Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis/Experiment 1
Subjects
- Location of subjects
- Taiwan
- 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
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- All Matched (AM) Rheumatoid Arthritis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All Matched (AM) Rheumatoid Arthritis Patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- 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
- V3-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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age, diabetes mellitus, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Text , Supplementary Figure S1A
Description: he composition of subgingival microbiota between the RA patients and controls in groups AM and PD were estimated by LEfSe with the parameter of the logarithmic LDA score > 2. In group AM, 176 discriminative taxa in total were found (Supplementary Figure S1A). Of the species level with the logarithmic LDA score > 4, Streptococcus
Abundance in Group 1: increased abundance in All Matched (AM) Rheumatoid Arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus anginosus | ||
| Treponema denticola | ||
| unclassified Fusobacterium |
Revision editor(s): Tislam, Peace Sandy
Signature 2
Source: Text , Supplementary Figure S1A
Description: he composition of subgingival microbiota between the RA patients and controls in groups AM and PD were estimated by LEfSe with the parameter of the logarithmic LDA score > 2. In group AM, 176 discriminative taxa in total were found (Supplementary Figure S1A). Of the species level with the logarithmic LDA score > 4, Streptococcus
Abundance in Group 1: decreased abundance in All Matched (AM) Rheumatoid Arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae | ||
| Streptococcus sanguinis |
Revision editor(s): Tislam, Peace Sandy
