1. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
- Author
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Steven R. Head, Emma Billings, Stephen Wandro, Jane M. Carlton, Alexandra Zhernakova, A. Murat Eren, Zhe Xue Quan, Anders S. Nilsson, Gyu Sung Cho, Udi Qimron, Martin M. Kowalewski, John Shimashita, Gillian A.O. Rice, Frank Møller Aarestrup, Elyse Stachler, Vito Adrian Cantu, Linsey C. Marr, Alessandro Rossi, Angela McCann, Colin Hill, Cristina García-Aljaro, Kristen M. Gulino, David A. Lipson, Rene S. Hendriksen, Bryan A. White, Bas E. Dutilh, Bashir Mukhtar Elwasila, Karla Mazankova, Alexander V. Tyakht, Julia M. Maritz, Ronan Strain, Rodrigo De la Iglesia, Ramy K. Aziz, Kyle Levi, Alan Twaddle, Alejandro Reyes Muñoz, Katelyn McNair, Alejandro A. Vega, Nathaniel J. Dominy, Abigail E. Asangba, Robert Edwards, Rasha Odeh, Olivia D. Nigro, Gunduz Ahmadov, Raúl R. Raya, Nam Nguyen, Charles M. A. P. Franz, Nicole Trefault, Adán Ramírez-Rojas, Michael P. Doane, Randall E. Junge, Patrick A. de Jonge, Jingyuan Fu, Taylor O'Connell, Mike Cranfield, German Tapia, Heikki Hyöty, Nicolás A. Villagra, Cisca Wijmenga, Henrike Zschach, Megan M. Morris, Franklin L. Nobrega, Elena N. Ilina, David Thomas McCarthy, Daniel Cazares, Silvia Monteiro, Lawrence Mugisha, Daniel A. Cuevas, Horst Neve, Przemyslaw Decewicz, John M. Haggerty, Ricardo Santos, Deepak Kumaresan, Shahar Molshanski-Mor, Andrew S. Whiteley, Benjamin Moreira-Grez, Rebecca M. Stumpf, Katrine Whiteson, Holly M. Norman, Jeremy J. Barr, Peter C. Fineran, Jeroen Wagemans, Samuel L. Díaz Muñoz, Kim Reasor, Elizabeth A. Dinsdale, Mitchell T. Irwin, Aaron J. Prussin, Mohammadali Khan Mirzaei, Maite Muniesa, Christelle Desnues, Montserrat Llagostera, Rob Lavigne, Abeer Alassaf, Tess Condeff, Petra Rainetova, María Mercedes Zambrano, Adrian Cazares, Elodie Ghedin, Alexander Kurilshikov, Lukasz Dziewit, Thomas C. Jeffries, Mary Ann Ugochi Ibekwe, Eugenia S. Lisitsyna, Juan Jofre, Pedro J. Torres, Maria Ohaeri, Mariana Piuri, Andrew Oliver, Steven R. Leigh, Ondrej Cinek, Stan J. J. Brouns, Josefa Antón, Pilar Cortés, Kyle Bibby, Lars C. Stene, Pablo Vinuesa, Scott T. Kelley, San Diego State University (SDSU), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Gene Technology, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Monash University [Clayton], University Medical Center Groningen [Groningen] (UMCG), Centro de Investigación Oceanográfica en el Pacífico Sur Oriental (COPAS), Universidad de Concepción - University of Concepcion [Chile], Dartmouth College [Hanover], Marine Biological Laboratory (MBL), University of Chicago, Department of Safety and Quality of Fruit and Vegetables, Federal Research Institute for Nutrition and Food, Department of Parasite and Virus Genomics, The Institute for Genomic Research (TIGR), The Scripps Research Institute [La Jolla, San Diego], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Queen's University [Belfast] (QUB), Hawkesbury Institute for the Environment [Richmond] (HIE), Western Sydney University, CREW - Center for Research on the English-speaking World - EA 4399 (CREW), Université Sorbonne Nouvelle - Paris 3, School of Microbiology, University College Cork (UCC), Université du Cap-Vert, université du Cap-Vert, Department of Microbiology [University of Barcelona], Dept Microbiol & Biotechnol, Max Rubner Inst, Department of Pharmaceutical Biosciences, Uppsala University, University of Manchester [Manchester], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Getulio Vargas Foundation, Centro Geofísico de Canarias, Instituto Geografico Nacional, Laboratorio de Patogénesis Molecular y Antimicrobianos, Facultad de Medicina , Universidad Andres Bello, University of Illinois, University of Illinois System, National Severe Storms Laboratory (NSSL), National Oceanic and Atmospheric Administration (NOAA), Department of Medical Genetics, HMNC Brain Health, Utrecht University [Utrecht], Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Universidad de Concepción [Chile], The SCRIPPS Research Institute (SCRIPPS), University of California [Los Angeles] (UCLA), University of California-University of California, Technical University of Denmark [Lyngby] (DTU), Biomolecular Imaging and Proteomics, National Center for Mass Spectrometry Imaging, Uppsala University, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Translational Immunology Groningen (TRIGR), and Center for Liver, Digestive and Metabolic Diseases (CLDM)
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DYNAMICS ,Male ,BACTERIAL ,ACCURACY ,Lineage (evolution) ,Filogeografia ,Microbiología ,Applied Microbiology and Biotechnology ,Genome ,Biological Coevolution ,MULTIPLE SEQUENCE ALIGNMENT ,TRACKING ,Feces ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Bacteriophages ,Viral ,Clade ,Phylogeny ,ComputingMilieux_MISCELLANEOUS ,2. Zero hunger ,0303 health sciences ,Environmental microbiology ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,crAssphage ,READ ALIGNMENT ,GENOME ,Phylogeography ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Female ,Life Sciences & Biomedicine ,Primates ,Microbiology (medical) ,Lineage (genetic) ,Evolution ,Immunology ,Coronacrisis-Taverne ,Microbiota intestinal ,BIOLOGY ,Biology ,Microbiology ,Virus ,DNA sequencing ,Article ,03 medical and health sciences ,All institutes and research themes of the Radboud University Medical Center ,SDG 3 - Good Health and Well-being ,Phylogenetics ,Genetics ,Animals ,Humans ,Human virome ,ALGORITHM ,Microbiome ,Genomes ,Gastrointestinal microbiome ,030304 developmental biology ,[SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health ,Science & Technology ,Widespread human gut virus ,Bacteroidetes ,030306 microbiology ,Genetic Variation ,DNA ,Cell Biology ,biology.organism_classification ,Gastrointestinal Microbiome ,MICROBIOME ,Evolutionary biology ,DNA, Viral - Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome. ispartof: NATURE MICROBIOLOGY vol:4 issue:10 pages:1727-1736 ispartof: location:England status: published
- Published
- 2019
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