Pleistocene reindeer dental calculus as a source for ancient oral and digestive flora

Dental calculus forms when the biofilm found on teeth calcifies during an individual’s lifetime, simultaneously encasing and preserving microorganisms and biomolecules, including DNA. Dental calculus contains genetic information from the oral microbiome, including potential pathogens, as well as DNA from food sources and a small amount of host DNA. In the case of ruminant animals, regurgitated gut microbes can also be detected. Under favorable conditions, DNA in dental calculus can be preserved for thousands of years and thus presents unique opportunities to study ancient metagenomic material from archaeological remains. Here, we present results from a project aiming to taxonomically characterize the ancient oral metagenome of reindeer (Rangifer tarandus) originating from Pleistocene archaeological sites in the Vézère Valley of southern France. This region served as a glacial refugium during the last glacial maximum, but reindeer subsequently became extinct there and are today found only in more northern arctic and boreal regions. We extracted DNA from the surface of 19 ancient reindeer teeth (15,000 – 25,000 years BP) for shotgun metagenomic sequencing and compared these results to microbiomes we obtained from reindeer dental calculus sampled from 45 wild reindeer from both extant and historical populations in Europe. We identified known components of the oral microbiome, and microbes likely originating from the rumen. While putative oral microbiomes differed considerably between ancient and modern samples, we identified six bacterial taxa detected in both ancient and modern samples, all of which are associated with the gastrointestinal tract. As soft tissue is often not preserved in ancient remains, the use of dental calculus of ruminant animals holds a unique opportunity to study both the oral microbiome composition and the microbiome of the digestive tract of extinct populations.