Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health

From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W, Bolstad AI
Journal
PloS one
Year
2018
OBJECTIVE: Rheumatoid arthritis (RA) and periodontitis are chronic inflammatory diseases that share common risk factors. However, the bidirectional relationship between RA and periodontal disease is not fully understood. This study was undertaken to describe the bacterial component of the subgingival microbiome in RA patients and to relate this to RA disease activity and periodontal status. METHODS: Patients with chronic established RA (N = 78) were periodontally examined and their subgingival plaque samples were collected; their clinical and laboratory data on RA status and medication were obtained from medical records. Bacterial DNA was quantified by universal 16S rDNA qPCR, and Porphyromonas gingivalis by species-specific qPCR. For microbiome assessment, 16S rDNA amplicon sequencing was performed. RESULTS: Active RA was diagnosed in 58% of the patients and periodontitis in 82% (mild: 9%, moderate: 55%, severe: 18%). P. gingivalis was present in 14% of the samples. Different levels of gingival bleeding, periodontal probing depth, RA disease status, prednisolone use and smoking were associated with significantly different microbiome compositions. Two subgingival microbial community types were discerned. CONCLUSION: In RA patients with active disease, anti-inflammatory medication as part of RA therapy was associated with better oral health status and a healthier subgingival microbiome compared to that of RA patients in remission, especially those in remission who were current smokers. RA patients in remission with current smoking status may particularly benefit from a systematic periodontal treatment program. The potential role of microbial community types in patient stratification and personalized therapy should be assessed in longitudinal studies.

Experiment 1


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2022/11/02

Curator: Tislam

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

Subjects

Location of subjects
Norway
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
Rheumatoid Arthritis (RA) Remission
Group 1 name Corresponds to the case (exposed) group for case-control studies
Active (RA) Rheumatoid Arthritis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals with active rheumatoid arthritis (RA)
Group 0 sample size Number of subjects in the control (unexposed) group
28
Group 1 sample size Number of subjects in the case (exposed) group
60
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
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2022/11/02

Curator: Tislam

Revision editor(s): Tislam, Peace Sandy

Source: Figure 3, text

Description: (B) Differentially discriminatory OTUs (N = 21) by RA disease activity status, as identified by linear discriminant analysis effect size (LEfSe) analysis. Active RA = grey bars; RA remission = black bars.

Abundance in Group 1: increased abundance in Active (RA) Rheumatoid Arthritis

NCBI Quality ControlLinks
Actinomyces
Corynebacterium
Prevotella
Streptococcus
Veillonella

Revision editor(s): Tislam, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2022/11/02

Curator: Tislam

Revision editor(s): Tislam

Source: Figure 2, text

Description: (B) Differentially discriminatory OTUs (N = 21) by RA disease activity status, as identified by linear discriminant analysis effect size (LEfSe) analysis. Active RA = grey bars; RA remission = black bars.

Abundance in Group 1: decreased abundance in Active (RA) Rheumatoid Arthritis

NCBI Quality ControlLinks
Atopobium
Clostridiales bacterium
Fusobacterium
Oribacterium
Prevotella
Rikenellaceae
Selenomonas

Revision editor(s): Tislam

Experiment 2


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

Subjects

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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
No prednisolone
Group 1 name Corresponds to the case (exposed) group for case-control studies
Prednisolone
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals who received prednisolone
Group 0 sample size Number of subjects in the control (unexposed) group
57
Group 1 sample size Number of subjects in the case (exposed) group
21

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: S4F Table

Description: Significantly discriminatory OTUs between the microbiome sample clusters (use - and non-use of prednisolone). From the 552 OTUs, 19 discriminated significantly use and non-use of prednisolone (LDA >2, p<0.05, LEfSe). Prednisolone (N=21)=black dots; no prednisolone (N=57)=grey dots.

Abundance in Group 1: increased abundance in Prednisolone

NCBI Quality ControlLinks
Kingella
Capnocytophaga
Streptococcus
Cardiobacterium
Selenomonas

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: S4F Table

Description: Significantly discriminatory OTUs between the microbiome sample clusters (use - and non-use of prednisolone). From the 552 OTUs, 19 discriminated significantly use and non-use of prednisolone (LDA >2, p<0.05, LEfSe). Prednisolone (N=21)=black dots; no prednisolone (N=57)=grey dots.

Abundance in Group 1: decreased abundance in Prednisolone

NCBI Quality ControlLinks
Atopobium
Clostridiales Family XIII bacterium
Coriobacteriaceae
Defluviitaleaceae
Dialister
Fretibacterium
Fusobacterium
Mogibacterium
Prevotella
Treponema

Revision editor(s): Peace Sandy

Experiment 3


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

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
Never Smokers
Group 1 name Corresponds to the case (exposed) group for case-control studies
Former Smokers
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Former Smokers
Group 0 sample size Number of subjects in the control (unexposed) group
29
Group 1 sample size Number of subjects in the case (exposed) group
35

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: S4A

Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.

Abundance in Group 1: increased abundance in Former Smokers

NCBI Quality ControlLinks
Actinomyces
Aggregatibacter
Bergeyella
Capnocytophaga
Cardiobacterium
Corynebacterium
Gemella
Haemophilus
Lautropia
Neisseria

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: S4A Table

Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.

Abundance in Group 1: decreased abundance in Former Smokers

NCBI Quality ControlLinks
Actinobaculum
Cardiobacterium
Leptotrichia
Neisseria

Revision editor(s): Peace Sandy

Experiment 4


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Current Smokers
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Current Smokers
Group 1 sample size Number of subjects in the case (exposed) group
14
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: S4A Table

Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.

Abundance in Group 1: increased abundance in Current Smokers

NCBI Quality ControlLinks
Fusobacterium
Synergistaceae
Fretibacterium
Paludibacter
Actinomyces
Treponema
Tannerella
Selenomonas
Mycoplasma
Defluviitaleaceae
Mogibacterium
Prevotella

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: S4A Table

Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.

Abundance in Group 1: decreased abundance in Current Smokers

NCBI Quality ControlLinks
Leptotrichia
Actinobaculum
Neisseria
Cardiobacterium

Revision editor(s): Peace Sandy

Experiment 5


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

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
Former Smokers
Group 0 sample size Number of subjects in the control (unexposed) group
35

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: S4A Table

Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.

Abundance in Group 1: increased abundance in Current Smokers

NCBI Quality ControlLinks
Fusobacterium
Synergistaceae
Fretibacterium
Paludibacter
Actinomyces
Treponema
Tannerella
Selenomonas
Mycoplasma
Defluviitaleaceae
Mogibacterium
Prevotella

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-20

Curated date: 2024/01/20

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: S4A Table

Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.

Abundance in Group 1: decreased abundance in Current Smokers

NCBI Quality ControlLinks
Neisseria
Corynebacterium
Haemophilus
Capnocytophaga
Aggregatibacter
Lautropia
Cardiobacterium
Gemella
Actinomyces
Bergeyella

Revision editor(s): Peace Sandy