New Results
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
View ORCID ProfileRobert A. Edwards, View ORCID ProfileAlejandro A. Vega, View ORCID ProfileHolly M. Norman, View ORCID ProfileMaria Ohaeri, View ORCID ProfileKyle Levi, View ORCID ProfileElizabeth A. Dinsdale, View ORCID ProfileOndrej Cinek, View ORCID ProfileRamy K. Aziz, View ORCID ProfileKatelyn McNair, View ORCID ProfileJeremy J. Barr, View ORCID ProfileKyle Bibby, View ORCID ProfileStan JJ. Brouns, View ORCID ProfileAdrian Cazares, View ORCID ProfilePatrick A. de Jonge, View ORCID ProfileChristelle Desnues, View ORCID ProfileSamuel L. Díaz Muñoz, View ORCID ProfilePeter C. Fineran, View ORCID ProfileAlexander Kurilshikov, View ORCID ProfileRob Lavigne, View ORCID ProfileKarla Mazankova, View ORCID ProfileDavid T. McCarthy, View ORCID ProfileFranklin L. Nobrega, View ORCID ProfileAlejandro Reyes Muñoz, View ORCID ProfileGerman Tapia, View ORCID ProfileNicole Trefault, View ORCID ProfileAlexander V. Tyakht, View ORCID ProfilePablo Vinuesa, View ORCID ProfileJeroen Wagemans, View ORCID ProfileAlexandra Zhernakova, View ORCID ProfileFrank M. Aarestrup, View ORCID ProfileGunduz Ahmadov, View ORCID ProfileAbeer Alassaf, View ORCID ProfileJosefa Anton, View ORCID ProfileAbigail Asangba, View ORCID ProfileEmma Billings, View ORCID ProfileVito Adrian Cantu, View ORCID ProfileJane M. Carlton, View ORCID ProfileDaniel Cazares, View ORCID ProfileGyu-Sung Cho, View ORCID ProfileTess Condeff, View ORCID ProfilePilar Cortés, View ORCID ProfileMike Cranfield, View ORCID ProfileDaniel A. Cuevas, View ORCID ProfileRodrigo De la Iglesia, View ORCID ProfilePrzemyslaw Decewicz, View ORCID ProfileMichael P. Doane, View ORCID ProfileNathaniel J. Dominy, View ORCID ProfileLukasz Dziewit, View ORCID ProfileBashir Mukhtar Elwasila, View ORCID ProfileA. Murat Eren, View ORCID ProfileCharles Franz, View ORCID ProfileJingyuan Fu, View ORCID ProfileCristina Garcia-Aljaro, View ORCID ProfileElodie Ghedin, View ORCID ProfileKristen M. Gulino, View ORCID ProfileJohn M. Haggerty, View ORCID ProfileSteven R. Head, View ORCID ProfileRene S. Hendriksen, View ORCID ProfileColin Hill, View ORCID ProfileHeikki Hyöty, View ORCID ProfileElena N. Ilina, View ORCID ProfileMitchell T. Irwin, View ORCID ProfileThomas Jeffries, View ORCID ProfileJuan Jofre Torroella, View ORCID ProfileRandall E. Junge, View ORCID ProfileScott T. Kelley, View ORCID ProfileMartin Kowalewski, View ORCID ProfileDeepak Kumaresan, View ORCID ProfileSteven Leigh, View ORCID ProfileEugenia S. Lisitsyna, View ORCID ProfileMontserrat Llagostera, View ORCID ProfileJulia M. Maritz, View ORCID ProfileLinsey C. Marr, Angela McCann, View ORCID ProfileMohammadali Khan Mirzaei, View ORCID ProfileShahar Molshanski-Mor, View ORCID ProfileSilvia Monteiro, View ORCID ProfileBen Moreira-Grez, View ORCID ProfileMegan Morris, View ORCID ProfileLawrence Mugisha, View ORCID ProfileMaite Muniesa, View ORCID ProfileHorst Neve, View ORCID ProfileNam-phuong Nguyen, View ORCID ProfileOlivia D. Nigro, View ORCID ProfileAnders S. Nilsson, View ORCID ProfileTaylor O’Connell, View ORCID ProfileRasha Odeh, View ORCID ProfileAndrew Oliver, View ORCID ProfileMariana Piuri, View ORCID ProfileAaron J. Prussin II, View ORCID ProfileUdi Qimron, View ORCID ProfileZhe-Xue Quan, View ORCID ProfilePetra Rainetova, View ORCID ProfileAdán Andrés Ramírez Rojas, View ORCID ProfileRaul Raya, Gillian A.O. Rice, View ORCID ProfileAlessandro Rossi, View ORCID ProfileRicardo Santos, John Shimashita, View ORCID ProfileElyse N. Stachler, View ORCID ProfileLars C. Stene, View ORCID ProfileRonan Strain, Rebecca Stumpf, View ORCID ProfilePedro J. Torres, View ORCID ProfileAlan Twaddle, View ORCID ProfileMaryAnn Ugochi Ibekwe, View ORCID ProfileNicolás Villagra, View ORCID ProfileStephen Wandro, View ORCID ProfileBryan White, View ORCID ProfileAndy Whitely, View ORCID ProfileKatrine L. Whiteson, View ORCID ProfileCisca Wijmenga, View ORCID ProfileMaria M. Zambrano, View ORCID ProfileHenrike Zschach, View ORCID ProfileBas E. Dutilh
