Tracking the transition to agriculture in souther europe through DNA analysis of dental calculus

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory till present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe, the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups. In particular, the human oral environment was dominated by a microbial species, Anaerolineaceae HOT439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic. Furthermore, the microbiota of ancient humans possessed a higher functional activity associated with the breakdown of dietary glycans, most likely due to plant food consumption. On the other hand, the functional profile of modern humans evolved to develop antibiotic resistance in recent times.