Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
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 |
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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 |
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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 |
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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