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Sci Rep. 2019 Dec 23;9(1):19637. doi: 10.1038/s41598-019-56074-x.

Metagenomic analysis of dental calculus in ancient Egyptian baboons.

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Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway.
Department of Oral and Maxillofacial Sciences, Diet and Ancient Technology Laboratory (DANTE), Sapienza University, Rome, Italy.
Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway.
University of Tartu, Institute of Genomics, Estonian Biocentre, 51010, Tartu, Estonia.
Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA.
School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.
Institute of Human Origins, Arizona State University, Tempe, AZ, USA.
Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy, and Prevention, University of Ferrara, 35-441221, Ferrara, Italy.
Laboratoire CNRS ASM ≪ Archéologie des Sociétés Méditerranéennes (UMR 5140), Université Paul-Valéry, LabEx Archimede, F-34199, Montpellier, France.
Royal Belgian Institute of Natural Sciences, B-1000, Brussels, Belgium.
KU Leuven-University of Leuven, Department of Biology, Laboratory of Biodiversity and Evolutionary Genomics, Center of Archaeological Sciences, B-3000, Leuven, Belgium.


Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th-6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.

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