The subgingival microbiome in patients with established 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
- 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
- Osteoarthritis with periodontitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rheumatoid Arthritis with periodontitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rheumatoid Arthritis patients with periodontitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 81
- Group 1 sample size Number of subjects in the case (exposed) group
- 99
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
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- comorbidity, marital status, race, smoking status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: text
Description: Excluding taxa for which >75% of patients in all four groups had zero values, there were 286 OTUs available for analysis. Among those with periodontitis, there were 10 OTUs (3.5% of OTUs examined) in lower abundance in RA vs OA samples in the base model with false discovery rate-adjusted P-values. These taxa included Catonella sp. (OTU 451), Clostridiales sp. (OTU 85), Lachnospiraceae sp. (OTU 96), Peptostreptococcaceae sp. (OTU 495), Porphyromonas sp. (OTU 285), Prevotella multiformis (OTU 685), Prevotella sp. (OTU 443), Selenomaonas sp. (OTU 479) and Treponema sp. (OTUs 230 and 236) (Table 4). Results were unchanged following full adjustment, with the exception that differential expression of Selenomaonas sp. was no longer significant. Although we observed evidence to suggest the under-abundance of Porphyromonas sp. in RA patients with periodontitis compared with OA patients with periodontitis, there was not similar evidence of differential expression for P. gingivalis (data not shown). In subjects without evidence of periodontitis, only one OTU was found in lower abundance in RA samples and in the fully adjusted model after accounting for false discovery rate, Streptococcus sp. (OTU 486), a difference that did not achieve statistical significance in the base model. There were no OTUs identified in the filtered data consistent with A. actinomycetemcomitans.
Abundance in Group 1: decreased abundance in Rheumatoid Arthritis with periodontitis
NCBI | Quality Control | Links |
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Catonella | ||
Clostridiales bacterium | ||
Lachnospiraceae | ||
Peptostreptococcaceae | ||
Porphyromonas | ||
Prevotella sp. | ||
Selenomonas | ||
Treponema sp. | ||
Prevotella multiformis |
Revision editor(s): Tislam