PeerJ (Apr 2020)
CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content
- Maxime Borry,
- Bryan Cordova,
- Angela Perri,
- Marsha Wibowo,
- Tanvi Prasad Honap,
- Jada Ko,
- Jie Yu,
- Kate Britton,
- Linus Girdland-Flink,
- Robert C. Power,
- Ingelise Stuijts,
- Domingo C. Salazar-García,
- Courtney Hofman,
- Richard Hagan,
- Thérèse Samdapawindé Kagoné,
- Nicolas Meda,
- Helene Carabin,
- David Jacobson,
- Karl Reinhard,
- Cecil Lewis,
- Aleksandar Kostic,
- Choongwon Jeong,
- Alexander Herbig,
- Alexander Hübner,
- Christina Warinner
Affiliations
- Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Bryan Cordova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Angela Perri
- Department of Archaeology, Durham University, Durham, UK
- Marsha Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA
- Tanvi Prasad Honap
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Jada Ko
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Jie Yu
- Department of History, Wuhan University, Wuhan, China
- Kate Britton
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Linus Girdland-Flink
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK
- Robert C. Power
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ingelise Stuijts
- The Discovery Programme, Dublin, Ireland
- Domingo C. Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria-Gasteiz, Spain
- Courtney Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Richard Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Thérèse Samdapawindé Kagoné
- Centre Muraz, Bobo-Dioulasso, Burkina Faso
- Nicolas Meda
- Centre Muraz, Bobo-Dioulasso, Burkina Faso
- Helene Carabin
- Département de pathologie et de microbiologie, Faculté de Médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
- David Jacobson
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Karl Reinhard
- School of Natural Resources, University of Nebraska, Lincoln, NE, USA
- Cecil Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Aleksandar Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA
- Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- DOI
- https://doi.org/10.7717/peerj.9001
- Journal volume & issue
-
Vol. 8
p. e9001
Abstract
Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.
Keywords
