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 Honap, Wing Tung 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: Working paper

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
PublisherbioRxiv
DOIs
Publication statusSubmitted - 15 Jan 2020

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Borry, M., Cordova, B., Perri, A., Wibowo, M. C., Honap, T., Jada Ko, W. T., ... Warinner, C. (2020). CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. bioRxiv. https://doi.org/10.1101/871533

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. / Borry, Maxime; Cordova, Bryan; Perri, Angela; Wibowo, Marsha C.; Honap, Tanvi; Jada Ko, Wing Tung; Yu, Jie; Britton, Kate; Girdland Flink, Linus; Power, Robert C.; Stuijts, Ingelise; Garcia, Domingo Salazar; Hofman, Courtney A.; Hagan, Richard W.; Kagone, Therese Samdapawinde; Meda, Nicolas; Carabin, Helene; Jacobson, David; Reinhard, Karl; Lewis, Jr., Cecil M.; Kostic, Aleksandar; Jeong, Choongwon ; Herbig, Alexander; Hubner, Alexander; Warinner, Christina .

bioRxiv, 2020.

Research output: Working paper

Borry, M, Cordova, B, Perri, A, Wibowo, MC, Honap, T, Jada Ko, WT, 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' bioRxiv. https://doi.org/10.1101/871533
Borry M, Cordova B, Perri A, Wibowo MC, Honap T, Jada Ko WT et al. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. bioRxiv. 2020 Jan 15. https://doi.org/10.1101/871533
Borry, Maxime ; Cordova, Bryan ; Perri, Angela ; Wibowo, Marsha C. ; Honap, Tanvi ; Jada Ko, Wing Tung ; Yu, Jie ; Britton, Kate ; Girdland Flink, Linus ; Power, Robert C. ; Stuijts, Ingelise ; Garcia, Domingo Salazar ; Hofman, Courtney A. ; Hagan, Richard W. ; Kagone, Therese Samdapawinde ; Meda, Nicolas ; Carabin, Helene ; Jacobson, David ; Reinhard, Karl ; Lewis, Jr., Cecil M. ; Kostic, Aleksandar ; Jeong, Choongwon ; Herbig, Alexander ; Hubner, Alexander ; Warinner, Christina . / CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. bioRxiv, 2020.
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title = "CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content",
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.",
author = "Maxime Borry and Bryan Cordova and Angela Perri and Wibowo, {Marsha C.} and Tanvi Honap and {Jada Ko}, {Wing Tung} 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 = "ACKNOWLEDGMENTS We thank David Petts, Zdenek Tvrd ˇ y, Susanne Stegmann-Rajt ´ ar, 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 to 2005 as part of the Lake Settlement Project. Thanks to the Servei d’Investigacio Prehist ´ orica of Val ` encia ` and Museu de la Valltorta of Catello for access to material. This work was supported by the US National ´ Institutes of Health R01GM089886 (to C.W. and C.M.L.), the Deutsche Forschungsgemeinschaft EXC 2051 #390713860 (to C.W.), and the Max Planck Society. Author contributions were as follows: M.B. and C.W. designed the research. B.C., M.C.W., D.J., C.A.H., and R.W.H. performed the laboratory experiments. M.B., C.J., M.C.W, and T.H. analyzed the data. M.B. developed the bioinformatics tools and pipelines. C.W., K.R., K.B., L.G.F., A.P., A.K., W.T.J.K, R.P., I.S., D.S.G., J.Y., T.S.K, N.M., H.C., and C.M.L. provided materials and resources. C.W., A.He., and A.Hu. supervised the research. M.B. ¨ wrote the article, with input from C.W., A.Hu., KR and the other co-authors. DATA AND CODE AVAILABILITY Genetic data are available in the European Nucleotide Archive (ENA) under the accessions PRJEB33577 and PRJEB35362. The code for the analysis is available at github.com/maxibor/coproid-article.",
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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

AU - Jada Ko, Wing Tung

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 - ACKNOWLEDGMENTS We thank David Petts, Zdenek Tvrd ˇ y, Susanne Stegmann-Rajt ´ ar, 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 to 2005 as part of the Lake Settlement Project. Thanks to the Servei d’Investigacio Prehist ´ orica of Val ` encia ` and Museu de la Valltorta of Catello for access to material. This work was supported by the US National ´ Institutes of Health R01GM089886 (to C.W. and C.M.L.), the Deutsche Forschungsgemeinschaft EXC 2051 #390713860 (to C.W.), and the Max Planck Society. Author contributions were as follows: M.B. and C.W. designed the research. B.C., M.C.W., D.J., C.A.H., and R.W.H. performed the laboratory experiments. M.B., C.J., M.C.W, and T.H. analyzed the data. M.B. developed the bioinformatics tools and pipelines. C.W., K.R., K.B., L.G.F., A.P., A.K., W.T.J.K, R.P., I.S., D.S.G., J.Y., T.S.K, N.M., H.C., and C.M.L. provided materials and resources. C.W., A.He., and A.Hu. supervised the research. M.B. ¨ wrote the article, with input from C.W., A.Hu., KR and the other co-authors. DATA AND CODE AVAILABILITY Genetic data are available in the European Nucleotide Archive (ENA) under the accessions PRJEB33577 and PRJEB35362. The code for the analysis is available at github.com/maxibor/coproid-article.

PY - 2020/1/15

Y1 - 2020/1/15

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.

AB - 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.

U2 - 10.1101/871533

DO - 10.1101/871533

M3 - Working paper

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

PB - bioRxiv

ER -