Assessing the Variation within the Oral Microbiome of Healthy Adults

Jacob T. Nearing, Vanessa DeClercq, Johan Van Limbergen, Morgan G.I. Langille

Research output: Contribution to journalArticlepeer-review

71 Citations (Scopus)

Abstract

More than 1,000 different species of microbes have been found to live within the human oral cavity, where they play important roles in maintaining both oral and systemic health. Several studies have identified the core members of this microbial community; however, the factors that determine oral microbiome composition are not well understood. In this study, we exam the salivary oral microbiome of 1,049 Atlantic Canadians using 16S rRNA gene sequencing to determine which dietary, lifestyle, and anthropometric features play a role in shaping microbial community composition. Features that were identified as being significantly associated with overall composition then were additionally examined for genera, amplicon sequence variants, and predicted pathway abundances that were associated with these features. Several associations were replicated in an additional secondary validation data set. Overall, we found that several anthropometric measurements, including waisthip ratio (WHR), height, and fat-free mass, as well as age and sex, were associated with overall oral microbiome structure in both our exploratory and validation data sets. We were unable to validate any dietary impacts on overall taxonomic oral microbiome composition but did find evidence to suggest potential contributions from factors such as the number of vegetable and refined grain servings an individual consumes. Interestingly, each one of these factors on its own was associated with only minor shifts in the overall taxonomic composition of the oral microbiome, suggesting that future biomarker identification for several diseases associated with the oral microbiome can be undertaken without the worry of confounding factors obscuring biological signals. IMPORTANCE The human oral cavity is inhabited by a diverse community of microbes, known as the human oral microbiome. These microbes play a role in maintaining both oral and systemic health and, as such, have been proposed to be useful biomarkers of disease. However, to identify these biomarkers, we first need to determine the composition and variation of the healthy oral microbiome. In this report, we investigate the oral microbiome of 1,049 healthy individuals to determine which genera and amplicon sequence variants are commonly found between individual oral microbiomes. We then further investigate how lifestyle, anthropometric, and dietary choices impact overall microbiome composition. Interestingly, the results from this investigation showed that while many features were significantly associated with oral microbiome composition, no single biological factor explained a variation larger than 2%. These results indicate that future work on biomarker detection may be encouraged by the lack of strong confounding factors.

Original languageEnglish
Article numbere00451-20
JournalmSphere
Volume5
Issue number5
DOIs
Publication statusPublished - Sept 2020

Bibliographical note

Funding Information:
J.T.N. is supported by both a Research Nova Scotia, Scotia Scholars award (2019 –2022) and a Nova Scotia Graduate Scholarship (2019 –2023). J.V.L. was supported by a Canadian Institutes of Health Research (CIHR)-Canadian Association of Gastroenterology-Crohn’s Colitis Canada New Investigator Award (2015–2019), a Canada Research Chair Tier 2 in Translational Microbiomics (2018 –2019), a Canadian Foundation of Innovation John R. Evans Leadership fund (awards 35235 and 36764), a Nova Scotia Health Research Foundation (NSHRF) establishment award (2015–2019), an IWK Health Centre Research Associateship, a Future Leaders in IBD project grant, a donation from the MacLeod family, and a CIHR-SPOR-Chronic Diseases grant (Inflammation, Microbiome, and Alimentation: Gastro-Intestinal and Neuropsychiatric Effects: the IMAGINE-SPOR Chronic Disease Network).

Funding Information:
This research was conducted using Atlantic PATH data and biosamples under application number 2018-103. We thank the Atlantic PATH participants who donated their time, personal health history, and biological samples to this project. We also thank the Atlantic PATH team members for data collection and management. J.T.N. is supported by both a Research Nova Scotia, Scotia Scholars award (2019-2022) and a Nova Scotia Graduate Scholarship (2019-2023). J.V.L. was supported by a Canadian Institutes of Health Research (CIHR)-Canadian Association of Gastroenterology-Crohn's Colitis Canada New Investigator Award (2015-2019), a Canada Research Chair Tier 2 in Translational Microbiomics (2018-2019), a Canadian Foundation of Innovation John R. Evans Leadership fund (awards 35235 and 36764), a Nova Scotia Health Research Foundation (NSHRF) establishment award (2015-2019), an IWK Health Centre Research Associateship, a Future Leaders in IBD project grant, a donation from the MacLeod family, and a CIHR-SPOR-Chronic Diseases grant (Inflammation, Microbiome, and Alimentation: Gastro-Intestinal and Neuropsychiatric Effects: the IMAGINE-SPOR Chronic Disease Network). The data used in this research were made available by the Atlantic Partnership for Tomorrow's Health (Atlantic PATH) study, which is the Atlantic Canada regional component of the Canadian Partnership for Tomorrow's Health Project, funded by the Canadian Partnership Against Cancer and Health Canada. The views expressed here represent the views of the authors and do not necessarily represent the views of Health Canada.

Funding Information:
The data used in this research were made available by the Atlantic Partnership for Tomorrow’s Health (Atlantic PATH) study, which is the Atlantic Canada regional component of the Canadian Partnership for Tomorrow’s Health Project, funded by the Canadian Partnership Against Cancer and Health Canada. The views expressed here represent the views of the authors and do not necessarily represent the views of Health Canada.

Publisher Copyright:
© 2020 Nearing et al. T. All Rights Reserved.

ASJC Scopus Subject Areas

  • Microbiology
  • Molecular Biology

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