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Proceedings of the National Academy of Sciences of the United States of America. pii: 2102116118. doi: 10.1073/pnas.2102116118

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

Ottoni C¹, Borić D², Cheronet O³, Sparacello V⁴, Dori I⁵, Coppa A⁶, Antonović D⁷, Vujević D⁸, Price TD⁹, Pinhasi R¹⁰, Cristiani E¹¹

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¹DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy; claudio.ottoni@uniroma2.it emanuela.cristiani@uniroma1.it.
²The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027.
³Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria.
⁴Department of Environmental and Life Sciences, University of Cagliari, 09042 Monserrato, Italy.
⁵Soprintendenza Archeologia, Belle Arti e Paesaggio per le province di Verona, Rovigo e Vicenza, 37121 Verona, Italy.
⁶Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy.
⁷Institute of Archaeology, 11000 Belgrade, Serbia.
⁸Department of Archaeology, University of Zadar, 23000 Zadar, Croatia.
⁹Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706.
¹⁰Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria.
¹¹DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy; claudio.ottoni@uniroma2.it emanuela.cristiani@uniroma1.it.

Abstract

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 until 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, and it was in particular associated with a higher abundance of the species sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, 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 and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

KEYWORDS: Southern Europe, ancient DNA, dental calculus, metagenomics

Publikations ID: 34312252
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