The relationship between cigarette smoking and the tongue microbiome in an East Asian population/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Subjects
- Location of subjects
- Japan
- 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
- Tongue Glossus,Tongue,tongue
- 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
- never smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- current smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- participants who underwent tongue-coating analysis in 2016 and 2017
- Group 0 sample size Number of subjects in the control (unexposed) group
- 384
- Group 1 sample size Number of subjects in the case (exposed) group
- 144
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)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, alcohol drinking, body mass index, dental caries, number of teeth measurement, peridontal microbiome, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 3(a)
Description: The result of comparison of bacterial abundance at the genus level
Abundance in Group 1: increased abundance in current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia | ||
| Streptococcus | ||
| Atopobium | ||
| Megasphaera | ||
| Corynebacterium | ||
| Paludibacter | ||
| Anaerovorax | ||
| Tannerella | ||
| Filifactor | ||
| Mycoplasma |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 3(a)
Description: The result of comparison of bacterial abundance at the genus level
Abundance in Group 1: decreased abundance in current smokers
