Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis

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Reviewed Marked as Reviewed by Atrayees on 2023-7-26

Curated date: 2022/11/08

Curator: Tislam

Revision editor(s): Tislam, WikiWorks, Aiyshaaaa, Atrayees

Subjects

Location of subjects: Canada

Host species Species from which microbiome was sampled (if applicable): 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

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

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

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Reviewed Marked as Reviewed by Atrayees on 2023-7-26

Curated date: 2023/04/01

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa

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

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Streptococcus
Rothia
Leptotrichia
Streptococcus salivarius
Rothia mucilaginosa
Selenomonas flueggei

Revision editor(s): Aiyshaaaa

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Flag for review

Reviewed Marked as Reviewed by Atrayees on 2023-7-26

Curated date: 2023/04/01

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa, Atrayees

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

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Capnocytophaga
Aggregatibacter
Porphyromonas
Fusobacterium
Porphyromonas endodontalis
Veillonella parvula
Granulicatella elegans
Fusobacterium periodonticum
Prevotella melaninogenica
Bacteroidota bacterium

Revision editor(s): Aiyshaaaa, Atrayees

Experiment 2

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Needs review

Curated date: 2023/07/26

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

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: 35

Lab analysis

Statistical Analysis

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

Needs review

Curated date: 2023/07/26

Curator: Atrayees

Revision editor(s): Atrayees

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”)

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Campylobacter rectus
Selenomonas artemidis
Corynebacterium durum
Capnocytophaga sputigena
Candidatus Absconditabacteria bacterium
Leptotrichia sp.

Revision editor(s): Atrayees

Signature 2

Needs review

Curated date: 2023/07/26

Curator: Atrayees

Revision editor(s): Atrayees

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”)

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Streptococcus salivarius

Revision editor(s): Atrayees

Experiment 3

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Needs review

Curated date: 2023/07/26

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

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

Needs review

Curated date: 2023/07/26

Curator: Atrayees

Revision editor(s): Atrayees

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”)

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Lancefieldella parvula

Revision editor(s): Atrayees

Signature 2

Needs review

Curated date: 2023/07/26

Curator: Atrayees

Revision editor(s): Atrayees

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”)

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Prevotella histicola
Megasphaera micronuciformis
Prevotella salivae
Candidatus Saccharibacteria
Catonella morbi
Veillonella rogosae
Oribacterium asaccharolyticum

Revision editor(s): Atrayees

Experiment 4

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Needs review

Curated date: 2023/07/26

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: All participants carrying the AVI/AVI genotype (“non-tasters”)
Group 1 name Corresponds to the case (exposed) group for case-control studies: All participants with the homozygous PAV/PAV (“supertasters”)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: All participants with the homozygous PAV/PAV (“supertasters”)
Group 0 sample size Number of subjects in the control (unexposed) group: 99
Group 1 sample size Number of subjects in the case (exposed) group: 99

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

Needs review

Curated date: 2023/07/26

Curator: Atrayees

Revision editor(s): Atrayees

Source: Figure 4(c)

Description: Most highly differentially abundant bacteria in all 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 All participants with the homozygous PAV/PAV (“supertasters”)

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Abiotrophia defectiva

Revision editor(s): Atrayees

Signature 2