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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
RA. Edwards, AA. Vega, HM. Norman, M. Ohaeri, K. Levi, EA. Dinsdale, O. Cinek, RK. Aziz, K. McNair, JJ. Barr, K. Bibby, SJJ. Brouns, A. Cazares, PA. de Jonge, C. Desnues, SL. Díaz Muñoz, PC. Fineran, A. Kurilshikov, R. Lavigne, K. Mazankova, DT....
Jazyk angličtina Země Velká Británie
Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem, Research Support, U.S. Gov't, Non-P.H.S.
Grantová podpora
T32 AI141346
NIAID NIH HHS - United States
NV15-29078A
MZ0
CEP - Centrální evidence projektů
NV15-31426A
MZ0
CEP - Centrální evidence projektů
Digitální knihovna NLK
Plný text - Článek
Plný text - Článek
Zdroj
Zdroj
NLK
ProQuest Central
od 2016-01-01 do Před 1 rokem
- MeSH
- Bacteroidetes klasifikace genetika virologie MeSH
- bakteriofágy klasifikace genetika MeSH
- DNA virů genetika MeSH
- feces virologie MeSH
- fylogeneze MeSH
- fylogeografie MeSH
- genetická variace MeSH
- koevoluce * MeSH
- lidé MeSH
- primáti virologie MeSH
- střevní mikroflóra * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
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 COVAB Makerere University Kampala Uganda
Centre of Epidemiology and Microbiology National Institute of Public Health Prague Czech Republic
Centro de Ciencias Genómicas Universidad Nacional Autónoma de México Cuernavaca Mexico
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
Departament de Genètica i de Microbiologia Universitat Autònoma De Barcelona Barcelona Spain
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 Biology San Diego State University San Diego CA USA
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 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 Medicine University of Chicago Chicago IL USA
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 Molecular Biology and Biochemistry University of California Irvine Irvine CA USA
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 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
Molecular Genetics Corporación Corpogen Bogotá Colombia
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
Wildlife Health Center University of California Davis Davis CA USA
Citace poskytuje Crossref.org
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- $a Edwards, Robert A $u 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.
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- $a Global phylogeography and ancient evolution of the widespread human gut virus crAssphage / $c RA. Edwards, AA. Vega, HM. Norman, M. Ohaeri, K. Levi, EA. Dinsdale, O. Cinek, RK. Aziz, K. McNair, JJ. Barr, K. Bibby, SJJ. Brouns, A. Cazares, PA. de Jonge, C. Desnues, SL. Díaz Muñoz, PC. Fineran, A. Kurilshikov, R. Lavigne, K. Mazankova, DT. McCarthy, FL. Nobrega, A. Reyes Muñoz, G. Tapia, N. Trefault, AV. Tyakht, P. Vinuesa, J. Wagemans, A. Zhernakova, FM. Aarestrup, G. Ahmadov, A. Alassaf, J. Anton, A. Asangba, EK. Billings, VA. Cantu, JM. Carlton, D. Cazares, GS. Cho, T. Condeff, P. Cortés, M. Cranfield, DA. Cuevas, R. De la Iglesia, P. Decewicz, MP. Doane, NJ. Dominy, L. Dziewit, BM. Elwasila, AM. Eren, C. Franz, J. Fu, C. Garcia-Aljaro, E. Ghedin, KM. Gulino, JM. Haggerty, SR. Head, RS. Hendriksen, C. Hill, H. Hyöty, EN. Ilina, MT. Irwin, TC. Jeffries, J. Jofre, RE. Junge, ST. Kelley, M. Khan Mirzaei, M. Kowalewski, D. Kumaresan, SR. Leigh, D. Lipson, ES. Lisitsyna, M. Llagostera, JM. Maritz, LC. Marr, A. McCann, S. Molshanski-Mor, S. Monteiro, B. Moreira-Grez, M. Morris, L. Mugisha, M. Muniesa, H. Neve, NP. Nguyen, OD. Nigro, AS. Nilsson, T. O'Connell, R. Odeh, A. Oliver, M. Piuri, AJ. Prussin Ii, U. Qimron, ZX. Quan, P. Rainetova, A. Ramírez-Rojas, R. Raya, K. Reasor, GAO. Rice, A. Rossi, R. Santos, J. Shimashita, EN. Stachler, LC. Stene, R. Strain, R. Stumpf, PJ. Torres, A. Twaddle, M. Ugochi Ibekwe, N. Villagra, S. Wandro, B. White, A. Whiteley, KL. Whiteson, C. Wijmenga, MM. Zambrano, H. Zschach, BE. Dutilh,
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- $a 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.
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