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

PeerJ

article

Maxime Borry¹  Bryan Cordova¹  Angela Perri²  Marsha Wibowo⁴  Tanvi Prasad Honap⁷  Jada Ko⁹  Jie Yu^1,10  Kate Britton³  Linus Girdland-Flink^1,11  Robert C. Power³  Ingelise Stuijts^1,14  Domingo C. Salazar-García^1,15  Courtney Hofman⁷  Richard Hagan¹  Thérèse Samdapawindé Kagoné^1,17  Nicolas Meda^1,17  Helene Carabin^1,18  David Jacobson⁷  Karl Reinhard^1,19  Cecil Lewis⁷  Aleksandar Kostic⁴  Choongwon Jeong¹  Alexander Herbig¹  Alexander Hübner¹  Christina Warinner¹ 

[1] Department of Archaeogenetics, Max Planck Institute for the Science of Human History;Department of Archaeology, Durham University;Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology;Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center;Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center;Department of Microbiology, Harvard Medical School;Department of Anthropology, University of Oklahoma;Laboratories of Molecular Anthropology and Microbiome Research ,(LMAMR), University of Oklahoma;Department of Anthropology, Harvard University;Department of History, Wuhan University;Department of Archaeology, University of Aberdeen;School of Natural Sciences and Psychology, Liverpool John Moores University;Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München;The Discovery Programme;Grupo de Investigación en Prehistoria IT-1223-19 ,(UPV-EHU), IKERBASQUE-Basque Foundation for Science;Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València;Centre Muraz;Département de pathologie et de microbiologie, Faculté de Médecine vétérinaire, Université de Montréal;School of Natural Resources, University of Nebraska, Lincoln;School of Biological Sciences, Seoul National University;Faculty of Biological Sciences, Friedrich-Schiller Universität Jena

关键词: Coprolite;    Paleofeces;    Microbiome;    Endogenous DNA;    Archeology;    Machine learning;    Nextflow;    Gut;    Human;    Dog;   

DOI  :  10.7717/peerj.9001

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY