Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 2023-6-16
Subjects
- Location of subjects
- India
- 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
- age-matched controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokers who were using either bidis or cigarettes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Smokers who were using either bidis (thin, hand-rolled cigarettes composed of tobacco wrapped in a “tendu” or “temburni” leaf) or cigarettes
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
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).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2023-6-16
Source: Figure 5
Description: Differentially abundant taxa identified in smokers and controls using DESeq2.
Abundance in Group 1: increased abundance in Smokers who were using either bidis or cigarettes
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Shuttleworthella | ||
| unclassified Candidatus Saccharibacteria |
