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

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.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-45AE-9 Version Permalink: http://hdl.handle.net/21.11116/0000-0006-45AF-8
Genre: Journal Article

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 Creators:
Borry, Maxime1, Author              
Cordova, Bryan1, Author              
Perri, Angela, Author
Wibowo, Marsha, Author
Honap, Tanvi Prasad, Author
Ko, Jada, Author
Yu, Jie, Author
Britton, Kate, Author
Girdland-Flink, Linus, Author
Power, Robert C., Author
Stuijts, Ingelise, Author
Salazar-García, Domingo C., Author
Hofman, Courtney, Author
Hagan, Richard1, Author              
Kagoné, Thérèse Samdapawindé, Author
Meda, Nicolas, Author
Carabin, Helene, Author
Jacobson, David, Author
Reinhard, Karl, Author
Lewis, Cecil, Author
Kostic, Aleksandar, AuthorJeong, Choongwon2, Author              Herbig, Alexander1, Author              Hübner, Alexander1, Author              Warinner, Christina1, Author               more..
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2Eurasia3angle, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2301699              

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Free keywords: Coprolite, Paleofeces, Microbiome, Endogenous DNA, Archeology, Machine learning, Nextflow, Gut, Human, Dog
 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.

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Language(s): eng - English
 Dates: 2020-04-17
 Publication Status: Published online
 Pages: 23
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Degree: -

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Title: PeerJ
  Other : PeerJ
Source Genre: Journal
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Publ. Info: London [u.a.] : PeerJ Inc.
Pages: - Volume / Issue: - Sequence Number: 8:e9001 Start / End Page: - Identifier: ISSN: 2167-8359
CoNE: https://pure.mpg.de/cone/journals/resource/2167-8359