Sociodemographic variation in the oral microbiome/Experiment 6
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-15
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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- 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
- Cigarette smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Secondhand smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Secondhand smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 86
- Group 1 sample size Number of subjects in the case (exposed) group
- 38
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- edgeR
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- 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
- smoking status
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-15
Source: Spreadsheet
Description: The relative abundance of selected species in cigarette smokers and secondhand smokers
Abundance in Group 1: decreased abundance in Secondhand smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Leptotrichia | ||
| Lactobacillus | ||
| Rothia | ||
| Streptococcus | ||
| Anaeroglobus | ||
| Actinomyces |
Revision editor(s): Atrayees
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-15
Source: Spreadsheet
Description: The relative abundance of selected species in cigarette smokers and secondhand smokers
Abundance in Group 1: increased abundance in Secondhand smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Bergeyella | ||
| Peptostreptococcus | ||
| Gemella | ||
| Alloprevotella | ||
| Neisseria | ||
| Prevotella |
Revision editor(s): Atrayees
