Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus

Significance The oral microbial community living in symbiosis with humans is a rich and diverse driver of health and disease that is strongly influenced by our ecology and lifestyle. However, its evolution across human prehistory remains elusive. By analyzing the DNA entrapped in archaeological dental calculus, we characterize the oral microbiomes of 44 prehistoric foragers and farmers from Southern Europe. We demonstrate that the genome of an oral bacteria diversified geographically and recorded one of the most dramatic changes in our biological and cultural history, the spread of farming. The transition to agriculture did not alter significantly the oral microbiome of ancient humans, whereas more significant changes occurred later in history, including the development of peculiar antibiotic resistance pathways.