Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening/Experiment 2
From BugSigDB
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
- 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
- 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
- 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
- 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
