Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31
Curated date: 2022/11/02
Curator: Tislam
Revision editor(s): Tislam, WikiWorks, Peace Sandy, LGeistlinger
Subjects
- Location of subjects
- United States of America
- 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 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
- Early Rheumatoid Arthritis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Early Rheumatoid Arthritis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 61
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- 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
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31
Source: Figure 3 (B)
Description: (b) Bar graph showing species and genera with an LDA score > 2.0. A star (*) by the species indicates that it was detected as influential in the OPLS-DA model too
Abundance in Group 1: increased abundance in Early Rheumatoid Arthritis
Revision editor(s): Tislam, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-31
Source: Figure 3 (B)
Description: (b) Bar graph showing species and genera with an LDA score > 2.0. A star (*) by the species indicates that it was detected as influential in the OPLS-DA model too
Abundance in Group 1: decreased abundance in Early Rheumatoid Arthritis
Revision editor(s): Tislam, Peace Sandy
