Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study

Study information

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study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31076212

DOI Digital object identifier for electronic documents.

https://doi.org/10.1016/j.annepidem.2019.03.005

URI

https://pubmed.ncbi.nlm.nih.gov/31076212/

Authors

Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE, Waldron L

Journal

Annals of epidemiology

Year

2019

Keywords:

16S, Human microbiome, Microbiota, Oral health, RNA, Ribosomal, Smoking, Tobacco

PURPOSE: The effect of tobacco exposure on the oral microbiome has not been established. METHODS: We performed amplicon sequencing of the 16S ribosomal RNA gene V4 variable region to estimate bacterial community characteristics in 259 oral rinse samples, selected based on self-reported smoking and serum cotinine levels, from the 2013-2014 New York City Health and Nutrition Examination Study. We identified differentially abundant operational taxonomic units (OTUs) by primary and secondhand tobacco exposure, and used "microbe set enrichment analysis" to assess shifts in microbial oxygen utilization. RESULTS: Cigarette smoking was associated with depletion of aerobic OTUs (Enrichment Score test statistic ES = -0.75, P = .002) with a minority (29%) of aerobic OTUs enriched in current smokers compared with never smokers. Consistent shifts in the microbiota were observed for current cigarette smokers as for nonsmokers with secondhand exposure as measured by serum cotinine levels. Differential abundance findings were similar in crude and adjusted analyses. CONCLUSIONS: Results support a plausible link between tobacco exposure and shifts in the oral microbiome at the population level through three lines of evidence: (1) a shift in microbiota oxygen utilization associated with primary tobacco smoke exposure; (2) consistency of abundance fold changes associated with current smoking and shifts along the gradient of secondhand smoke exposure among nonsmokers; and (3) consistency after adjusting for a priori hypothesized confounders.

Experiment 1

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Curated date: 2023/03/28

Curator: Atrayees

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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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

tobacco smoke exposure measurement tobacco smoke exposure measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Never smokers

Group 1 name Corresponds to the case (exposed) group for case-control studies

Current cigarette smokers

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Participants who reported smoking more than 100 cigarettes in their lifetime, smoking a cigarette in the last 5 days, and not using any alternative tobacco product in the last 5 days (the 90 with highest measured serum cotinine were selected)

Group 0 sample size Number of subjects in the control (unexposed) group

43

Group 1 sample size Number of subjects in the case (exposed) group

86

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

Statistical test

edgeR

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

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, diabetes mellitus, physical activity, education level, race, sex, Confounders controlled for: "self-reported gum disease" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.self-reported gum disease

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Chao1 Abundance-based estimator of species richness

unchanged

Signature 1

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Source: Supplementary Fig. 4

Description: Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers.

Abundance in Group 1: decreased abundance in Current cigarette smokers

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Actinobacillus
Bergeyella
Bifidobacterium
Gemella
Lachnoanaerobaculum
Lactococcus
Lautropia
Porphyromonas
Streptococcus
Neisseria
Cardiobacterium
Haemophilus

Revision editor(s): Atrayees

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Source: Supplementary Fig. 4

Description: Differentially abundant OTUs, taxonomically assigned to 28 different genera identified between current cigarette smokers and never smokers.

Abundance in Group 1: increased abundance in Current cigarette smokers

NCBI	Quality Control	Links
Alloprevotella
Anaeroglobus
Campylobacter
Fretibacterium
Lactobacillus
Leptotrichia
Megasphaera
Prevotella
Pseudomonas
Rothia
Treponema
Veillonella
Muribaculaceae

Revision editor(s): Atrayees, Peace Sandy

Signature 3

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Source: Supplementary Fig. 5

Description: Differentially abundant microbes found in the current smokers and the never smokers at the phylum level (obtained by crude differential analysis).

Abundance in Group 1: decreased abundance in Current cigarette smokers

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Pseudomonadota

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Signature 4

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Source: Supplementary Fig. 5

Description: Differentially abundant microbes found in the current smokers and the never smokers at the phylum level (obtained by crude differential analysis).

Abundance in Group 1: increased abundance in Current cigarette smokers

NCBI	Quality Control	Links
Synergistota
Actinomycetota
Candidatus Saccharibacteria
Spirochaetota

Revision editor(s): Atrayees