doi: https://doi.org/10.1101/527796
Robert A. Edwards
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
2Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Alejandro A. Vega
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Holly M. Norman
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Maria Ohaeri
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Kyle Levi
3Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Elizabeth A. Dinsdale
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Ondrej Cinek
4Department of Pediatrics, Charles University in Prague, Ovocný trh 3-5, Prague, Czech Republic
Ramy K. Aziz
5Department of Microbiology and Immunology, Cairo University, Qasr El-Ainy Street, Cairo, 11562, Egypt
Katelyn McNair
2Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Jeremy J. Barr
6School of Biological Sciences, Monash University, 17 Rainforest Walk, School of Biological Sciences, Clayton, VIC, 3800, Australia
Kyle Bibby
7Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN, 46556, USA
Stan JJ. Brouns
8Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
Adrian Cazares
9Institute of Infection and Global Health, University of Liverpool, 8 W Derby St, Liverpool, L7 3EA, UK
Patrick A. de Jonge
10Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
8Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
Christelle Desnues
11Microbes, Evolution, Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, 19-21 Bd Jean Moulin, Marseille, PACA, 13005, France
Samuel L. Díaz Muñoz
12Center for Genomics and Systems Biology & Department of Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
13Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
Peter C. Fineran
14Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
Alexander Kurilshikov
15Department of Genetics, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
Rob Lavigne
16Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 - box 2462, Leuven, B-3001, Belgium
Karla Mazankova
4Department of Pediatrics, Charles University in Prague, Ovocný trh 3-5, Prague, Czech Republic
David T. McCarthy
17Environmental and Public Health Microbiology Laboratory (EPHM Lab), Civil Engineering Department, Monash University, Building 60, Wellington Road, Clayton, VIC, 3800, Australia
Franklin L. Nobrega
8Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
Alejandro Reyes Muñoz
18Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Carrera 1 #18A-12, Bogotá, 111711, Colombia
German Tapia
19Department of Child Health, Norwegian Institute of Public Health, Marcus Thranes gate 6, Oslo, NO-0473, Norway
Nicole Trefault
20GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago, Chile
Alexander V. Tyakht
21Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
22Department of Informational Technologies, ITMO University, 49 Kronverksky Pr., Saint-Petersburg, 197101, Russia
Pablo Vinuesa
23Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P. 62210, Cuernavaca, Morelos, 62210, México
Jeroen Wagemans
16Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 - box 2462, Leuven, B-3001, Belgium
Alexandra Zhernakova
15Department of Genetics, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
Frank M. Aarestrup
24National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Søltofts Plads 221, Kongens Lyngby, 2800, Denmark
