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

Autor: Edwards RA; Department of Biology, San Diego State University, San Diego, CA, USA. redwards@sdsu.edu.; The Viral Information Institute, San Diego State University, San Diego, CA, USA. redwards@sdsu.edu., Vega AA; Department of Biology, San Diego State University, San Diego, CA, USA., Norman HM; Department of Biology, San Diego State University, San Diego, CA, USA., Ohaeri M; Department of Biology, San Diego State University, San Diego, CA, USA., Levi K; Department of Computer Science, San Diego State University, San Diego, CA, USA., Dinsdale EA; Department of Biology, San Diego State University, San Diego, CA, USA., Cinek O; Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic., Aziz RK; Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt., McNair K; Computational Sciences Research Center, San Diego State University, San Diego, CA, USA., Barr JJ; School of Biological Sciences, Monash University, Clayton, Victoria, Australia., Bibby K; Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA., Brouns SJJ; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands., Cazares A; Institute of Infection and Global Health, University of Liverpool, Liverpool, UK., de Jonge PA; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.; Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands., Desnues C; MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France.; Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France., Díaz Muñoz SL; Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA.; Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA., Fineran PC; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand., Kurilshikov A; Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands., Lavigne R; Department of Biosystems, KU Leuven, Leuven, Belgium., Mazankova K; Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic., McCarthy DT; EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia., Nobrega FL; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands., Reyes Muñoz A; Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia., Tapia G; Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway., Trefault N; GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile., Tyakht AV; Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia.; Department of Informational Technologies, ITMO University, Saint Petersburg, Russia., Vinuesa P; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico., Wagemans J; Department of Biosystems, KU Leuven, Leuven, Belgium., Zhernakova A; Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands., Aarestrup FM; National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark., Ahmadov G; Endocrine Centre Baku, Baku, Azerbaijan., Alassaf A; Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan., Anton J; Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain., Asangba A; Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Billings EK; Department of Biology, San Diego State University, San Diego, CA, USA., Cantu VA; Computational Sciences Research Center, San Diego State University, San Diego, CA, USA., Carlton JM; Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA., Cazares D; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico., Cho GS; Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany., Condeff T; Department of Biology, San Diego State University, San Diego, CA, USA., Cortés P; Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain., Cranfield M; Wildlife Health Center, University of California, Davis, Davis, CA, USA., Cuevas DA; Computational Sciences Research Center, San Diego State University, San Diego, CA, USA., De la Iglesia R; Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile., Decewicz P; Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland., Doane MP; Department of Biology, San Diego State University, San Diego, CA, USA., Dominy NJ; Department of Anthropology, Dartmouth College, Hanover, NH, USA., Dziewit L; Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland., Elwasila BM; Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan., Eren AM; Department of Medicine, University of Chicago, Chicago, IL, USA., Franz C; Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany., Fu J; Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands., Garcia-Aljaro C; Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain., Ghedin E; Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA., Gulino KM; Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA., Haggerty JM; Department of Biology, San Diego State University, San Diego, CA, USA., Head SR; Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA., Hendriksen RS; National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark., Hill C; School of Microbiology, University College Cork, Cork, Ireland., Hyöty H; Department of Virology, School of Medicine, University of Tampere, Tampere, Finland., Ilina EN; Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia., Irwin MT; Department of Anthropology, Northern Illinois University, DeKalb, IL, USA., Jeffries TC; School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia., Jofre J; Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain., Junge RE; Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA., Kelley ST; Department of Biology, San Diego State University, San Diego, CA, USA., Khan Mirzaei M; Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada., Kowalewski M; Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina., Kumaresan D; UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia., Leigh SR; Department of Anthropology, University of Colorado, Boulder, CO, USA., Lipson D; Department of Biology, San Diego State University, San Diego, CA, USA., Lisitsyna ES; Department of Research and Development, Lytech Ltd., Moscow, Russia., Llagostera M; Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain., Maritz JM; Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA., Marr LC; Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA., McCann A; APC Microbiome Institute, University College Cork, Cork, Ireland., Molshanski-Mor S; Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel., Monteiro S; Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal., Moreira-Grez B; UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia., Morris M; Department of Biology, San Diego State University, San Diego, CA, USA., Mugisha L; CEHA, Kampala, Uganda.; COVAB, Makerere University, Kampala, Uganda., Muniesa M; Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain., Neve H; Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany., Nguyen NP; Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA., Nigro OD; College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA., Nilsson AS; Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden., O'Connell T; Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA., Odeh R; Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan., Oliver A; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA., Piuri M; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina., Prussin Ii AJ; Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA., Qimron U; Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel., Quan ZX; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China., Rainetova P; Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic., Ramírez-Rojas A; Molecular Genetics, Corporación Corpogen, Bogotá, Colombia., Raya R; CERELA, Tucumán, Argentina., Reasor K; Department of Biology, San Diego State University, San Diego, CA, USA., Rice GAO; Department of Anthropology, Dartmouth College, Hanover, NH, USA., Rossi A; Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.; Department of Biology, University of Padova, Padova, Italy., Santos R; Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal., Shimashita J; Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA., Stachler EN; Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA., Stene LC; Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway., Strain R; APC Microbiome Institute, University College Cork, Cork, Ireland., Stumpf R; Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Torres PJ; Department of Biology, San Diego State University, San Diego, CA, USA., Twaddle A; Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA., Ugochi Ibekwe M; Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria., Villagra N; Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile., Wandro S; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA., White B; Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Whiteley A; UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia., Whiteson KL; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA., Wijmenga C; Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands., Zambrano MM; Molecular Genetics, Corporación Corpogen, Bogotá, Colombia., Zschach H; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark., Dutilh BE; Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands. bedutilh@gmail.com.; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands. bedutilh@gmail.com.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2019 Oct; Vol. 4 (10), pp. 1727-1736. Date of Electronic Publication: 2019 Jul 08.
DOI: 10.1038/s41564-019-0494-6
Abstrakt: 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.
Databáze: MEDLINE