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

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

doi:10.7717/peerj.9001

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

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Borry, Maxime
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons221555

Cordova, Bryan
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons221741

Hagan, Richard
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons205106

Jeong, Choongwon
Eurasia3angle, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons179620

Herbig, Alexander
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

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Hübner, Alexander
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons221103

Warinner, Christina
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

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Citation

Borry, M., Cordova, B., Perri, A., Wibowo, M., Honap, T. P., Ko, J., et al. (2020). CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ, 8:e9001. doi:10.7717/peerj.9001.

Cite as: https://hdl.handle.net/21.11116/0000-0006-45AE-9

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.