Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome.

Jaelle C Brealey,Henrique G Leitão,Love Dalén,Wenbo Xu,Katia Bougiouri,Tom Van Der Valk,Katerina Guschanski,Daniel Falush

doi:10.1093/molbev/msaa135

Jaelle C Brealey, Henrique G Leitão + Show 6 more

Open Access

https://doi.org/10.1093/molbev/msaa135

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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.

Highlights

Dental plaque is the microbial biofilm that forms on mammalian teeth (Jin and Yip 2002)
Dental calculus on healthy teeth differed in appearance between the three host species and lacked the three-dimensional structure commonly observed in humans (Warinner et al 2014)
It is possible that the dental calculus of ruminants captures a subset of the rumen microbiome, which may contribute to the comparatively lower proportion of oral taxa we observed in reindeer dental calculus

Summary

Introduction

Dental plaque is the microbial biofilm that forms on mammalian teeth (Jin and Yip 2002). Archaeological dental calculus has been shown to be a rich source of information on the oral microbial community, potential pathogens, host DNA, and dietary components (Armitage 1975; Dobney and Brothwell 1988; Adler et al 2013; de la Fuente et al 2013; Warinner et al 2014). Dental calculus provides the opportunity to study oral microbiome evolution through time and to integrate investigations of microbial, dietary, and host genetic factors from the same source material (Adler et al 2013; Warinner et al 2014; Weyrich et al 2017; Mann et al 2018; Ottoni et al 2019; Ozga et al 2019; Modi et al 2020)

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