Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8
Subjects
- Location of subjects
- Turkey
- 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
- Buccal mucosa Buccal mucosa,buccal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking behavior smoking,Smoking behavior,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who smoke cigarettes that fulfilled the inclusion criteria for good health: no use of antibiotics in the past 3 months, no respiratory infections, no oral aphthous lesions on buccal mucosa, and absence of dental problems
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- 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
- V2-V9
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8
Source: Table 2
Description: Comparison of statistically significant differences between smoker and non-smoker groups at genus and species levels
Abundance in Group 1: increased abundance in smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Veillonella | ||
| Streptococcus australis | ||
| Segatella salivae | ||
| Prevotella melaninogenica | ||
| Rothia mucilaginosa | ||
| Veillonella atypica |
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