TY - JOUR T1 - Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study JF - bioRxiv DO - 10.1101/470286 SP - 470286 AU - Francesco Beghini AU - Audrey Renson AU - Christine P. Zolnik AU - Ludwig Geistlinger AU - Mykhaylo Usyk AU - Thomas U. Moody AU - Lorna Thorpe AU - Jennifer B. Dowd AU - Robert Burk AU - Nicola Segata AU - Heidi E. Jones AU - Levi Waldron Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/11/14/470286.abstract N2 - 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 2013-14 New York City Health and Nutrition Examination Study. We identified differentially abundant operational taxonomic units (OTUs) by primary and secondhand tobacco exposure, and employed “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 = 0.002) with a minority (29%) of aerobic OTUs enriched in current smokers compared to never smokers. Consistent shifts in the microbiota were observed for current cigarette smokers as for non-smokers with secondhand exposure as measured by serum cotinine levels. Differential abundance findings were similar in crude and adjusted analyses.Conclusion 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 non-smokers, and 3) consistency after adjusting for a priori hypothesized confounders.Cigarette smoke was associated with microbial anaerobiosis in oral rinse specimensThe microbiome shifts associated with smoking and secondhand exposure were correlatedShifts in oral bacterial oxygen utilization may mediate smoking and health outcomesWe propose “microbe set enrichment analysis” for interpreting shifts in the microbiomeList of abbreviationsCIConfidence IntervalCUNYCity University of New YorkDNADeoxyribonucleic AcidESEnrichment ScoreFDRFalse Discovery RateGSEAGene Set Enrichment AnalysisGSVAGene Set Variation AnalysisHMPHuman MIcrobiome ProjectIRBInstitutional Review BoardNHANESNational Health Nutrition and Examination SurveyNYC DOHMHNew York City Department of Health and Mental HygieneNYC HANESNew York City Health Nutrition and Examination SurveyOROdds RatioORAOver-representation AnalysisOTUOperational Taxonomic UnitPCOAPrincipal Coordinates AnalysisPERMANOVAPermutational Multivariate Analysis of VarianceRNARibonucleic AcidrRNARibosomal Ribonucleic Acid ER -