Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Canada
- 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
- Internal cheek pouch Internal buccal pouch,Internal cheek pouch,internal cheek pouch
- 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
- Non Rheumatoid Arthritis
- 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
- Individual who have been diagnosed with Rheumatoid Arthritis(RA).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3(a&b)
Description: Linear discriminant analysis (LDA) effect size (LEfSe) analysis demonstrated differences in the relative abundance of some taxa between RA and non-RA controls at genus and species level.
Abundance in Group 1: increased abundance in Rheumatoid Arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Rothia | ||
| Leptotrichia | ||
| Streptococcus salivarius | ||
| Rothia mucilaginosa | ||
| Selenomonas flueggei |
Revision editor(s): Aiyshaaaa
Signature 2
Source: Figure 3(a&b)
Description: Linear discriminant analysis (LDA) effect size (LEfSe) analysis demonstrated differences in the relative abundance of some taxa between RA and non-RA controls at genus and species level.
Abundance in Group 1: decreased abundance in Rheumatoid Arthritis
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sensory perception of bitter taste bitter taste perception,bitter taste sensitivity,Sensory perception of bitter taste,sensory perception of bitter taste
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 4(a)
Description: Most highly differentially abundant bacteria in RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE
Abundance in Group 1: decreased abundance in rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”)
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter rectus | ||
| Selenomonas artemidis | ||
| Corynebacterium durum | ||
| Capnocytophaga sputigena | ||
| Candidatus Absconditabacteria bacterium | ||
| Leptotrichia sp. |
Revision editor(s): Atrayees
Signature 2
Source: Figure 4(b)
Description: Most highly differentially abundant bacteria in RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE
Abundance in Group 1: increased abundance in rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus salivarius |
Revision editor(s): Atrayees
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-rheumatoid arthritis patients carrying the AVI/AVI genotype (“non-tasters”)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 64
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 4(b)
Description: Most highly differentially abundant bacteria in non-RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE
Abundance in Group 1: decreased abundance in Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”)
| NCBI | Quality Control | Links |
|---|---|---|
| Lancefieldella parvula |
Revision editor(s): Atrayees
Signature 2
Source: Figure 4(b)
Description: Most highly differentially abundant bacteria in non-RA patients in buccal swab samples from participants with the homozygous AVI/AVI and PAV/PAV TAS2R38 genotypes by the LEfSE
Abundance in Group 1: increased abundance in Non-rheumatoid arthritis patients with the homozygous PAV/PAV (“supertasters”)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella histicola | ||
| Megasphaera micronuciformis | ||
| Segatella salivae | ||
| Candidatus Saccharibacteria | ||
| Catonella morbi | ||
| Veillonella rogosae | ||
| Oribacterium asaccharolyticum |
Revision editor(s): Atrayees
