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The importance of commensal microbes for human health is increasingly recognized1-5, yet the impacts of evolutionary changes in human diet and culture on commensal microbiota remain almost unknown. Two of the greatest dietary shifts in human evolution involved the adoption of carbohydrate-rich Neolithic (farming) diets6,7 (beginning ~10,000 years before the present6,8) and the more recent advent of industrially processed flour and sugar (in ~1850)9. Here, we show that calcified dental plaque (dental calculus) on ancient teeth preserves a detailed genetic record throughout this period. Data from 34 early European skeletons indicate that the transition from hunter-gatherer to farming shifted the oral microbial community to a disease-associated configuration. The composition of oral microbiota remained unexpectedly constant between Neolithic and medieval times, after which (the now ubiquitous) cariogenic bacteria became dominant, apparently during the Industrial Revolution. Modern oral microbiotic ecosystems are markedly less diverse than historic populations, which might be contributing to chronic oral (and other) disease in postindustrial lifestyles.
Commensal microbiota comprise the majority of cells in the body and have a key role in human health1-5,10. However, their evolution remains poorly understood, and detailed genetic records from commensal bacteria have yet to be recovered from the archaeological record. Dental calculus is ubiquitous in both present-day and ancient human populations11, and microscopic analysis has shown that it accurately preserves bacterial morphology over millennia12-14. Dental calculus develops when dental plaque, an extremely dense bacterial biofilm15, becomes mineralized with calcium phosphate16. Bacteria in calculus become locked in a crystalline matrix similar to bone16 (Supplementary Fig. 1), with deposits occurring both above and below the gum or gingiva (supra- and subgingivally)17. Calculus represents one of the few sources of preserved human and hominid microbiota, and genetic analysis has the potential to create a powerful new record of dietary impacts, health changes and oral pathogen genomic evolution deep into the past. In addition, oral bacteria are transferred vertically from the primary caregiver(s) in early childhood18 and horizontally between family members later in life18,19, making archaeological dental calculus a potentially unique means of tracing population structure, movement and admixture in ancient cultures, as well as the spread of diseases.
The increased consumption of domesticated cereals (wheat and barley in the Near East) beginning with the Neolithic period was associated with...