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

doi:10.1101/871533

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

Archaeology

Research output: Contribution to journal › Article › peer-review

29 Citations (Scopus)

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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 language	English
Article number	e9001
Number of pages	23
Journal	PeerJ
Volume	8
Early online date	17 Apr 2020
DOIs	https://doi.org/10.1101/871533 https://doi.org/10.7717/peerj.9001 https://doi.org/10.7717/peerj.9001/supp-1
Publication status	Published - 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

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Borry_et_al_PeerJ_CoproIDPredicts_VoR
© 2020 Borry et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. https://creativecommons.org/licenses/by/4.0/
Final published version, 8.03 MBLicence: CC BY

Cite this

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, Article e9001. https://doi.org/10.1101/871533, https://doi.org/10.7717/peerj.9001, https://doi.org/10.7717/peerj.9001/supp-1

Borry, M, Cordova, B, Perri, A, Wibowo, MC, Honap, TP, Ko, J, Yu, J, Britton, K , Girdland Flink, L, Power, RC, Stuijts, I, Garcia, DS, Hofman, CA, Hagan, RW, Kagone, TS, Meda, N, Carabin, H, Jacobson, D, Reinhard, K, Lewis, Jr., CM, Kostic, A, Jeong, C, Herbig, A, Hubner, A & Warinner, C 2020, 'CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content', PeerJ, vol. 8, e9001. https://doi.org/10.1101/871533, https://doi.org/10.7717/peerj.9001, https://doi.org/10.7717/peerj.9001/supp-1

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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.",

keywords = "Coprolite, Paleofeces, Microbiome, Endogenous DNA, Archaeology, Machine learning, Nextflow, Gut, Human, Dog",

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

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, Zden{\v e}k Tvrd{\'y}, Susanne Stegmann-Rajt{\'a}r, 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{\textquoteright}Investigaci{\'o} Prehist{\`o}rica of Val{\`e}ncia and Museu de la Valltorta of Catell{\'o} 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.",

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T1 - CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

AU - Borry, Maxime

AU - Cordova, Bryan

AU - Perri, Angela

AU - Wibowo, Marsha C.

AU - Honap, Tanvi Prasad

AU - Ko, Jada

AU - Yu, Jie

AU - Britton, Kate

AU - Girdland Flink, Linus

AU - Power, Robert C.

AU - Stuijts, Ingelise

AU - Garcia, Domingo Salazar

AU - Hofman, Courtney A.

AU - Hagan, Richard W.

AU - Kagone, Therese Samdapawinde

AU - Meda, Nicolas

AU - Carabin, Helene

AU - Jacobson, David

AU - Reinhard, Karl

AU - Lewis, Jr., Cecil M.

AU - Kostic, Aleksandar

AU - Jeong, Choongwon

AU - Herbig, Alexander

AU - Hubner, Alexander

AU - Warinner, Christina

N1 - 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.

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N2 - 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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KW - Paleofeces

KW - Microbiome

KW - Endogenous DNA

KW - Archaeology

KW - Machine learning

KW - Nextflow

KW - Gut

KW - Human

KW - Dog

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DO - 10.1101/871533

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SN - 2167-8359

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JO - PeerJ

JF - PeerJ

M1 - e9001

ER -

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

Abstract

Bibliographical note

Keywords

Access to Document

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