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

2019; Nature Portfolio; Volume: 4; Issue: 10 Linguagem: Inglês

10.1038/s41564-019-0494-6

2058-5276

Robert A. Edwards, Alejandro A. Vega, Holly M. Norman, Maria Cynthia Ohaeri, Kyle Levi, Elizabeth A. Dinsdale, Ondřej Cinek, Ramy K. Aziz, Katelyn McNair, Jeremy J. Barr, Kyle Bibby, Stan J. J. Brouns, Adrián Cazares, Patrick A. de Jonge, Christelle Desnues, Samuel L. Díaz‐Muñoz, Peter C. Fineran, Alexander Kurilshikov, Rob Lavigne, Karla Mazankova, David McCarthy, Franklin L. Nóbrega, Alejandro Reyes, German Tapia, Nicole Trefault, Alexander Tyakht, Pablo Vinuesa, Jeroen Wagemans, Alexandra Zhernakova, Frank M. Aarestrup, Gunduz Ahmadov, Abeer Alassaf, A. Aldaz, Abigail E. Asangba, E Billings, Adrian Cantu, Jane M. Carlton, Daniel Cazares, Gyu-Sung Cho, Tess Condeff, Pilar Cortés, Mike Cranfield, Daniel Cuevas, Rodrigo De la Iglesia, Przemysław Decewicz, Michael P. Doane, Nathaniel J. Dominy, Łukasz Dziewit, Bashir Mukhtar Elwasila, A. Murat Eren, Charles M. A. P. Franz, Jingyuan Fu, Cristina García‐Aljaro, Elodie Ghedin, Kristen Gulino, John M. Haggerty, Steven R. Head, René S. Hendriksen, Colin Hill, Heikki Hyöty, Elena N. Ilina, Mitchell T. Irwin, Thomas C. Jeffries, Juan Jofre, Randall E. Junge, Scott T. Kelley, Mohammadali Khan Mirzaei, Martín M. Kowalewski, Deepak Kumaresan, Steven R. Leigh, David A. Lipson, Eugenia Lisitsyna, M. Casas, Julia M. Maritz, Linsey C. Marr, Angela McCann, Shahar Molshanski-Mor, Sílvia Monteiro, Benjamin Moreira‐Grez, Megan M. Morris, Lawrence Mugisha, Maite Muniesa, Horst Neve, Nam Nguyen, Olivia D. Nigro, Anders Nilsson, Taylor O’Connell, Rasha Odeh, Andrew Oliver, Mariana Piuri, Aaron J. Prussin, Udi Qimron, Zhe‐Xue Quan, Petra Rainetová, Adán Andrés Ramírez Rojas, Raúl R. Raya, Kim Reasor, Gillian A. O. Rice, Alessandro Rossi, Ricardo Santos, John Shimashita, Elyse Stachler, Lars C. Stene, Ronan Strain, Rebecca M. Stumpf, Pedro J. Torres, Alan Twaddle, MaryAnn Ugochi Ibekwe, Nicolás A. Villagra, Stephen Wandro, Bryan A. White, Andrew S. Whiteley, Katrine Whiteson, Cisca Wijmenga, María Mercedes Zambrano, Henrike Zschach, Bas E. Dutilh,

Gut microbiota and health

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. Here, the authors describe the global distribution of crAssphage, its presence in Old-World and New-World primates, and its association with gut bacterial communities and dietary factors, providing insights into the origin, evolution and epidemiology of human gut crAssphage.