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)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31

Curated date: 2022/11/02

Curator: Tislam

Revision editor(s): Tislam, Peace Sandy

Source: Figure 3 (B)

Description: (b) Bar graph showing species and genera with an LDA score > 2.0. A star (*) by the species indicates that it was detected as influential in the OPLS-DA model too

Abundance in Group 1: increased abundance in Early Rheumatoid Arthritis

NCBI Quality ControlLinks
Alloprevotella tannerae
Fusobacterium polymorphum
Capnocytophaga leadbetteri
Prevotella sp. oral taxon 314
Porphyromonas endodontalis
Fusobacterium vincentii
Neisseria elongata
Prevotella intermedia
Hoylesella pleuritidis
Prevotella veroralis
Aggregatibacter sp.
Treponema denticola
Campylobacter gracilis
Filifactor alocis
Parvimonas micra
TM7 phylum sp. oral taxon 349
Hoylesella saccharolytica
Treponema sp.
Segatella maculosa
Prevotella dentalis
Bulleidia extructa
Fretibacterium sp.
Capnocytophaga
Treponema
Lactobacillus
Dialister
Filifactor
Fretibacterium
Bulleidia
Bacteroidota

Revision editor(s): Tislam, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31

Curated date: 2022/11/02

Curator: Tislam

Revision editor(s): Tislam, Peace Sandy

Source: Figure 3 (B)

Description: (b) Bar graph showing species and genera with an LDA score > 2.0. A star (*) by the species indicates that it was detected as influential in the OPLS-DA model too

Abundance in Group 1: decreased abundance in Early Rheumatoid Arthritis

NCBI Quality ControlLinks
Actinomyces
Actinomyces sp.
Campylobacter concisus
Catonella
Catonella morbi
Lautropia
Lautropia mirabilis
Oribacterium
Oribacterium sinus
Stomatobaculum
Veillonella
Veillonella rogosae
uncultured Stomatobaculum sp.

Revision editor(s): Tislam, Peace Sandy