Gunduz Ahmadov
25Endocrine Centre Baku, Str. I. Hashimov 4A, Baku, AZ1114, Azerbaijan
Abeer Alassaf
26Department of Pediatrics, School of Medicine, University of Jordan, Queen Rania Street, Amman, 11942, Jordan
Josefa Anton
27Department of Physiology, Genetics and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, 03080 Alicante, Spain
Abigail Asangba
28Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana Champaign, 607 S Mathews Ave, Urbana, IL, 61801, USA
Emma Billings
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Vito Adrian Cantu
2Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Jane M. Carlton
12Center for Genomics and Systems Biology & Department of Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
Daniel Cazares
23Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P. 62210, Cuernavaca, Morelos, 62210, México
Gyu-Sung Cho
29Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, Kiel, 24103, Germany
Tess Condeff
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Pilar Cortés
30Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Avinguda de l’Eix Central / Carrer dels Til·lers, Bellaterra, 8193, Spain
Mike Cranfield
31Wildlife Health Center, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
Daniel A. Cuevas
2Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Rodrigo De la Iglesia
32Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Portugal 49, Santiago, Metropolitana, 8330025, Chile
Przemyslaw Decewicz
33Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
Michael P. Doane
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Nathaniel J. Dominy
34Department of Anthropology, Dartmouth College, 6047 Silsby Hall, Hanover, NH, 03755-3529, USA
Lukasz Dziewit
33Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
Bashir Mukhtar Elwasila
35Department of Pediatrics and Child Health, University of Khartoum, Faculty of Medicine, El Qasr Ave, Khartoum, Sudan
A. Murat Eren
36Department of Medicine, University of Chicago, 900 E. 57th St., Chicago, IL, 60637, USA
Charles Franz
29Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, Kiel, 24103, Germany
Jingyuan Fu
37Department of Pediatrics, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
Cristina Garcia-Aljaro
38Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Av. Diagonal, 643 Barcelona, 08028, Spain
Elodie Ghedin
12Center for Genomics and Systems Biology & Department of Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
Kristen M. Gulino
12Center for Genomics and Systems Biology & Department of Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
John M. Haggerty
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Steven R. Head
39Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, CA, 92037, USA
Rene S. Hendriksen
24National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Søltofts Plads 221, Kongens Lyngby, 2800, Denmark
Colin Hill
40School of Microbiology, University College Cork, BioSciences Building, Western Road, Cork, T12 YT20, Ireland
Heikki Hyöty
41Department of Virology, School of Medicine, University of Tampere, Kalevantie 4, Tampere, FI33520, Finland
Elena N. Ilina
42Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
Mitchell T. Irwin
43Anthropology, Northern Illinois University, 1425 W Lincoln Hwy, DeKalb, IL, 60115, USA
Thomas Jeffries
44School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
Juan Jofre Torroella
38Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Av. Diagonal, 643 Barcelona, 08028, Spain
Randall E. Junge
45Department of Animal Health, Columbus Zoo and Aquarium, 9990 Riverside Drive, Powell, OH, 43065, USA
Scott T. Kelley
