Dental calculus as a tool to study the evolution of the mammalian oral microbiome

Jaelle C. Brealey*, Henrique G. Leitão, Tom Van-Der-Valk, Wenbo Xu, Katia Bougiouri, Love Dalén, Katerina Guschanski

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
Original languageEnglish
Pages (from-to)3003-3022
Number of pages20
JournalMolecular Biology and Evolution
Volume37
Issue number10
DOIs
Publication statusPublished - 28 May 2020

Keywords

  • ancient DNA
  • antimicrobial resistance
  • metagenome-assembled genomes
  • metagenomics
  • oral pathogens

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