The first detailed analysis of ancient oral microbiome ecology and function has revealed that despite significant changes in diet and lifestyle over the last 1,000 years, the oral cavity has been a long-term host for opportunistic pathogens that initiate oral and respiratory diseases, as well as bacteria associated with the development of heart disease and other systemic diseases.

The study published in Nature Genetics analysed four adult human skeletons from the medieval monastic site of Dalheim, Germany (c. 950-1200 AD), which presented evidence of mild to severe periodontal diseases, as well as the dental calculus of nine twenty-first century individuals with known dental histories. Previously, five common oral bacteria have been identified in historic dental calculus, but by applying shotgun DNA sequencing the researchers were able to distinguish 40 putative opportunistic pathogens, finding the calculus strongly dominated by bacterial DNA.

DNA sequences also revealed antibiotic resistance genes, suggesting that even before therapeutic antibiotics were used by humans, the oral cavity functioned as a source of low-level antibiotic resistance. Forty-three human proteins were identified in the calculus, 25 of which are involved in the innate immune system, driving inflammation and host defence processes. The wealth of inflammatory proteins supports the evidence of attachment loss and active periodontal disease.

As well as the researchers providing direct insight into common diseases of the human evolutionary past, their study also used plant and animal DNA sequences recovered from the ancient calculus to provide a high-resolution taxonomic characterisation of their diet. Animal tissue, plant bast fibres and starch granules from cereals were among their findings. These results have significant implications for archaeological studies but also future medical and microbiome research. Warinner et al. conclude that 'dental calculus is a robust, long-term biomolecular reservoir of ancient disease and dietary information'.