Oral Microbiota Perturbations Are Linked to High Risk for 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
- China
- 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
- Pre - High risk Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA, anti-citrullinated protein antibodies;
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Individuals having a history of antibiotics treatment or surgery in the last 3 months were excluded
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
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- age, ethnic group, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 3B, text
Description: FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.
Abundance in Group 1: increased abundance in Pre - High risk Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Gemella |
Revision editor(s): Tislam, Atrayees, Peace Sandy
Signature 2
Source: Figure 3, text
Description: FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.
Abundance in Group 1: decreased abundance in Pre - High risk Patients
Revision editor(s): Tislam, Peace Sandy
Experiment 2
Subjects
- 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 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
- Patients with Rheumatoid Arthritis
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 3, text
Description: FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.
Abundance in Group 1: increased abundance in Rheumatoid Arthritis
Revision editor(s): Peace Sandy
Signature 2
Source: Figure 3, text
Description: FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.
Abundance in Group 1: decreased abundance in Rheumatoid Arthritis
Revision editor(s): Peace Sandy
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Rheumatoid Arthritis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pre - High risk Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pre, “pre-clinical” at risk for RA individuals; RF, rheumatoid factor; ACPA, anti-citrullinated protein antibodies;
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 3, text
Description: FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.
Abundance in Group 1: increased abundance in Pre - High risk Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Gemella |
Revision editor(s): Peace Sandy
Signature 2
Source: Figure 3, text
Description: FIGURE 3 LEfSe analysis revealed the specific taxa changes in high-risk individuals (Pre) and RA patients. LefSe analysis was applied to identify differentially abundant taxa and for which the LDA scores more than 3 are shown (B). LefSe, the LDA effect size. *p < 0.05; **p < 0.01; and ***p < 0.001.
Abundance in Group 1: decreased abundance in Pre - High risk Patients
Revision editor(s): Peace Sandy
