Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Alcohol drinking alcohol consumption,Alcohol drinking,alcohol drinking
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-drinkers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Moderate drinkers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- > 0 but ≤ 1 drinks per day, on average, for women, and > 0 but ≤ 2 drinks per day, on average, for men
- Group 0 sample size Number of subjects in the control (unexposed) group
- 270
- Group 1 sample size Number of subjects in the case (exposed) group
- 614
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NA
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
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- 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, body mass index, education level, race, sex, smoking status
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Source: Figure 3a
Description: Heatmap of fold changes and the correlations of the taxa related to alcohol drinking level
Abundance in Group 1: increased abundance in Moderate drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Prevotella | ||
| Bergeyella | ||
| Corynebacterium | ||
| Fusobacterium | ||
| Leptotrichia | ||
| Pasteurellaceae | ||
| Aggregatibacter | ||
| Cardiobacterium | ||
| Eikenella | ||
| Kingella | ||
| Neisseria | ||
| Bacteroidales |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Source: Figure 3a
Description: Heat map fold changes and the correlations of the taxa related to alcohol drinking level
Abundance in Group 1: decreased abundance in Moderate drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Granulicatella adiacens | ||
| Granulicatella elegans |
