Host Genetic Control of the Oral Microbiome in Health and Disease

Andres Gomez, Josh L. Espinoza, Derek M. Harkins, Pamela Leong, Richard Saffery, Michelle Bockmann, Manolito Torralba, Claire Kuelbs, Rohith Kodukula, Jason Inman, Toby Hughes, Jeffrey M. Craig, Sarah K. Highlander, Marcus B. Jones, Chris L. Dupont, Karen E. Nelson

Research output: Contribution to journalArticlepeer-review

97 Scopus citations


Host-associated microbial communities are influenced by both host genetics and environmental factors. However, factors controlling the human oral microbiome and their impact on disease remain to be investigated. To determine the combined and relative effects of host genotype and environment on oral microbiome composition and caries phenotypes, we profiled the supragingival plaque microbiome of 485 dizygotic and monozygotic twins aged 5–11. Oral microbiome similarity always increased with shared host genotype, regardless of caries state. Additionally, although most of the variation in the oral microbiome was determined by environmental factors, highly heritable oral taxa were identified. The most heritable oral bacteria were not associated with caries state, did not tend to co-occur with other taxa, and decreased in abundance with age and sugar consumption frequency. Thus, while the human oral microbiome composition is influenced by host genetic background, potentially cariogenic taxa are likely not controlled by genetic factors. Gomez et al. examine the supragingival plaque microbiome of 5- to 11-year-old twins and find that the early oral microbiome is shaped by both heritable and environmental factors. However, the most heritable bacteria diminish in abundance with age, and potentially cariogenic taxa are not controlled by host genetics.

Original languageEnglish (US)
Pages (from-to)269-278.e3
JournalCell Host and Microbe
Issue number3
StatePublished - Sep 13 2017

Bibliographical note

Funding Information:
We wish to thank all twins and their families; Grant Townsend and Nicky Kilpatrick for their dental expertise; and Tina Vaiano, Jane Loke, Anna Czajko, Blessy Manil, Chrissie Robinson, Mihiri Silva, and Supriya Raj for their expertise and assistance with collection of data and samples. We also want to thank Dr. Anna Edlund, Dr. Nicholas Schork, and Thomas Clarke at the JCVI. The research in this publication was supported by the National Institute of Dental and Craniofacial Research of the National Institutes of Health under Award Number R01DE019665 to K.E.N. The Peri/Postnatal Epigenetic Twins Study (PETS) was supported by grants from the Australian National Health and Medical Research Council (grant numbers 437015 and 607358 to J.M.C. and R.S.), the Bonnie Babes Foundation (grant number BBF20704 to J.M.C.), the Financial Markets Foundation for Children (grant number 032-2007 to J.M.C.), and the Victorian Government’s Operational Infrastructure Support Program . The Craniofacial Biology Research Group (CBRG) was supported by grants from the Australian National Health and Medical Research Council (grant numbers 349448 and 1006294 to T.H.) and the Financial Markets Foundation for Children (grant number 223-2009 to T.H.).

Publisher Copyright:
© 2017 Elsevier Inc.


  • 16S
  • human microbiome
  • oral microbiome
  • twins


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