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

The microbiome and its host have a long history of co-evolution, defined by a complex interplay between environmental and host genetic factors. Yet, we have a very limited understanding of how the host-associated microbiome is influenced by extrinsic and intrinsic long-term processes, such as climate change and host demography. To this end, we need to study microbiome changes through time, over known historical events that have affected the host. Dental calculus, the calcified form of the microbial biofilm that forms on vertebrate teeth, is one of few microbial substrates that preserves virtually unchanged through time. Metagenomics sequencing of ancient dental calculus has provided valuable insights in humans, but few studies have attempted to characterise the dental calculus microbiome of non-human animals. We establish dental calculus as a valuable research tool for the study of host-associated microbiome evolution. We recover a recognisable oral microbiome signature from species as diverse as gorillas, bears and reindeer, and identify a subset of microorganisms that may be unique to each host species. We detect oral pathogens in specimens with evidence of oral disease, identify microbial metabolic pathways, characterise antibiotic resistance genes and recover host DNA using metagenomic analyses of dental calculus. In addition, we identify important strategies and current limitations for working with historical metagenomics data from non-human mammals. With this new tool in hand, we can now study changes in microbiome composition and function as result of extrinsic and intrinsic processes in host history over millennia.