MetadeNTin - De novo assembly of ancient metagenomic data from dental calculus to disentangle the Neolithic transition in Southern Europe

Abstract:

The Neolithic transition was one of the main demographic events affecting Europe 10,000 years ago, characterized by the shift from hunting- gathering to farming as the main subsistence strategy. The adoption of a new lifestyle triggered important changes in the evolution of both humans and their oral microbiome being possibly associated with a higher abundance of two bacterial species: Olsenella sp. oral taxon 807 (OT807) and Anaerolineaceae bacterium oral taxon 439 (OT439). Few studies analyzed the human oral microbiome during this transition and most focused on changes of bacterial relative abundance across time and poorly characterized their genetic structure and phylogeographical pattern. Moreover, most studies align sequences against modern reference genomes, limiting discoveries to known taxa and their close relatives. A way to overcome this issue is performing a de novo assembly of metagenomes, resulting in a set of genomes of all the species present in the sample, however, to date, there is not a golden standard to follow when analyzing ancient metagenomic data. Here I propose to create a pipeline optimize to efficiently reconstruct ancient metagenome-assembled genomes (MAGs). Furthermore, by combining metagenomic and population genetic analysis, this project aims to expand the number of samples from Palaeolithic to Bronze Age periods in understudied geographical areas of Italy and reconstruct the genomes of OT807 and OT439 bacteria to explore their genetic variability in ancient human communities. The proposal includes transfer of knowledge to the host institution and the training of the candidate in innovative ancient metagenomics and development of new methodologies to analyze metagenomic datasets. Altogether, this project guarantees the two-way transfer of knowledge and represents a solid investment of funds from which the fellow, the host institutions and the European society will largely benefit.