The subgingival microbiome of clinically healthy current and never smokers
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Mason MR, Preshaw PM, Nagaraja HN, Dabdoub SM, Rahman A, Kumar PS
Journal
The ISME journal
Year
2015
Dysbiotic oral bacterial communities have a critical role in the etiology and progression of periodontal diseases. The goal of this study was to investigate the extent to which smoking increases risk for disease by influencing the composition of the subgingival microbiome in states of clinical health. Subgingival plaque samples were collected from 200 systemically and periodontally healthy smokers and nonsmokers. 16S pyrotag sequencing was preformed generating 1,623,713 classifiable sequences, which were compared with a curated version of the Greengenes database using the quantitative insights into microbial ecology pipeline. The subgingival microbial profiles of smokers and never-smokers were different at all taxonomic levels, and principal coordinate analysis revealed distinct clustering of the microbial communities based on smoking status. Smokers demonstrated a highly diverse, pathogen-rich, commensal-poor, anaerobic microbiome that is more closely aligned with a disease-associated community in clinically healthy individuals, suggesting that it creates an at-risk-for-harm environment that is primed for a future ecological catastrophe.
Statistical test
T-Test
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-3-28
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
- smoking behavior smoking,smoking behavior
- 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
- Healthy Current Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- people who are current smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 100
- 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-V9
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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)?
- No
- Matched on Factors on which subjects have been matched on in a case-control study
- age, education level, race, sex, socioeconomic status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Subject page title: | The subgingival microbiome of clinically healthy current and never smokers/Experiment 1/Signature 1 |
---|---|
Reviewer: | Claregrieve1 |
Review date: | 2023-3-28 |
Review state: | Reviewed |
Quality control tags: |
Needs review
Source: Text
Description: The relative abundance of selected species in current smokers and nonsmokers.
Abundance in Group 1: increased abundance in Healthy Current Smokers
Revision editor(s): Kelvin Joseph, Claregrieve1
Signature 2
Subject page title: | The subgingival microbiome of clinically healthy current and never smokers/Experiment 1/Signature 2 |
---|---|
Reviewer: | Claregrieve1 |
Review date: | 2023-3-28 |
Review state: | Reviewed |
Quality control tags: |
Needs review
Source: Text
Description: The relative abundance of selected species in current smokers and nonsmokers.
Abundance in Group 1: decreased abundance in Healthy Current Smokers
Revision editor(s): Kelvin Joseph, Claregrieve1
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