Warinner, Christina5; Rodrigues, João F Matias6; Vyas, Rounak6; Trachsel, Christian7; Shved, Natallia5; Grossmann, Jonas7; Radini, Anita8; Hancock, Y15; Tito, Raul Y10; Fiddyment, Sarah15; Speller, Camilla15; Hendy, Jessica15; Charlton, Sophy15; Luder, Hans Ulrich11; Salazar-García, Domingo C12; Eppler, Elisabeth13; Seiler, Roger5; Hansen, Lars H.16; Samaniego Castruita, Jose Alfredo17; Barkow-Oesterreicher, Simon7; Teoh, Kai Yik15; Kelstrup, Christian18; Olsen, Jesper Velgaard18; Nanni, Paolo7; Kawai, Toshihisa14; Willerslev, Eske17; von Mering, Christian6; Lewis, Cecil M10; Collins, Matthew J15; Gilbert, M. Thomas P.17; Rühli, Frank5; Cappellini, Enrico17
1 Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Københavns Universitet2 Microbiology, Department of Biology, Faculty of Science, Københavns Universitet3 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet4 Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Københavns Universitet5 Centre for Evolutionary Medicine, Institute of Anatomy, University of Zürich, Zürich, Switzerland.6 Institute of Molecular Life Sciences, University of Zürich7 Functional Genomics Center Zürich, University of Zürich/Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.8 BioArCh, Department of Archaeology, University of York9 University of York10 Department of Anthropology, University of Oklahoma, Norman, Oklahoma, USA.11 Centre of Dental Medicine, Institute of Oral Biology, University of Zürich, Zürich, Switzerland.12 Research Group on Plant Foods in Hominin Dietary Ecology, Max Planck Institute for Evolutionary Anthropology13 Research Group Neuro-Endocrine-Immune Interactions, Institute of Anatomy, University of Zürich, Zürich, Switzerland.14 Department of Immunology and Infectious Diseases, Forsyth Institute15 University of York16 Microbiology, Department of Biology, Faculty of Science, Københavns Universitet17 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet18 Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Københavns Universitet
Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past.