Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening
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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
Authors
Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi Z, Gai X, Heng C, Zhang J, Yang L, Zhang
Journal
Scientific reports
Year
2018
The key to arthritis management is early diagnosis and treatment to prevent further joint destruction and maximize functional ability. Osteoarthritis (OA) and rheumatoid arthritis (RA) are two common types of arthritis that the primary care provider must differentiate, in terms of diagnosis and treatment. Effective and non-invasive strategies for early detection and disease identification are sorely needed. Growing evidence suggests that RA has a correlation with oral microbiome and may be affected by its dynamic variations. There is already a study comparing oral microbiome in patients with RA and OA, however, it did not screen for potential biomarkers for arthritis. In this study, we assessed the oral microbiome in saliva samples from 110 RA patients, 67 OA patients and 155 healthy subjects, using 16S rRNA gene amplicon sequencing. The structure and differences in oral microbiome between RA, OA and healthy subjects were analyzed. Eight oral bacterial biomarkers were identified to differentiate RA from OA. This report provides proof of oral microbiota as an informative source for discovering non-invasive biomarkers for arthritis screening.
Experiment 1
Reviewed Marked as Reviewed by Chloe on 2022/03/22
Subjects
- Location of subjects
- China
- 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 , Osteoarthritis 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,Arthritides, Degenerative,Arthritis, Degenerative,arthrosis,Degenerative Arthritides,Degenerative Arthritis,degenerative arthritis,degenerative joint disease,hypertrophic arthritis,OA,Osteoarthritides,osteoarthritis,Osteoarthroses,Osteoarthrosis,osteoarthrosis,osteoarthrosis and allied disorder,Osteoarthrosis Deformans,Osteoarthritis
- 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
- arthritis patient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- arthritis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 155
- Group 1 sample size Number of subjects in the case (exposed) group
- 177
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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)
- .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
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Chloe on 2022/03/22
Source: Figure 2, text
Description: (c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).
Abundance in Group 1: increased abundance in arthritis patient
Revision editor(s): Tislam
Signature 2
Reviewed Marked as Reviewed by Chloe on 2022/03/22
Source: Figure 2, text
Description: (c) Histogram of the LDA scores, where the LDA score indicates the effective size and ranking of each differentially abundant taxon (LDA > 2).
Abundance in Group 1: decreased abundance in arthritis patient
Revision editor(s): Tislam
Experiment 2
Reviewed Marked as Reviewed by Chloe on 2022/03/22
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Rheumatoid arthritis , Osteoarthritis 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,Arthritides, Degenerative,Arthritis, Degenerative,arthrosis,Degenerative Arthritides,Degenerative Arthritis,degenerative arthritis,degenerative joint disease,hypertrophic arthritis,OA,Osteoarthritides,osteoarthritis,Osteoarthroses,Osteoarthrosis,osteoarthrosis,osteoarthrosis and allied disorder,Osteoarthrosis Deformans,Osteoarthritis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Osteoarthritis
- 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
- patient with rheumatoid arthritis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 67
- Group 1 sample size Number of subjects in the case (exposed) group
- 110
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Chloe on 2022/03/22
Source: Figure 2, text
Description: c) Histogram of the LDA scores, where the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).
Abundance in Group 1: increased abundance in rheumatoid arthritis
Revision editor(s): Tislam
Signature 2
Reviewed Marked as Reviewed by Chloe on 2022/03/22
Source: Figure 2
Description: (c) Histogram of the LDA scores, where the LDA score indicates the efective size and ranking of each diferentially abundant taxon (LDA>2).
Abundance in Group 1: decreased abundance in rheumatoid arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Actinomyces | ||
| Lautropia | ||
| Rothia | ||
| Granulicatella | ||
| Rothia dentocariosa | ||
| Ruminococcus | ||
| Oribacterium | ||
| Mediterraneibacter gnavus | ||
| Abiotrophia |
Revision editor(s): Tislam
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