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Martin Kowalewski
46Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, 9 de Julio 392 8D, Corrientes, 3400, Argentina
Deepak Kumaresan
47School of Earth and Environment, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
Steven Leigh
48Department of Anthropology, not College, University of Colorado, Boulder, 1350 Pleasant St., Boulder, CO, 80309, USA
Eugenia S. Lisitsyna
49Department of Research and Development, Lytech Ltd., Malaya Semenovskaya 3a, Moscow, 107023, Russia
Montserrat Llagostera
30Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Avinguda de l’Eix Central / Carrer dels Til·lers, Bellaterra, 8193, Spain
Julia M. Maritz
12Center for Genomics and Systems Biology & Department of Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
Linsey C. Marr
50Department of Civil and Environmental Engineering, Virginia Tech, 750 Drillfield Drive, Blacksburg, VA, 24060, USA
Angela McCann
51APC Microbiome Institute, University College Cork, Room 3.39 BioSciences Building, Cork, Ireland
Mohammadali Khan Mirzaei
52Department of Molecular Biosciences, Stockholm University, Svante Arrhenius väg 20C, Stockholm, Sweden
Shahar Molshanski-Mor
53Clinical Microbiology & Immunology, Sackler school of Medicine, Tel-Aviv University, 55 Levanon St., Tel-Aviv, 6997878, Israel
Silvia Monteiro
54Laboratorio de Analises, Instituto Superior Tecnico, Av. Rovisco Pais, Lisboa, Lisboa, 1049-001, Portugal
Ben Moreira-Grez
47School of Earth and Environment, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
Megan Morris
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Lawrence Mugisha
55Conservation and Ecosystem Health Alliance (CEHA), P.O. Box, 34153, Kampala, Uganda
56College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
Maite Muniesa
38Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Av. Diagonal, 643 Barcelona, 08028, Spain
Horst Neve
29Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, Kiel, 24103, Germany
Nam-phuong Nguyen
57Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0404, USA
Olivia D. Nigro
58Department of Biology, Hawai’i Pacific University, 45-045 Kamehameha Highway, Ste. 206, Kaneohe, Hi, 96744-5297, USA
Anders S. Nilsson
52Department of Molecular Biosciences, Stockholm University, Svante Arrhenius väg 20C, Stockholm, Sweden
Taylor O’Connell
59Biological and Medical Informatics Program, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Rasha Odeh
26Department of Pediatrics, School of Medicine, University of Jordan, Queen Rania Street, Amman, 11942, Jordan
Andrew Oliver
60Department of Molecular Biology & Biochemistry, University of California, Irvine, 3315 McGaugh Hall, Irvine, CA, 92697, USA
Mariana Piuri
61Departamento de Química Biológica, Ciudad Universitaria, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires, 1428, Argentina
Aaron J. Prussin II
50Department of Civil and Environmental Engineering, Virginia Tech, 750 Drillfield Drive, Blacksburg, VA, 24060, USA
Udi Qimron
62Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 55 Levanon St., Tel Aviv, 69978, Israel
Zhe-Xue Quan
63Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, 2005 Songhu-Road, Shanghai, 200438, P. R. China
Petra Rainetova
64Centre of Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 49/48, Prague, Czech Republic
Adán Andrés Ramírez Rojas
65Molecular Genetics, Corporación Corpogen, Carrera 5 #66A-34, Bogotá, DC, 110231, Colombia
Raul Raya
66CERELA, Chacabuco 145 - (T4000ILC), San Miguel de Tucumán, Tucumán, Argentina
Gillian A.O. Rice
34Department of Anthropology, Dartmouth College, 6047 Silsby Hall, Hanover, NH, 03755-3529, USA
Alessandro Rossi
10Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
67Molecular medicine, University of Padova, Via Gabelli 63, Padova, Veneto, 35121, Italy
Ricardo Santos
54Laboratorio de Analises, Instituto Superior Tecnico, Av. Rovisco Pais, Lisboa, Lisboa, 1049-001, Portugal
John Shimashita
50Department of Civil and Environmental Engineering, Virginia Tech, 750 Drillfield Drive, Blacksburg, VA, 24060, USA
Elyse N. Stachler
68Swanson School of Engineering, University of Pittsburgh, 3700 O’Hara Street, Pittsburgh, PA, 15261, USA
Lars C. Stene
19Department of Child Health, Norwegian Institute of Public Health, Marcus Thranes gate 6, Oslo, NO-0473, Norway
Ronan Strain
51APC Microbiome Institute, University College Cork, Room 3.39 BioSciences Building, Cork, Ireland
Rebecca Stumpf
28Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana Champaign, 607 S Mathews Ave, Urbana, IL, 61801, USA
Pedro J. Torres
1Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
Alan Twaddle
12Center for Genomics and Systems Biology & Department of Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
MaryAnn Ugochi Ibekwe
69Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Udensi Road, Abakaliki, Nigeria
Nicolás Villagra
70Lab. Patogénesis Molecular y Antimicrobianos, Universidad Andres Bello, Av. República 239, Santiago, Chile
Stephen Wandro
60Department of Molecular Biology & Biochemistry, University of California, Irvine, 3315 McGaugh Hall, Irvine, CA, 92697, USA
Bryan White
28Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana Champaign, 607 S Mathews Ave, Urbana, IL, 61801, USA
Andy Whitely
47School of Earth and Environment, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
Katrine L. Whiteson
60Department of Molecular Biology & Biochemistry, University of California, Irvine, 3315 McGaugh Hall, Irvine, CA, 92697, USA
Cisca Wijmenga
15Department of Genetics, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
Maria M. Zambrano
65Molecular Genetics, Corporación Corpogen, Carrera 5 #66A-34, Bogotá, DC, 110231, Colombia
Henrike Zschach
71Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, Kongens Lyngby, 2800, Denmark
Bas E. Dutilh
10Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
72Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands
Abstract
Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered 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 to other environments. Here we investigate the origin, evolution, and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboratory, we obtained DNA sequences of crAssphage from over one-third of the world’s countries, and showed that its phylogeography is locally clustered within countries, cities, and individuals. We also found colinear crAssphage-like genomes in both Old-World and New-World primates, challenging genomic mosaicism and suggesting that the association of crAssphage with primates may be millions of years old. We conclude that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Posted January 26, 2019.
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Robert A. Edwards, Alejandro A. Vega, Holly M. Norman, Maria Ohaeri, Kyle Levi, Elizabeth A. Dinsdale, Ondrej Cinek, Ramy K. Aziz, Katelyn McNair, Jeremy J. Barr, Kyle Bibby, Stan JJ. Brouns, Adrian Cazares, Patrick A. de Jonge, Christelle Desnues, Samuel L. Díaz Muñoz, Peter C. Fineran, Alexander Kurilshikov, Rob Lavigne, Karla Mazankova, David T. McCarthy, Franklin L. Nobrega, Alejandro Reyes Muñoz, German Tapia, Nicole Trefault, Alexander V. Tyakht, Pablo Vinuesa, Jeroen Wagemans, Alexandra Zhernakova, Frank M. Aarestrup, Gunduz Ahmadov, Abeer Alassaf, Josefa Anton, Abigail Asangba, Emma Billings, Vito Adrian Cantu, Jane