PROMETEO · Reconstructing human oral microbiome composition changes over the last 8000 years with proteomics and metagenomics approaches

This project aims at reconstructing the evolution of human oral health in Northern Europeans, from the late Mesolithic to modern days, by genomics and proteomics investigation of: human ancient microbiota, human immune response proteins, and food remains preserved in mineralised dental plaque (archaeological dental calculus).The human microbiota is essential to maintain health, but capable of eliciting disease. Ecological shifts and imbalances (dysbiosis) of the oral microbiota can significantly impact health and cause severe forms of oral pathologies resulting in systemic disease at different body sites. Taxonomic reconstruction of ancient microbiomes and identification of which genes have been gained or lost in their genomes in connection with major lifestyle changes in human history will contribute to the development of more effective preventive and therapeutic approaches for this disease.The two main research objectives are:• Reconstruction of the evolution of the oral microbiome composition over the last 8000 years, and• Characterisation of the associated human immune responses.Genomic and proteomics biomolecular evidence will be retrieved from archaeological human dental calculus: a rich, but so far mostly neglected, source of ancient oral biomolecules. Ancient DNA and proteins extracted from archaeological dental calculus will be analysed using state-of-the-art proteomics and metagenomics approaches at the Centre for GeoGenetics, by high-resolution mass spectrometry and high-throughput DNA sequencing-by-synthesis methods. CGG recently led a high-profile study demonstrating the potential of this approach and will further develop this concept using approximately 80 Northern European samples from a wide chronological range. The Researcher’s skills in computational proteomics will be beneficial to ancient proteomics analysis, and his skills extended to the field of metagenomics.