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

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., Yu, J., Britton, K., Girdland-Flink, L., Power, R. C., Stuijts, I., Salazar-García, D. C., Hofman, C., Hagan, R., Samdapawindé Kagoné, T., Meda, N., Carabin, H., Jacobson, D., Reinhard, K., Lewis, C., …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
• Public URL: https://durham-repository.worktribe.com/output/1271318