Ancient DNA from dental calculus records past dietary changes

Human evolution has been punctuated by major changes in diet, with important impacts on our biology. Two of the biggest dietary shifts involved the increasingly carbohydrate-rich diets associated with the adoption of Neolithic (farming) diets from ~10,000 years BP and the industrial processing of staples such as flour and sugar in the Industrial Revolution (~1800 AD). Increased signs of physiological stress in Neolithic skeletal records suggest that these changes directly underpin many diseases associated with modern lifestyles. Major shifts in human diet are likely to have considerable impacts on commensal bacteria, and co-evolved host-microbiota mutualisms whose role is increasingly recognized in human health and disease. However, the evolutionary history of human microbiota is poorly quantified, and genetic records from commensal bacterial have not yet been recovered from fossil remains.

Methods:

Here we show that dental calculus on ancient human teeth preserves a detailed record of past bacterial DNA diversity and health changes. We collected dental calculus samples (n=28) from ancient European agriculturist groups spanning the Neolithic to Medieval periods. Bacterial DNA was extracted from the sterilised calculus samples and used to generate PCR amplicon libraries of the 16S rRNA gene, which were sequenced using 454 technology.

Results:

We found that dental calculus from early European farming communities had higher oral microbe diversity compared to modern populations, with a dominance of bacteria associated with periodontal disease. The latter maintain relatively constant levels after the introduction of agriculture. The composition of oral microbiota remained surprisingly constant between Neolithic and Medieval times, after which (the now ubiquitous) caries-forming bacteria became dominant, probably during the Industrial Revolution.

Conclusions:

The data suggests the ecosystem of the human mouth has recently undergone changes, and provides insight into the pathogenic consequences. Archaeological dental calculus provides a method to track the evolution of oral diseases.