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Klapper M, Hübner A, Ibrahim A, Wasmuth I, Borry M, Haensch VG, Zhang S, Al-Jammal WK, Suma H, Fellows Yates JA, Frangenberg J, Velsko IM, Chowdhury S, Herbst R, Bratovanov EV, Dahse HM, Horch T, Hertweck C, González Morales MR, Straus LG, Vilotijevic I, Warinner C, Stallforth P. Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. Science 2023; 380:619-624. [PMID: 37141315 DOI: 10.1126/science.adf5300] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.
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Affiliation(s)
- Martin Klapper
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Ina Wasmuth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Veit G Haensch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Shuaibing Zhang
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Walid K Al-Jammal
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Harikumar Suma
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - James A Fellows Yates
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jasmin Frangenberg
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Rosa Herbst
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Evgeni V Bratovanov
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Therese Horch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Manuel Ramon González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, 39071 Santander, Spain
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA
- Grupo I+D+i EvoAdapta, Departmento de Ciencias Históricas, Universidad de Cantabria, 39005 Santander, Spain
| | - Ivan Vilotijevic
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
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2
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Borry M, Hübner A, Rohrlach AB, Warinner C. PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly. PeerJ 2021; 9:e11845. [PMID: 34395085 PMCID: PMC8323603 DOI: 10.7717/peerj.11845] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/01/2021] [Indexed: 01/19/2023] Open
Abstract
DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets.
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Affiliation(s)
- Maxime Borry
- Microbiome Sciences Group, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany
| | - Alexander Hübner
- Microbiome Sciences Group, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany.,Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany
| | - Adam B Rohrlach
- Population Genetics Group, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, Australia
| | - Christina Warinner
- Microbiome Sciences Group, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany.,Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany.,Department of Anthropology, Harvard University, Cambridge, MA, United States of America
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3
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Wibowo MC, Yang Z, Borry M, Hübner A, Huang KD, Tierney BT, Zimmerman S, Barajas-Olmos F, Contreras-Cubas C, García-Ortiz H, Martínez-Hernández A, Luber JM, Kirstahler P, Blohm T, Smiley FE, Arnold R, Ballal SA, Pamp SJ, Russ J, Maixner F, Rota-Stabelli O, Segata N, Reinhard K, Orozco L, Warinner C, Snow M, LeBlanc S, Kostic AD. Reconstruction of ancient microbial genomes from the human gut. Nature 2021; 594:234-239. [PMID: 33981035 PMCID: PMC8189908 DOI: 10.1038/s41586-021-03532-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/12/2021] [Indexed: 12/26/2022]
Abstract
Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces. Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.
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Affiliation(s)
- Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kun D Huang
- CIBIO Department, University of Trento, Trento, Italy.,Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Samuel Zimmerman
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philipp Kirstahler
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tre Blohm
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Francis E Smiley
- Department of Anthropology, Northern Arizona University, Flagstaff, AZ, USA
| | - Richard Arnold
- Pahrump Paiute Tribe and Consolidated Group of Tribes and Organizations, Pahrump, NV, USA
| | - Sonia A Ballal
- Department of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Russ
- Morrison Microscopy Core Research Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, Harvard University, Cambridge, MA, USA.,Faculty of Biological Sciences, Friedrich-Schiller University, Jena, Germany
| | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Steven LeBlanc
- Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA, USA
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA. .,Department of Microbiology, Harvard Medical School, Boston, MA, USA.
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4
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Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 2021; 9:e10947. [PMID: 33777521 PMCID: PMC7977378 DOI: 10.7717/peerj.10947] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.
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Affiliation(s)
- James A. Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Thiseas C. Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stephen Clayton
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxime U. Garcia
- National Genomics Infrastructure, Science for Life Laboratory, Stockholm, Sweden
- Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Alexander Peltzer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Quantitative Biology Center, Eberhard-Karls University Tübingen, Tübingen, Germany
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5
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Fellows Yates JA, Andrades Valtueña A, Vågene ÅJ, Cribdon B, Velsko IM, Borry M, Bravo-Lopez MJ, Fernandez-Guerra A, Green EJ, Ramachandran SL, Heintzman PD, Spyrou MA, Hübner A, Gancz AS, Hider J, Allshouse AF, Zaro V, Warinner C. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Sci Data 2021; 8:31. [PMID: 33500403 PMCID: PMC7838265 DOI: 10.1038/s41597-021-00816-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/13/2020] [Indexed: 01/05/2023] Open
Abstract
Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at 10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies. Measurement(s) | genome • Metagenome • Metadata • Ancient DNA | Technology Type(s) | digital curation | Factor Type(s) | geographic location • sample age |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13241537
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Affiliation(s)
- James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. .,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, München, 80539, Germany.
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
| | - Åshild J Vågene
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Becky Cribdon
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
| | - Miriam J Bravo-Lopez
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Queretaro, 76230, Mexico
| | - Antonio Fernandez-Guerra
- Section for GeoGenetics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1350, Denmark.,Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Eleanor J Green
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, United Kingdom.,Department of Earth Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
| | | | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, 9037, Norway
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Abigail S Gancz
- Department of Anthropology, Pennsylvania State University, Pennsylvania, PA, 16802, USA
| | - Jessica Hider
- Department of Anthropology, McMaster University, Hamilton, L8S4L9, Canada.,McMaster Ancient DNA Centre, McMaster University, Hamilton, L8S4L10, Canada
| | - Aurora F Allshouse
- Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA.,Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA
| | - Valentina Zaro
- Department of Biology, Università degli Studi di Firenze, Florence, 50122, Italy
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Jena, Germany. .,Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA.
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6
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Borry M, Cordova B, Perri A, Wibowo M, Prasad Honap T, Ko J, Yu J, Britton K, Girdland-Flink L, Power RC, Stuijts I, Salazar-García DC, Hofman C, Hagan R, Samdapawindé Kagoné T, Meda N, Carabin H, Jacobson D, Reinhard K, Lewis C, Kostic A, Jeong C, Herbig A, Hübner A, Warinner C. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ 2020; 8:e9001. [PMID: 32337106 PMCID: PMC7169968 DOI: 10.7717/peerj.9001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/26/2020] [Indexed: 12/11/2022] Open
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.
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Affiliation(s)
- Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Bryan Cordova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Angela Perri
- Department of Archaeology, Durham University, Durham, UK
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marsha Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Tanvi Prasad Honap
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Jada Ko
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Jie Yu
- Department of History, Wuhan University, Wuhan, China
| | - Kate Britton
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK
| | - Linus Girdland-Flink
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Robert C. Power
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, München, Germany
| | | | - Domingo C. Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria-Gasteiz, Spain
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
| | - Courtney Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Richard Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | | | - Helene Carabin
- Département de pathologie et de microbiologie, Faculté de Médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - David Jacobson
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska, Lincoln, NE, USA
| | - Cecil Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Aleksandar Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany
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