CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

Authors

Maxime Borry, Max Planck Institute for the Science of Human HistoryFollow
Bryan Cordova, Max Planck Institute for the Science of Human HistoryFollow
Angela Perri, Durham University and Max Planck Institute for Evolutionary Anthropology
Marsha Wibowo, Joslin Diabetes Center and Harvard Medical School
Tanvi Prasad Honap, University of OklahomaFollow
Jada Ko, Harvard UniversityFollow
Kate Britton, Max Planck Institute for Evolutionary Anthropology and University of AberdeenFollow
Linus Girdland-Flink, University of Aberdeen and Liverpool John Moores UniversityFollow
Robert C. Power, Max Planck Institute for Evolutionary Anthropology and Ludwig-Maximilians-Universität München
Ingelise Stuijts, The Discovery Programme, Dublin, Ireland
Domingo C. Salazar-García, IKERBASQUE-Basque Foundation for Science and Universitat de València
Courtney Hofman, University of OklahomaFollow
Richard Hagan, Max Planck Institute for the Science of Human HistoryFollow
Thérèse Samdapawindé Kagoné, Centre Muraz, Bobo-Dioulasso, Burkina Faso
Nicolas Meda, Centre Muraz, Bobo-Dioulasso, Burkina Faso
Helene Carabin, Université de MontréalFollow
David Jacobson, University of Oklahoma
Karl Reinhard, University of Nebraska-LincolnFollow
Cecil Lewis, University of OklahomaFollow
Aleksandar Kostic, Joslin Diabetes Center and Harvard Medical SchoolFollow
Choongwon Jeong, Max Planck Institute for the Science of Human History and Seoul National UniversityFollow
Alexander Herbig, Max Planck Institute for the Science of Human HistoryFollow
Alexander Hübner, Max Planck Institute for the Science of Human HistoryFollow
Christina Warinner, Max Planck Institute for the Science of Human History, Harvard University, and Friedrich-Schiller Universität JenaFollow

Document Type

Article

Date of this Version

2020

Citation

Borry M, Cordova B, Perri A, Wibowo M, Prasad Honap T, Ko J, Yu J, Britton K, Girdland-Flink L, Power RC, Stuijts I, Salazar-García DC, Hofman C, Hagan R, Samdapawindé Kagoné T, Meda N, Carabin H, Jacobson D, Reinhard K, Lewis C, Kostic A, Jeong C, Herbig A, Hübner A, Warinner C. 2020. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ 8:e9001 DOI 10.7717/peerj.9001

Comments

Copyright 2020 Borry et al.

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.