Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users/Experiment 6
From BugSigDB
Subjects
- Location of subjects
- United States of America
- 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 epithelium Buccal epithelium,buccal epithelium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking behaviour measurement Smoking behaviour measurement,smoking behaviour measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Smokeless tobacco user (ST).
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-tobacco users (NU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Users who had never used a tobacco product in their lifetime.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 Months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- Kruskall-Wallis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- age, race, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig 5B
Description: Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: increased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Streptococcus sp. | ||
| uncultured Actinomyces sp. | ||
| uncultured Mogibacteriaceaeuncultured Mogibacteriaceae | ||
| uncultured Oribacterium sp. | ||
| uncultured Peptostreptococcus sp. |
Revision editor(s): Shulamite
Signature 2
Source: Fig 5B
Description: Relative abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between (a) non-users (NU) and cigarette users (CG) and (b) non-users (NU) and smokeless tobacco users (ST).
Abundance in Group 1: decreased abundance in Non-tobacco users (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Neisseria sp. | ||
| uncultured Achromobacter sp. | ||
| Neisseria subflava | ||
| Haemophilus parainfluenzae |
Revision editor(s): Shulamite
