Abstract
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.
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Acknowledgements
We thank the Kantonale Ethik-Kommission Zürich, the Functional Genomics Center Zürich, the Center for Microscopy and Image Analysis, and the Institute of Oral Biology at the University of Zürich; the PRIDE Team; G. Akgül, K. Alt, D. Ashford, P. Ashton, H. Barton, A. Bouwman, C. Burger, D. Coulthard, J. Hublin, V. Meskenaite, F. Najar, M. Richards, K. Sankaranarayanan, R. Schlapbach, L. Shillito, T. Stöllner, O. Ullrich and H. Zbinden for assistance with data collection, analysis and management; and M. Carver, F. Dewhirst, A. Tanner, K. Hardy and A. Henry for helpful comments on early drafts and data analyses. This work was supported by the Mäxi Foundation Zürich, the Swiss Foundation for Nutritional Research, Danish Research Foundation grant 29396, Danish Council for Independent Research grant 10-081390, Lundbeck Foundation grants R52-A5062 and R44-A4384, US National Institutes of Health grants R01-HG005172, R01-GM089886, R01-DE018499 and R21-DE018310, European Research Council grant UMICIS/242870, Marie Curie grants EUROTAST FP7-PEOPLE-2010 MC ITN, PALIMPSEST FP7-PEOPLE-2011-IEF 299101 and ORCA FP7-PEOPLE-2011-IOF 299075, a C2D2 Research Priming Fund grant partly funded by Wellcome Trust 097829, Swiss National Science Foundation grant 31003A-135688, the Novartis Foundation, the Novo Nordisk Foundation, the Max Planck Society and the University of York.
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Contributions
C.W. conceived the project, with input from M.J.C. R.S. and F.R. contributed samples. C.W., E.C., M.J.C., M.T.P.G., C.v.M., A.R. and Y.H. designed the experiments. C.W., E.C., N.S., C.T., A.R., Y.H., D.C.S.-G., S.C., S.F., H.U.L., P.N., C.D.K., J.V.O., K.Y.T. and E.E. performed the experiments. J.F.M.R., R.V., C.W., C.v.M., J.G., A.R., Y.H., R.Y.T., S.F., C.S., S.C., D.C.S.-G., J.H., J.A.S.C., L.H.H. and T.K. analyzed the data. S.B.-O., Y.H., E.W., C.M.L., M.T.P.G., M.J.C. and F.R. contributed material support to the project. Y.H. wrote the supplementary Raman section. C.W. wrote the manuscript, with critical input from C.M.L., M.T.P.G., M.J.C., C.v.M., E.W., E.C. and the remaining authors.
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Supplementary Text and Figures
Supplementary Figures 1–23, Supplementary Tables 1 and 5–29, and Supplementary Note (PDF 11364 kb)
Supplementary Table 2
Comparison of putative pathogens identified in ancient dental calculus and HMP healthy cohort dental plaque samples. (XLSX 124 kb)
Supplementary Table 3
Specific virulence factors and mobile elements identified within ancient dental calculus metagenomic and metaproteomic data. (XLSX 4997 kb)
Supplementary Table 4
Putative antibiotic resistance genes identified from ancient dental calculus metagenomic data. (XLS 185 kb)
Supplementary Data Set 1
Ancient dental samples BIOM file for 454 data. (TXT 449 kb)
Supplementary Data Set 2
Ancient dental and HMP samples BIOM file for 454 data. (TXT 7461 kb)
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Warinner, C., Rodrigues, J., Vyas, R. et al. Pathogens and host immunity in the ancient human oral cavity. Nat Genet 46, 336–344 (2014). https://doi.org/10.1038/ng.2906
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DOI: https://doi.org/10.1038/ng.2906
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