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

Author:

Borry Maxime1ORCID,Cordova Bryan1,Perri Angela23,Wibowo Marsha456,Prasad Honap Tanvi78,Ko Jada9,Yu Jie10,Britton Kate311ORCID,Girdland-Flink Linus1112,Power Robert C.313ORCID,Stuijts Ingelise14,Salazar-García Domingo C.1516,Hofman Courtney78,Hagan Richard1,Samdapawindé Kagoné Thérèse17,Meda Nicolas17,Carabin Helene18ORCID,Jacobson David78,Reinhard Karl19,Lewis Cecil78ORCID,Kostic Aleksandar456ORCID,Jeong Choongwon120ORCID,Herbig Alexander1ORCID,Hübner Alexander1ORCID,Warinner Christina1921

Affiliation:

1. Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany

2. Department of Archaeology, Durham University, Durham, UK

3. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

4. Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA

5. Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA

6. Department of Microbiology, Harvard Medical School, Boston, MA, USA

7. Department of Anthropology, University of Oklahoma, Norman, OK, USA

8. Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA

9. Department of Anthropology, Harvard University, Cambridge, MA, USA

10. Department of History, Wuhan University, Wuhan, China

11. Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK

12. School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK

13. Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, München, Germany

14. The Discovery Programme, Dublin, Ireland

15. Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria-Gasteiz, Spain

16. Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain

17. Centre Muraz, Bobo-Dioulasso, Burkina Faso

18. Département de pathologie et de microbiologie, Faculté de Médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada

19. School of Natural Resources, University of Nebraska, Lincoln, NE, USA

20. School of Biological Sciences, Seoul National University, Seoul, South Korea

21. Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany

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.

Publisher

PeerJ

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

Reference59 articles.

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3. maxibor/anonymap: Anonymap v1.0;Borry,2019a

4. Sourcepredict: prediction of metagenomic sample sources using dimension reduction followed by machine learning classification;Borry;Journal of Open Source Software,2019b

5. Patterns of damage in genomic DNA sequences from a Neandertal;Briggs;Proceedings of the National Academy of Sciences of The United States of America,2007

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