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

Borry, Maxime; Cordova, Bryan; Perri, Angela; Wibowo, Marsha; Prasad Honap, Tanvi; Ko, Jada; Yu, Jie; Britton, Kate; Girdland-Flink, Linus; Power, Robert C.; Stuijts, Ingelise; Salazar-García, Domingo C.; Hofman, Courtney; Hagan, Richard; Samdapawindé Kagoné, Thérèse; Meda, Nicolas; Carabin, Helene; Jacobson, David; Reinhard, Karl; Lewis, Cecil; Kostic, Aleksandar; Jeong, Choongwon; Herbig, Alexander; Hübner, Alexander; Warinner, Christina

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


Authors

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



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.

Citation

Borry, M., Cordova, B., Perri, A., Wibowo, M., Prasad Honap, T., Ko, J., …Warinner, C. (2020). CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ – the Journal of Life & Environmental Sciences, 8, Article e9001. https://doi.org/10.7717/peerj.9001

Journal Article Type Article
Acceptance Date Mar 26, 2020
Online Publication Date Apr 17, 2020
Publication Date 2020
Deposit Date May 6, 2020
Publicly Available Date May 7, 2020
Journal PeerJ
Publisher PeerJ
Peer Reviewed Peer Reviewed
Volume 8
Article Number e9001
DOI https://doi.org/10.7717/peerj.9001

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Published Journal Article (8.6 Mb)
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Publisher Licence URL
http://creativecommons.org/licenses/by/4.0/

Copyright Statement
Copyright © 2020 Borry et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.




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