Tongue microbiome of smokeless tobacco users/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-12
Subjects
- Location of subjects
- Saudi Arabia
- 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
- non-shammah users
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- shammah users
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- participants who used shammah daily for at least one year without a period of cessation and those who had no history of shammah use
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
- 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
- V1-V3
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.015
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-12
Source: Figure 3 a & b
Description: Differentially abundant taxa
Abundance in Group 1: increased abundance in shammah users
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-12
Source: Figure 3 a & b
Description: Differentially abundant taxa
Abundance in Group 1: decreased abundance in shammah users
| NCBI | Quality Control | Links |
|---|---|---|
| Eikenella | ||
| Peptostreptococcus | ||
| Oribacterium | ||
| Eikenella corrodens | ||
| Streptococcus sp. | ||
| Oribacterium asaccharolyticum | ||
| Oribacterium sinus | ||
| Leptotrichia sp. | ||
| Archangium |
Revision editor(s): WikiWorks
