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

Francesco Beghini, Audrey Renson, Christine P. Zolnik, Ludwig Geistlinger, Mykhaylo Usyk, Thomas U. Moody, Lorna Thorpe, Jennifer B. Dowd, Robert Burk, Nicola Segata, Heidi E. Jones, Levi Waldron

Research output: Contribution to journalArticlepeer-review


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. Highlights 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 microbiome

Original languageEnglish (US)
JournalUnknown Journal
StatePublished - Nov 14 2018


  • human microbiome
  • microbiota
  • oral health
  • RNA, Ribosomal, 16S
  • smoking
  • tobacco

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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