Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users/Experiment 7
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 mucosa Buccal mucosa,buccal mucosa
- 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
- Non-tobacco users at Time 1 (NU)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-tobacco users at Time 4 (NU)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who had either never used tobacco products or had smoked less than 20 cigarettes or used smokeless tobacco less than 20 times in their lifetime at time point 4.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- 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
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2a
Description: Differential abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.
Abundance in Group 1: increased abundance in Non-tobacco users at Time 4 (NU)
Signature 2
Source: Figure 2a
Description: Differential abundance of bacterial OTUs in buccal swab samples that were statistically significantly different (α = 0.001) between time-points 1 and 4. The OTUs are colored by user groups (cigarette user (CG), orange; smokeless tobacco user (ST), green; non-user (NU), grey). A positive log2-fold change value denotes an OTU that is significantly higher in time-point 1 samples, while a negative log2-fold change indicates an OTU that is significantly higher in time-point 4 samples.
Abundance in Group 1: decreased abundance in Non-tobacco users at Time 4 (NU)
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Lactobacillus | ||
| unclassified Blautia | ||
| unclassified Staphylococcus | ||
| Enterobacter cloacae | ||
| Streptococcus lutetiensis |
Revision editor(s): Victoria
