Subgingival microbiome of deep and shallow periodontal sites in patients with rheumatoid arthritis: a pilot study/Experiment 1
Curated date: 2022/11/02
Curator: Tislam
Revision editor(s): WikiWorks, Tislam, Aiyshaaaa, Peace Sandy
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
- 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
- Healthy Non-RA Controls
- 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
- Biologic Naive Rheumatoid Arthritis patient
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- 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
- 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).
- relative abundances
- Statistical test
- LEfSe
- 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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Curated date: 2022/11/02
Curator: Tislam
Revision editor(s): WikiWorks, Tislam, Aiyshaaaa, Peace Sandy
Source: Figure 6
Description: Differentially abundant OTUs in RA and non-RA controls. Differentially abundant OTUs were identified by LEfSe with a minimum LDA threshold of 2. Taxa enriched in non-RA controls are indicated by green bars. Those enriched in RA subjects are indicated by yellow bars. The OTUs associated with RA or non-RA controls shown were observed for both shallow and deep sites. OTU, Operational taxonomic unit
Abundance in Group 1: increased abundance in Rheumatoid Arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Schaalia meyeri | ||
| Streptococcus parasanguinis |
Revision editor(s): WikiWorks, Tislam, Aiyshaaaa, Peace Sandy
Signature 2
Curated date: 2022/11/02
Curator: Tislam
Revision editor(s): WikiWorks, Tislam, Aiyshaaaa, Peace Sandy
Source: Figure 6
Description: Differentially abundant OTUs in RA and non-RA controls. Differentially abundant OTUs were identified by LEfSe with a minimum LDA threshold of 2. Taxa enriched in non-RA controls are indicated by green bars. Those enriched in RA subjects are indicated by yellow bars. The OTUs associated with RA or non-RA controls shown were observed for both shallow and deep sites. OTU, Operational taxonomic unit
Abundance in Group 1: increased abundance in Rheumatoid Arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella morbillorum | ||
| Kingella denitrificans | ||
| Leptotrichia | ||
| Prevotella melaninogenica |
Revision editor(s): WikiWorks, Tislam, Aiyshaaaa, Peace Sandy
