Differences in the Oral Microbiome in Patients With Early Rheumatoid Arthritis and Individuals at Risk of Rheumatoid Arthritis Compared to Healthy Individuals/Experiment 1
Curated date: 2022/11/09
Curator: Tislam
Revision editor(s): Tislam, Claregrieve1, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- Netherlands
- 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
- Arthritis arthritic joint disease,arthritides,arthritis,inflammation of skeletal joint,inflammatory disorder of joint,skeletal joint inflammation,Arthritis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Early Rheumatoid Arthritis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Early Rheumatoid Arthritis patients (diagnosed within the previous year)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
- 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
- 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)
- 0.05
- 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
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Table 3
Description: Saliva: a summary of the most significant zero-radius operational taxonomic units (zOTUs) that differentiated among the early rheumatoid arthritis (RA) group, at-risk group, and control group, sorted on linear discriminant analysis (LDA) score per group. Differences in relative abundance among the groups were tested with a Kruskal-Wallis test (false discovery rate corrected level of significance of 0.02), and post-hoc Mann-Whitney U tests. Results for zOTUs with a median relative abundance ≥0.01 for ≥1 group are marked with an outline.
Abundance in Group 1: decreased abundance in Early Rheumatoid Arthritis
Signature 2
Source: Supplementary Table 3
Description: Saliva: a summary of the most significant zero-radius operational taxonomic units (zOTUs) that differentiated among the early rheumatoid arthritis (RA) group, at-risk group, and control group, sorted on linear discriminant analysis (LDA) score per group. Differences in relative abundance among the groups were tested with a Kruskal-Wallis test (false discovery rate corrected level of significance of 0.02), and post-hoc Mann-Whitney U tests. Results for zOTUs with a median relative abundance ≥0.01 for ≥1 group are marked with an outline.
Abundance in Group 1: increased abundance in Early Rheumatoid Arthritis
