Subgingival microbiome of deep and shallow periodontal sites in patients with rheumatoid arthritis: a pilot study
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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
- United States of America
- 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
- Subgingival dental plaque Subgingival 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy shallow
- 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
- 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
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Figure 6, text
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: decreased abundance in Rheumatoid Arthritis
NCBI | Links |
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Leptotrichia | |
Prevotella melaninogenica | |
Kingella denitrificans | |
Gemella morbillorum |
Revision editor(s): Tislam
Signature 2
Source: Figure 6, text
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 | Links |
---|---|
Streptococcus parasanguinis | |
Schaalia meyeri |
Revision editor(s): Tislam