The subgingival microbiome in patients with established rheumatoid arthritis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-27
Curated date: 2022/11/02
Curator: Tislam
Revision editor(s): WikiWorks, Tislam, Peace Sandy, Victoria
Subjects
- 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
- 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
- Osteoarthritis (OA)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rheumatoid Arthritis (RA)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Rheumatoid Arthritis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 296
- Group 1 sample size Number of subjects in the case (exposed) group
- 260
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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).
- raw counts
- Statistical test
- Linear Regression
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- comorbidity, marital status, race, smoking status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-27
Source: text
Description: Differential expression of OTUs between RA and OA patients based on periodontitis status
Differential expression analysis conducted using two separate linear models: the first fitted with RA vs OA status, periodontitis status and the interaction between these factors (base model); and the second fitted with the same factors as the base model in addition to race, marital status and smoking (fully adjusted model). OTU: operational taxonomic unit; FDR: false discovery rate.
Abundance in Group 1: decreased abundance in Rheumatoid Arthritis (RA)
| NCBI | Quality Control | Links |
|---|---|---|
| Catonella | ||
| Clostridiales bacterium | ||
| Lachnospiraceae | ||
| Peptostreptococcaceae | ||
| Porphyromonas | ||
| Prevotella multiformis | ||
| Prevotella sp. | ||
| Selenomonas | ||
| Treponema sp. |
Revision editor(s): Tislam, Peace Sandy
