Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-10
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.

Experiment 1


Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/12

Curator: Brian

Revision editor(s): Claregrieve1, Brian, Atrayees, Suwaiba, Victoria

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

Curated date: 2023/03/15

Curator: Brian

Revision editor(s): Brian, Suwaiba, Atrayees

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 ControlLinks
Streptococcus
Prevotella
Bergeyella
Corynebacterium
Fusobacterium
Leptotrichia
Pasteurellaceae
Aggregatibacter
Cardiobacterium
Eikenella
Kingella
Neisseria
Bacteroidales

Revision editor(s): Brian, Suwaiba, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/15

Curator: Brian

Revision editor(s): Brian, Suwaiba

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 ControlLinks
Bacilli
Granulicatella adiacens
Granulicatella elegans

Revision editor(s): Brian, Suwaiba

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/20

Curator: Suwaiba

Revision editor(s): Suwaiba, Victoria

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

Curated date: 2023/03/24

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees

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

NCBI Quality ControlLinks
Actinomyces
Actinomyces graevenitzii
Aggregatibacter
Bergeyella
Lachnoanaerobaculum
Leptotrichia
Neisseria
Pasteurellaceae
Streptococcus
Tannerella
Granulicatella elegans
Bacteroidales

Revision editor(s): Suwaiba, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/24

Curator: Suwaiba

Revision editor(s): Suwaiba

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 ControlLinks
Bacilli
Lactobacillales
Granulicatella adiacens
Granulicatella elegans

Revision editor(s): Suwaiba

Experiment 3


Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/20

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees, Victoria

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

Curated date: 2023/03/24

Curator: Suwaiba

Revision editor(s): Suwaiba

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 ControlLinks
Aggregatibacter
Corynebacteriaceae
Corynebacterium
Eikenella

Revision editor(s): Suwaiba

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/24

Curator: Suwaiba

Revision editor(s): Suwaiba

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 ControlLinks
Bacillota
Bacteroidota
Peptococcaceae
Peptococcus
Prevotella
Mogibacterium

Revision editor(s): Suwaiba

Experiment 4


Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/24

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees, Victoria

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

Curated date: 2023/03/24

Curator: Suwaiba

Revision editor(s): Suwaiba

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 ControlLinks
Aggregatibacter
Parascardovia

Revision editor(s): Suwaiba

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/25

Curator: Suwaiba

Revision editor(s): Suwaiba

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 ControlLinks
Bacillota
Bacteroidota
Clostridia
Eubacteriales
Oribacterium
Porphyromonas
Prevotella
Stomatobaculum

Revision editor(s): Suwaiba

Experiment 5


Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/25

Curator: Suwaiba

Revision editor(s): Suwaiba, Atrayees, Victoria

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

Curated date: 2023/03/25

Curator: Suwaiba

Revision editor(s): Suwaiba

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 ControlLinks
Lachnospiraceae
Prevotella

Revision editor(s): Suwaiba

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-23

Curated date: 2023/03/25

Curator: Suwaiba

Revision editor(s): Suwaiba

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 ControlLinks
Bacillota
Bacteroidota
Clostridia
Eubacteriales
Lachnospiraceae
Mogibacterium
Oribacterium
Parascardovia
Prevotella
Stomatobaculum

Revision editor(s): Suwaiba