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

Maxime Borry*, Bryan Cordova, Angela Perri, Marsha C. Wibowo, Tanvi Prasad Honap, Jada Ko, Jie Yu, Kate Britton, Linus Girdland Flink, Robert C. Power, Ingelise Stuijts, Domingo Salazar Garcia, Courtney A. Hofman, Richard W. Hagan, Therese Samdapawinde Kagone, Nicolas Meda, Helene Carabin, David Jacobson, Karl Reinhard, Cecil M. Lewis, Jr.Aleksandar Kostic, Choongwon Jeong, Alexander Herbig, Alexander Hubner, Christina Warinner*

*Corresponding author for this work

Research output: Contribution to journalArticle

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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.
Original languageEnglish
Article numbere9001
Number of pages23
JournalPeerJ
Volume8
Early online date17 Apr 2020
DOIs
Publication statusPublished - 17 Apr 2020

Keywords

  • Coprolite
  • Paleofeces
  • Microbiome
  • Endogenous DNA
  • Archaeology
  • Machine learning
  • Nextflow
  • Gut
  • Human
  • Dog

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    Borry, M., Cordova, B., Perri, A., Wibowo, M. C., Honap, T. P., Ko, J., Yu, J., Britton, K., Girdland Flink, L., Power, R. C., Stuijts, I., Garcia, D. S., Hofman, C. A., Hagan, R. W., Kagone, T. S., Meda, N., Carabin, H., Jacobson, D., Reinhard, K., ... Warinner, C. (2020). CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ, 8, [e9001]. https://doi.org/10.1101/871533, https://doi.org/10.7717/peerj.9001, https://doi.org/10.7717/peerj.9001/supp-1