Recent genomic data have revealed multiple interactions between Neanderthals and modern humans1, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering2,3. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess4 and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)—the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

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We thank G. Manzi, the Odontological Collection of the Royal College of Surgeons, Royal Belgian Institute of Natural Sciences, Museo Nacional de Ciencias Naturales, and Adelaide University for access to dental calculus material. We thank A. Croxford for DNA sequencing and A. Walker, J. Krause and A. Herbig for feedback. The Australian Research Council supported this work through the Discovery Project and Fellowship schemes. We acknowledge the fundamental contribution of D. Brothwell (1933-2016) to this research by initiating the archaeological study of dental calculus.

Author information


  1. Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia

    • Laura S. Weyrich
    • , Julien Soubrier
    • , Luis Arriola
    • , Bastien Llamas
    • , James Breen
    • , Andrew G. Farrer
    • , Wolfgang Haak
    •  & Alan Cooper
  2. Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, Australia

    • Sebastian Duchene
    •  & Edward C. Holmes
  3. Department of Human Biology, University of Cape Town, Cape Town, South Africa

    • Alan G. Morris
  4. Danube Private University, Krems, Austria

    • Kurt W. Alt
  5. State Office for Heritage Management and Archaeology, Saxony-Anhalt, Germany

    • Kurt W. Alt
    •  & Veit Dresely
  6. Heritage Museum, Halle, Germany

    • Kurt W. Alt
    •  & Veit Dresely
  7. Institute for Prehistory and Archaeological Science, Basel University, Switzerland

    • Kurt W. Alt
  8. Department of Biology, University of Florence, Florence, Italy

    • David Caramelli
  9. Human Origins and Palaeo Environments Group, Oxford Brookes University, Oxford, UK

    • Milly Farrell
  10. Paleoanthropology, Senckenberg Centre for Human Evolution and Paleoenvironments, Eberhard Karls University of Tübingen, Tübingen, Germany

    • Michael Francken
    •  & Katerina Harvati
  11. School of Dentistry, The University of Adelaide, Adelaide, Australia

    • Neville Gully
    • , John Kaidonis
    •  & Grant Townsend
  12. Catalan Institution for Research and Advanced Studies (ICREA), Pg Lluís Companys 23, 08010 Barcelona, Catalonia, Spain

    • Karen Hardy
  13. Departament de Prehistòria, Facultat de Filosofia i Lletres, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain

    • Karen Hardy
  14. Institute of Anthropology, University of Mainz, Mainz, Germany

    • Petra Held
  15. Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain

    • Carles Lalueza-Fox
  16. Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, Oviedo, Spain

    • Marco de la Rasilla
  17. Paleoanthropology Group, Department of Paleobiology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain

    • Antonio Rosas
  18. Scientific Service Heritage, Royal Belgian Institute of Natural Sciences, Brussels, Belgium

    • Patrick Semal
  19. Department of Bioarchaeology, Institute of Archaeology, University of Warsaw, Warsaw, Poland

    • Arkadiusz Soltysiak
  20. Istituto Italiano per l’Africa e l’Oriente (IsIAO), Rome, Italy

    • Donatella Usai
  21. State Office for Cultural Heritage Management Baden-Württemberg, Esslingen, Germany

    • Joachim Wahl
  22. Department of Algorithms in Bioinformatics, University of Tübingen, Tübingen, Germany

    • Daniel H. Huson
  23. Department of Archaeology, Classics and Egyptology, School of Histories, Languages and Cultures, University of Liverpool, Liverpool, UK

    • Keith Dobney
  24. Department of Archaeology, University of Aberdeen, Aberdeen, UK

    • Keith Dobney
  25. Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada

    • Keith Dobney


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L.S.W., K.D. and A.C. designed the study; A.G.M., K.W.A., D.C., V.D., M.Fa., M.Fr., N.G., W.H., K.Hard., K.Harv., P.H., J.K., C.L.F., M.d.l.R., A.R., P.S., A.S., D.U. and J.W. provided samples and interpretations of associated archaeological goods; L.S.W. performed experiments; L.S.W., S.D., E.C.H., J.S., B.L., J.B., L.A., A.G.F. and A.C. performed bioinformatics analysis and interpretation of the data; D.H.H. developed bioinformatics tools; N.G., J.K., and G.T. analysed medical relevance of data; L.S.W. and A.C. wrote the paper; and all authors contributed to editing the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Laura S. Weyrich or Alan Cooper.

Reviewer Information Nature thanks P. Ungar and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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