Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Liu X, Tian K, Ma X, Wang S, Luo C, Du Q
Journal
Saudi journal of biological sciences
Year
2020
OBJECTIVE: Periodontitis (PD) and rheumatoid arthritis (RA) share similar pathogenesis. Evidences indicated that oral bacteria play an important role in the etiology of both diseases. For example, Porphyromonas gingvialis connect the two diseases through immune responses. We designed this study to compare bacterial diversity in RA, PD and healthy subjects and to investigate whether there are other oral bacteria play an potential role in linking the two diseases. METHODS: This study included 3 groups of Chinese participants who visited Sichuan Provincial People's Hospital during August 2018 and March 2019. Subgingival plaques were collected from RA group (n = 54), PD group (n = 45) and normal group (n = 44). Illumina MiSeq was used to compare the composition of subgingival microbiota and analyze correlations between oral bacteria and both diseases. RESULTS: Alpha diversity Analysis reflected similar microbiome profile in RA, PD and healthy groups. But we found Treponema was significantly more abundant in the PD and RA groups than healthy group at each taxonomic level from the phylum down to the genus level. Porphyromonas, Prevotella, and Veilonella were significantly more abundant in RA while Streptococcus, Gemella, Planobacterium were verified the opposite results. CONCLUSIONS: We found no significant group differences referent to either microbial diversity or richness. But we picked out Spirochaetes which may link the two diseases. Upper/lower regulation of some microbia in RA may remind us a direction to explore the role they play in pathogenesis.
Statistical test
Mann-Whitney (Wilcoxon)
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Supragingival dental plaque Supragingival plaque,Supragingival 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
- 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 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- rheumatoid arthritis patients RA
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 54
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Three 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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 5
Description: Different relative abundance of bacterial taxonomy profiles of RA, PD and control group
Abundance in Group 1: increased abundance in rheumatoid arthritis patients
| NCBI | Links |
|---|---|
| Bacteroidia | |
| Spirochaetia | |
| Spirochaetales | |
| Spirochaetaceae | |
| Treponema |
Revision editor(s): Sophy
Signature 2
Source: Figure 6
Description: The profile of periodontal pathogens in RA and PE groups compared with controls (*P < 0.05).
Abundance in Group 1: increased abundance in rheumatoid arthritis patients
| NCBI | Links |
|---|---|
| Porphyromonas | |
| Treponema | |
| Tannerella |
Revision editor(s): Sophy
Signature 3
Source: Figure 7
Description: The profile of competitive genuses of periodontal pathogens in RA and PE groups compared with controls (*P < 0.05).
Abundance in Group 1: increased abundance in rheumatoid arthritis patients
| NCBI | Links |
|---|---|
| Prevotella |
Revision editor(s): Sophy
Signature 4
Source: Figure 7
Description: The profile of competitive genuses of periodontal pathogens in RA and PE groups compared with controls (*P < 0.05).
Abundance in Group 1: decreased abundance in rheumatoid arthritis patients
| NCBI | Links |
|---|---|
| Streptococcus |
Revision editor(s): Sophy
Experiment 2
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- periodontitis chronic pericementitis,inflammation of periodontium,Pericementitides,Pericementitis,Periodontitides,periodontitis,Periodontitis (disorder),Periodontitis, NOS,periodontium inflammation,periodontosis
- 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
- periodontal disease patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- periodontal disease patients PA
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Three months
Lab analysis
- Sequencing type
- 16S
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
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