M. Carlton, Daniel Cazares, Gyu-Sung Cho, Tess Condeff, Pilar Cortés, Mike Cranfield, Daniel A. Cuevas, Rodrigo De la Iglesia, Przemyslaw Decewicz, Michael P. Doane, Nathaniel J. Dominy, Lukasz Dziewit, Bashir Mukhtar Elwasila, A. Murat Eren, Charles Franz, Jingyuan Fu, Cristina Garcia-Aljaro, Elodie Ghedin, Kristen M. Gulino, John M. Haggerty, Steven R. Head, Rene S. Hendriksen, Colin Hill, Heikki Hyöty, Elena N. Ilina, Mitchell T. Irwin, Thomas Jeffries, Juan Jofre Torroella, Randall E. Junge, Scott T. Kelley, Martin Kowalewski, Deepak Kumaresan, Steven Leigh, Eugenia S. Lisitsyna, Montserrat Llagostera, Julia M. Maritz, Linsey C. Marr, Angela McCann, Mohammadali Khan Mirzaei, Shahar Molshanski-Mor, Silvia Monteiro, Ben Moreira-Grez, Megan Morris, Lawrence Mugisha, Maite Muniesa, Horst Neve, Nam-phuong Nguyen, Olivia D. Nigro, Anders S. Nilsson, Taylor O’Connell, Rasha Odeh, Andrew Oliver, Mariana Piuri, Aaron J. Prussin II, Udi Qimron, Zhe-Xue Quan, Petra Rainetova, Adán Andrés Ramírez Rojas, Raul Raya, Gillian A.O. Rice, Alessandro Rossi, Ricardo Santos, John Shimashita, Elyse N. Stachler, Lars C. Stene, Ronan Strain, Rebecca Stumpf, Pedro J. Torres, Alan Twaddle, MaryAnn Ugochi Ibekwe, Nicolás Villagra, Stephen Wandro, Bryan White, Andy Whitely, Katrine L. Whiteson, Cisca Wijmenga, Maria M. Zambrano, Henrike Zschach, Bas E. Dutilh
bioRxiv 527796; doi: https://doi.org/10.1101/527796
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Robert A. Edwards, Alejandro A. Vega, Holly M. Norman, Maria Ohaeri, Kyle Levi, Elizabeth A. Dinsdale, Ondrej Cinek, Ramy K. Aziz, Katelyn McNair, Jeremy J. Barr, Kyle Bibby, Stan JJ. Brouns, Adrian Cazares, Patrick A. de Jonge, Christelle Desnues, Samuel L. Díaz Muñoz, Peter C. Fineran, Alexander Kurilshikov, Rob Lavigne, Karla Mazankova, David T. McCarthy, Franklin L. Nobrega, Alejandro Reyes Muñoz, German Tapia, Nicole Trefault, Alexander V. Tyakht, Pablo Vinuesa, Jeroen Wagemans, Alexandra Zhernakova, Frank M. Aarestrup, Gunduz Ahmadov, Abeer Alassaf, Josefa Anton, Abigail Asangba, Emma Billings, Vito Adrian Cantu, Jane M. Carlton, Daniel Cazares, Gyu-Sung Cho, Tess Condeff, Pilar Cortés, Mike Cranfield, Daniel A. Cuevas, Rodrigo De la Iglesia, Przemyslaw Decewicz, Michael P. Doane, Nathaniel J. Dominy, Lukasz Dziewit, Bashir Mukhtar Elwasila, A. Murat Eren, Charles Franz, Jingyuan Fu, Cristina Garcia-Aljaro, Elodie Ghedin, Kristen M. Gulino, John M. Haggerty, Steven R. Head, Rene S. Hendriksen, Colin Hill, Heikki Hyöty, Elena N. Ilina, Mitchell T. Irwin, Thomas Jeffries, Juan Jofre Torroella, Randall E. Junge, Scott T. Kelley, Martin Kowalewski, Deepak Kumaresan, Steven Leigh, Eugenia S. Lisitsyna, Montserrat Llagostera, Julia M. Maritz, Linsey C. Marr, Angela McCann, Mohammadali Khan Mirzaei, Shahar Molshanski-Mor, Silvia Monteiro, Ben Moreira-Grez, Megan Morris, Lawrence Mugisha, Maite Muniesa, Horst Neve, Nam-phuong Nguyen, Olivia D. Nigro, Anders S. Nilsson, Taylor O’Connell, Rasha Odeh, Andrew Oliver, Mariana Piuri, Aaron J. Prussin II, Udi Qimron, Zhe-Xue Quan, Petra Rainetova, Adán Andrés Ramírez Rojas, Raul Raya, Gillian A.O. Rice, Alessandro Rossi, Ricardo Santos, John Shimashita, Elyse N. Stachler, Lars C. Stene, Ronan Strain, Rebecca Stumpf, Pedro J. Torres, Alan Twaddle, MaryAnn Ugochi Ibekwe, Nicolás Villagra, Stephen Wandro, Bryan White, Andy Whitely, Katrine L. Whiteson, Cisca Wijmenga, Maria M. Zambrano, Henrike Zschach, Bas E. Dutilh
bioRxiv 527796; doi: https://doi.org/10.1101/527796
Subject Area
Subject Areas
- Biochemistry (9173)
- Bioengineering (6806)
- Bioinformatics (24064)
- Biophysics (12155)
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