Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB, Ahn J
Journal
Microbiome
Year
2018
Keywords:
16s rRNA genes, Alcohol consumption, Large population-based study, Oral microbiome
BACKGROUND: Dysbiosis of the oral microbiome can lead to local oral disease and potentially to cancers of the head, neck, and digestive tract. However, little is known regarding exogenous factors contributing to such microbial imbalance. RESULTS: We examined the impact of alcohol consumption on the oral microbiome in a cross-sectional study of 1044 US adults. Bacterial 16S rRNA genes from oral wash samples were amplified, sequenced, and assigned to bacterial taxa. We tested the association of alcohol drinking level (non-drinker, moderate drinker, or heavy drinker) and type (liquor, beer, or wine) with overall microbial composition and individual taxon abundance. The diversity of oral microbiota and overall bacterial profiles differed between heavy drinkers and non-drinkers (α-diversity richness p = 0.0059 and β-diversity unweighted UniFrac p = 0.0036), and abundance of commensal order Lactobacillales tends to be decreased with higher alcohol consumption (fold changes = 0.89 and 0.94 for heavy and moderate drinkers, p trend = 0.005 [q = 0.064]). Additionally, certain genera were enriched in subjects with higher alcohol consumption, including Actinomyces, Leptotrichia, Cardiobacterium, and Neisseria; some of these genera contain oral pathogens, while Neisseria can synthesize the human carcinogen acetaldehyde from ethanol. Wine drinkers may differ from non-drinkers in microbial diversity and profiles (α-diversity richness p = 0.048 and β-diversity unweighted UniFrac p = 0.059) after controlling for drinking amount, while liquor and beer drinkers did not. All significant differences between drinkers and non-drinkers remained after exclusion of current smokers. CONCLUSIONS: Our results, from a large human study of alcohol consumption and the oral microbiome, indicate that alcohol consumption, and heavy drinking in particular, may influence the oral microbiome composition. These findings may have implications for better understanding the potential role that oral bacteria play in alcohol-related diseases.
Statistical test
DESeq2
Experiment 1
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 (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- alcohol drinking alcohol consumption,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).
- relative abundances
- 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 |
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Heavy drinkers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women and men who had greater than one or two drinks per day respectively
- Group 1 sample size Number of subjects in the case (exposed) group
- 160
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
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 fold changes and the correlations of the taxa related to alcohol drinking level
Abundance in Group 1: increased abundance in Heavy drinkers
Signature 2
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: decreased abundance in Heavy drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillales | ||
| Granulicatella adiacens | ||
| Granulicatella elegans |
Revision editor(s): Suwaiba
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Wine drinkers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Alcohol drinkers who drank exclusively wine
- Group 1 sample size Number of subjects in the case (exposed) group
- 101
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.10
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, alcohol drinking, body mass index, education level, race, sex, smoking status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Source: Figure 4a
Description: Heatmap of fold changes and the correlations of taxa related to alcohol drinking type
Abundance in Group 1: increased abundance in Wine drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Corynebacteriaceae | ||
| Corynebacterium | ||
| Eikenella |
Revision editor(s): Suwaiba
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Source: Figure 4a
Description: Heatmap of fold changes and the correlations of taxa related to alcohol drinking type
Abundance in Group 1: decreased abundance in Wine drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacteroidota | ||
| Peptococcaceae | ||
| Peptococcus | ||
| Prevotella | ||
| Mogibacterium |
Revision editor(s): Suwaiba
Experiment 4
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Beer drinkers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Alcohol drinkers who drink beer exclusively
- Group 1 sample size Number of subjects in the case (exposed) group
- 39
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Source: Figure 4a
Description: Heatmap of fold changes of correlations of the taxa related to alcohol drinking type
Abundance in Group 1: increased abundance in Beer drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Parascardovia |
Revision editor(s): Suwaiba
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Source: Figure 4a
Description: Heatmap of fold changes and the correlations of the taxa related to alcohol drinking type
Abundance in Group 1: decreased abundance in Beer drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacteroidota | ||
| Clostridia | ||
| Eubacteriales | ||
| Oribacterium | ||
| Porphyromonas | ||
| Prevotella | ||
| Stomatobaculum |
Revision editor(s): Suwaiba
Experiment 5
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Liquor drinkers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Alcohol drinkers who exclusively drank liquor
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Source: Figure 4a
Description: Heatmap of fold changes and correlations of the taxa related to alcohol drinking type
Abundance in Group 1: decreased abundance in Liquor drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Prevotella |
Revision editor(s): Suwaiba
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-23
Source: Figure 4a
Description: Heatmap fold changes and correlations of taxa related to alcohol drinking type
Abundance in Group 1: decreased abundance in Liquor drinkers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacteroidota | ||
| Clostridia | ||
| Eubacteriales | ||
| Lachnospiraceae | ||
| Mogibacterium | ||
| Oribacterium | ||
| Parascardovia | ||
| Prevotella | ||
| Stomatobaculum |
Revision editor(s): Suwaiba
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