Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

. 2019 Oct ; 4 (10) : 1727-1736. [epub] 20190708

Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem, Research Support, U.S. Gov't, Non-P.H.S.

Perzistentní odkaz   https://www.medvik.cz/link/pmid31285584

Grantová podpora
K99 AI119401 NIAID NIH HHS - United States
R00 AI119401 NIAID NIH HHS - United States
T32 AI141346 NIAID NIH HHS - United States

Odkazy

PubMed 31285584
PubMed Central PMC7440971
DOI 10.1038/s41564-019-0494-6
PII: 10.1038/s41564-019-0494-6
Knihovny.cz E-zdroje

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.

APC Microbiome Institute University College Cork Cork Ireland

Biological and Medical Informatics Program San Diego State University San Diego CA USA

Carl R Woese Institute of Genomic Biology University of Illinois at Urbana Champaign Urbana IL USA

CEHA Kampala Uganda

Center for Genomics and Systems Biology and Department of Biology New York University New York NY USA

Centre for Molecular and Biomolecular Informatics Radboud Institute for Molecular Life Sciences Radboud University Medical Centre Nijmegen The Netherlands

Centre of Epidemiology and Microbiology National Institute of Public Health Prague Czech Republic

Centro de Ciencias Genómicas Universidad Nacional Autónoma de México Cuernavaca Mexico

CERELA Tucumán Argentina

Civil and Environmental Engineering and Earth Sciences University of Notre Dame Notre Dame IN USA

Clinical Microbiology and Immunology Sackler school of Medicine Tel Aviv University Tel Aviv Israel

College of Natural and Computational Sciences Hawai'i Pacific University Kaneohe HI USA

Computational Sciences Research Center San Diego State University San Diego CA USA

Computer Science and Engineering University of California San Diego La Jolla CA USA

COVAB Makerere University Kampala Uganda

Departament de Genètica i de Microbiologia Universitat Autònoma De Barcelona Barcelona Spain

Departamento de Genética Molecular y Microbiología Pontificia Universidad Católica de Chile Santiago Chile

Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina

Department Estacion Biologica Corrientes Institution Museo Arg Cs Naturales CONICET Corrientes Argentina

Department of Animal Health Columbus Zoo and Aquarium Powell OH USA

Department of Anthropology Dartmouth College Hanover NH USA

Department of Anthropology Northern Illinois University DeKalb IL USA

Department of Anthropology University of Colorado Boulder CO USA

Department of Bacterial Genetics Institute of Microbiology Faculty of Biology University of Warsaw Warsaw Poland

Department of Biology San Diego State University San Diego CA USA

Department of Biology University of Padova Padova Italy

Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Delft The Netherlands

Department of Biosystems KU Leuven Leuven Belgium

Department of Child Health Norwegian Institute of Public Health Oslo Norway

Department of Civil and Environmental Engineering Virginia Tech Blacksburg VA USA

Department of Clinical Microbiology and Immunology Sackler School of Medicine Tel Aviv University Tel Aviv Israel

Department of Computer Science San Diego State University San Diego CA USA

Department of Genetics Microbiology and Statistics Universitat de Barcelona Barcelona Spain

Department of Genetics University Medical Center Groningen Groningen The Netherlands

Department of Informational Technologies ITMO University Saint Petersburg Russia

Department of Medicine University of Chicago Chicago IL USA

Department of Microbiology and Biotechnology Max Rubner Institut Federal Research Institute of Nutrition and Food Kiel Germany

Department of Microbiology and Immunology Faculty of Pharmacy Cairo University Cairo Egypt

Department of Microbiology and Immunology McGill University Montreal Quebec Canada

Department of Microbiology and Immunology University of Otago Dunedin New Zealand

Department of Microbiology and Molecular Genetics University of California Davis Davis CA USA

Department of Molecular Biology and Biochemistry University of California Irvine Irvine CA USA

Department of Molecular Biology and Genetics Federal Research and Clinical Center of Physical Chemical Medicine Moscow Russia

Department of Molecular Biosciences Stockholm University Stockholm Sweden

Department of Pediatrics 2nd Faculty of Medicine Charles University Prague Prague Czech Republic

Department of Pediatrics and Child Health Faculty of Medicine University of Khartoum Khartoum Sudan

Department of Pediatrics Federal Teaching Hospital Abakaliki Ebonyi State University Abakaliki Nigeria

Department of Pediatrics School of Medicine University of Jordan Amman Jordan

Department of Pediatrics University Medical Center Groningen Groningen The Netherlands

Department of Physiology Genetics and Microbiology University of Alicante Alicante Spain

Department of Research and Development Lytech Ltd Moscow Russia

Department of Virology School of Medicine University of Tampere Tampere Finland

Endocrine Centre Baku Baku Azerbaijan

EPHM Lab Civil Engineering Department Monash University Clayton Victoria Australia

Escuela de Tecnología Médica Universidad Andres Bello Santiago Chile

GEMA Center for Genomics Ecology and Environment Universidad Mayor Huechuraba Chile

Institute of Infection and Global Health University of Liverpool Liverpool UK

Laboratorio de Analises Instituto Superior Tecnico Universidade Lisboa Lisboa Portugal

Laboratory of Bioinformatics Federal Research and Clinical Center of Physical Chemical Medicine Moscow Russia

Max Planck Tandem Group in Computational Biology Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia

Mediterranean Institute of Oceanography Aix Marseille Université Université de Toulon CNRS IRD UM 110 Marseille France

MEPHI Aix Marseille Université IRD AP HM CNRS IHU Méditerranée Infection Marseille France

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering Fudan University Shanghai China

Molecular Genetics Corporación Corpogen Bogotá Colombia

National Food Institute Research Group for Genomic Epidemiology Technical University of Denmark Kongens Lyngby Denmark

Next Generation Sequencing and Microarray Core Facility The Scripps Research Institute La Jolla CA USA

School of Biological Sciences Monash University Clayton Victoria Australia

School of Microbiology University College Cork Cork Ireland

School of Science and Health Western Sydney University Penrith New South Wales Australia

Swanson School of Engineering University of Pittsburgh Pittsburgh PA USA

The Bioinformatics Centre Department of Biology University of Copenhagen Copenhagen Denmark

The Viral Information Institute San Diego State University San Diego CA USA

Theoretical Biology and Bioinformatics Science4Life Utrecht University Utrecht The Netherlands

UWA School of Agriculture and Environment University of Western Australia Perth Western Australia Australia

Wildlife Health Center University of California Davis Davis CA USA

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