Investigating the transition from hunter-gathering to farming in Southern Italy through metagenomic and population genetic analysis of ancient human dental calculus

Several archaeological and genetic evidence have shown that the Neolithic transition have deeply affected human recent evolutionary history through the adoption of new ways for foods processing and cooking. Such transition in human dietary habits triggered important changes in the evolution of both humans and of the microbes associated with them. Despite these numerous signals suggest that a strong human microbiome transformation occurred, only very few scientific studies have analysed the composition of past oral microbial communities during this transition, depicting sometimes contrasting scenarios. Moreover, it has been demonstrated that bacterial oral taxa show patterns of phylogenetic diversification able to distinguish coeval populations based on their geographical distribution.
This project will focus on a peculiar archaeological remain: the dental calculus, a highly informative substrate that retains biological information from both host and microbial communities, as well as residues of food and materials introduced in the oral cavity. Combining metagenomic and population genetics analysis on a large dataset of Palaeolithic, Neolithic and Eneolithic individuals from Central-Southern Italy, the project aims to: 1) reconstruct the oral microbiomes of ancient human populations in Italy, to infer changes in diet, health and lifestyle during the Neolithic transition compared to previous time; 2) investigate the evolutionary and demographic processes associated to the Neolithic transition in Italy and in the Mediterranean Europe, through the analysis of genomes of commensal species; 3) developing new methodological approaches for the genetic analysis of dietary components in ancient dental calculus.
In particular the project aim to expand the number of samples from Palaeolithic period, exploiting one of the most important pre-Neolithic archaeological site in Italy, in order to explore the oral microbiome variability within ancient hunter-gatherer communities that are still poorly investigated. Moreover, providing a high number of samples from different time transects covering a wide temporal scale in a restricted geographical area will be crucial to unveil the genetic impact of this cultural revolution in finer detail.
The project will be developed through the collaboration of two Research Units (Firenze and Ferrara), that possess research infrastructures and renowned expertise in different fields covering the operative plan of the project (molecular analysis applied on ancient DNA, bioinformatics, metagenomics and population genetics). The complementary skills of the researchers will provide an integrated genetic approach to investigate lifestyle conditions, evolutionary and demographic processes associated to the Palaeolithic-Neolithic transition, from the perspective of ancient human dental calculus. The expected results will have multiple scientific, clinical, cultural, educational and social outcomes.