Dysbiotic Subgingival Microbial Communities in Periodontally Healthy Patients With Rheumatoid Arthritis

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-5
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
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


Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-5

Curated date: 2022/11/10

Curator: Tislam

Revision editor(s): WikiWorks, Claregrieve1, Tislam, Victoria

Subjects

Location of subjects
United Kingdom
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
Rheumatoid Arthritis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
periodontally healthy patients with Rheumatoid Arthritis
Group 0 sample size Number of subjects in the control (unexposed) group
19
Group 1 sample size Number of subjects in the case (exposed) group
22
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
12 weeks

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V9
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).
raw counts
Statistical test
DESeq2
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-5

Curated date: 2022/11/10

Curator: Tislam

Revision editor(s): Tislam, Aiyshaaaa, Claregrieve1

Source: Supplemental Table 1

Description: Differential microbial abundance between RA patients and controls

Abundance in Group 1: increased abundance in Rheumatoid Arthritis

NCBI Quality ControlLinks
Schaalia cardiffensis
Actinomyces dentalis
Actinomyces israelii
Actinomyces johnsonii
Actinomyces naeslundii
Actinomyces oris
Actinomyces radicidentis
Anaeroglobus geminatus
Lancefieldella parvula
Lancefieldella rimae
Bacteroidaceae
Bifidobacterium breve
Bifidobacterium dentium
Bifidobacterium longum
Bifidobacterium scardovii
Chloroflexia
Cryptobacterium curtum
Desulfobulbus
Desulfovibrio
Dialister invisus
Dialister sp.
Erysipelotrichaceae
Fretibacterium fastidiosum
Fretibacterium sp.
Johnsonella
Lachnoanaerobaculum orale
Lachnoanaerobaculum saburreum
Limosilactobacillus fermentum
Limosilactobacillus reuteri
Leptotrichia hongkongensis
Leptotrichia shahii
Leptotrichia wadei
Megasphaera
Megasphaera micronuciformis
Mitsuokella
Moryella
Metamycoplasma faucium
Metamycoplasma orale
Metamycoplasma salivarium
Olsenella
Olsenella uli
Oribacterium sp. oral taxon 078
Parascardovia denticolens
Prevotella dentalis
Prevotella denticola
Prevotella histicola
Segatella maculosa
Segatella oulorum
Hoylesella oralis
Segatella salivae
Propionibacterium acidifaciens
Scardovia wiggsiae
Selenomonas flueggei
Selenomonas sp. oral taxon 136
Selenomonas sp. oral taxon 140
Selenomonas sp. oral taxon 143
Selenomonas noxia
Selenomonas sputigena
Slackia exigua
Solobacterium moorei
Streptococcus anginosus
Streptococcus downei
Tannerella sp. oral taxon 808
TM7 phylum sp. oral taxon 346
Treponema parvum
Treponema socranskii
Treponema vincentii
Veillonella dispar
Veillonella sp. oral taxon 780
Veillonellaceae bacterium oral taxon 132
Veillonellaceae bacterium oral taxon 145
Veillonellaceae bacterium oral taxon 148
Veillonellaceae bacterium oral taxon 150
Veillonellaceae bacterium oral taxon 155
Veillonellaceae bacterium oral taxon 483

Revision editor(s): Tislam, Aiyshaaaa, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-5

Curated date: 2022/11/10

Curator: Tislam

Revision editor(s): Tislam, Claregrieve1

Source: Supplementary Table 1

Description: Differential microbial abundance between RA patients and healthy controls

Abundance in Group 1: decreased abundance in Rheumatoid Arthritis

NCBI Quality ControlLinks
Acinetobacter baumannii
Acinetobacter sp. oral taxon 408
Aggregatibacter sp. oral taxon 458
Aggregatibacter sp. oral taxon 513
Aggregatibacter segnis
Alloprevotella rava
Alloprevotella sp. oral taxon 308
Shouchella clausii
Bergeyella sp. oral taxon 322
Campylobacter showae
Capnocytophaga haemolytica
Capnocytophaga sputigena
Catonella sp. oral taxon 164
Catonella sp. oral taxon 451
Catonella morbi
Comamonas testosteroni
Desulfomicrobium orale
Eikenella corrodens
Enterococcus italicus
Enterococcus saccharolyticus
Gemella haemolysans
Gemella morbillorum
Gemella sanguinis
Granulicatella adiacens
Haemophilus haemolyticus
Haemophilus sp. oral taxon 035
Haemophilus sp. oral taxon 036
Haemophilus influenzae
Haemophilus parainfluenzae
Johnsonella ignava
Kingella oralis
Kingella denitrificans
Kingella sp. oral taxon 012
Kingella sp. oral taxon 459
Kingella kingae
Lactobacillus crispatus
Lactobacillus gasseri
Leptothrix sp. oral taxon 025
Leptotrichia sp. oral taxon 212
Lysinibacillus fusiformis
Neisseria bacilliformis
Neisseria flava
Neisseria flavescens
Neisseria meningitidis
Neisseria polysaccharea
Ottowia sp. oral taxon 894
Parvimonas sp.
Parvimonas sp. oral taxon 393
Peptococcus sp. oral taxon 167
Peptostreptococcaceae bacterium oral taxon 106
Porphyromonas catoniae
Porphyromonas sp. oral taxon 279
Porphyromonas sp. oral taxon 284
Prevotella intermedia
Hoylesella shahii
Cutibacterium acnes
Rothia dentocariosa
Rothia mucilaginosa
Pseudomonas fluorescens
Stutzerimonas stutzeri
Ectopseudomonas oleovorans
Staphylococcus caprae
Staphylococcus epidermidis
Staphylococcus warneri
Stenotrophomonas maltophilia
Streptococcus australis
Streptococcus intermedius
Streptococcus mitis
Streptococcus oralis
Streptococcus pyogenes
Streptococcus salivarius
Streptococcus vestibularis
Terrahaemophilus aromaticivorans
Treponema sp. oral taxon 250
Veillonella rogosae

Revision editor(s): Tislam, Claregrieve1