Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health
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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
- Norway
- 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
- 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
- Rheumatoid Arthritis (RA) Remission
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Active (RA) Rheumatoid Arthritis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with active rheumatoid arthritis (RA)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
- 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
- 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
- decreased
Signature 1
Source: Figure 3, text
Description: (B) Differentially discriminatory OTUs (N = 21) by RA disease activity status, as identified by linear discriminant analysis effect size (LEfSe) analysis. Active RA = grey bars; RA remission = black bars.
Abundance in Group 1: increased abundance in Active (RA) Rheumatoid Arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Corynebacterium | ||
| Prevotella | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): Tislam, Peace Sandy
Signature 2
Source: Figure 2, text
Description: (B) Differentially discriminatory OTUs (N = 21) by RA disease activity status, as identified by linear discriminant analysis effect size (LEfSe) analysis. Active RA = grey bars; RA remission = black bars.
Abundance in Group 1: decreased abundance in Active (RA) Rheumatoid Arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Atopobium | ||
| Clostridiales bacterium | ||
| Fusobacterium | ||
| Oribacterium | ||
| Prevotella | ||
| Rikenellaceae | ||
| Selenomonas |
Revision editor(s): Tislam
Experiment 2
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No prednisolone
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prednisolone
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals who received prednisolone
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: S4F Table
Description: Significantly discriminatory OTUs between the microbiome sample clusters (use - and non-use of prednisolone). From the 552 OTUs, 19 discriminated significantly use and non-use of prednisolone (LDA >2, p<0.05, LEfSe). Prednisolone (N=21)=black dots; no prednisolone (N=57)=grey dots.
Abundance in Group 1: increased abundance in Prednisolone
| NCBI | Quality Control | Links |
|---|---|---|
| Kingella | ||
| Capnocytophaga | ||
| Streptococcus | ||
| Cardiobacterium | ||
| Selenomonas |
Revision editor(s): Peace Sandy
Signature 2
Source: S4F Table
Description: Significantly discriminatory OTUs between the microbiome sample clusters (use - and non-use of prednisolone). From the 552 OTUs, 19 discriminated significantly use and non-use of prednisolone (LDA >2, p<0.05, LEfSe). Prednisolone (N=21)=black dots; no prednisolone (N=57)=grey dots.
Abundance in Group 1: decreased abundance in Prednisolone
| NCBI | Quality Control | Links |
|---|---|---|
| Atopobium | ||
| Clostridiales Family XIII bacterium | ||
| Coriobacteriaceae | ||
| Defluviitaleaceae | ||
| Dialister | ||
| Fretibacterium | ||
| Fusobacterium | ||
| Mogibacterium | ||
| Prevotella | ||
| Treponema |
Revision editor(s): Peace Sandy
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Never Smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Former Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Former Smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: S4A
Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.
Abundance in Group 1: increased abundance in Former Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Aggregatibacter | ||
| Bergeyella | ||
| Capnocytophaga | ||
| Cardiobacterium | ||
| Corynebacterium | ||
| Gemella | ||
| Haemophilus | ||
| Lautropia | ||
| Neisseria |
Revision editor(s): Peace Sandy
Signature 2
Source: S4A Table
Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.
Abundance in Group 1: decreased abundance in Former Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobaculum | ||
| Cardiobacterium | ||
| Leptotrichia | ||
| Neisseria |
Revision editor(s): Peace Sandy
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Current Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Current Smokers
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- 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
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: S4A Table
Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.
Abundance in Group 1: increased abundance in Current Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Synergistaceae | ||
| Fretibacterium | ||
| Paludibacter | ||
| Actinomyces | ||
| Treponema | ||
| Tannerella | ||
| Selenomonas | ||
| Mycoplasma | ||
| Defluviitaleaceae | ||
| Mogibacterium | ||
| Prevotella |
Revision editor(s): Peace Sandy
Signature 2
Source: S4A Table
Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.
Abundance in Group 1: decreased abundance in Current Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Leptotrichia | ||
| Actinobaculum | ||
| Neisseria | ||
| Cardiobacterium |
Revision editor(s): Peace Sandy
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Former Smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: S4A Table
Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.
Abundance in Group 1: increased abundance in Current Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Synergistaceae | ||
| Fretibacterium | ||
| Paludibacter | ||
| Actinomyces | ||
| Treponema | ||
| Tannerella | ||
| Selenomonas | ||
| Mycoplasma | ||
| Defluviitaleaceae | ||
| Mogibacterium | ||
| Prevotella |
Revision editor(s): Peace Sandy
Signature 2
Source: S4A Table
Description: S4A Table. Significantly discriminatory OTUs between the microbiome sample clusters (Smoking status). From the 552 OTUs, 37 discriminated significantly between smoking status (LDA >2, p<0.05, LEfSe). Never smokers (N=29)=green bars; former smokers (N=35)=blue bars; current smokers (N=14)=red bars.
Abundance in Group 1: decreased abundance in Current Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Corynebacterium | ||
| Haemophilus | ||
| Capnocytophaga | ||
| Aggregatibacter | ||
| Lautropia | ||
| Cardiobacterium | ||
| Gemella | ||
| Actinomyces | ||
| Bergeyella |
Revision editor(s): Peace Sandy
