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 journalArticlepeer-review

30 Citations (Scopus)
11 Downloads (Pure)

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

Bibliographical note

Funding
This work was supported by the US National Institutes of Health R01GM089886 (to Christina Warinner and Cecil Lewis), the Deutsche Forschungsgemeinschaft EXC 2051 #390713860 (to Christina Warinner), and the Max Planck Society. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Acknowledgements
We thank David Petts, Zdeněk Tvrdý, Susanne Stegmann-Rajtár, and Zuzana Rajtarova for contributing archaeological samples to this study. We thank the Guildford Museum (Guildford Borough Council Heritage Service) and Catriona Wilson for allowing us to analyze the chamber pot paleofeces sample from Surrey, UK. The sample from Derragh, Ireland was excavated by Discovery Programme, an all-Ireland public center of archaeological research supported by the Heritage Council, during field work in 2003–2005 as part of the Lake Settlement Project. Thanks to the Servei d’Investigació Prehistòrica of València and Museu de la Valltorta of Catelló for access to material.

Data Availability
The following information was supplied regarding data availability:

The code for the analysis is available at GitHub: https://github.com/maxibor/coproid-article and Zenodo:

Maxime Borry, Alexander Peltzer, & James A. Fellows Yates. (2019, April 29). nf-core/coproid: coproID v1.0 - Dioptre Walrus (Version 1.0). Zenodo. DOI 10.5281/zenodo.2653757.

Keywords

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

Fingerprint

Dive into the research topics of 'CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content'. Together they form a unique fingerprint.

Cite this