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 J. J. 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; null et al

doi:10.1038/s41564-019-0494-6

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 J. J. Brouns, Adrian Cazares, Patrick A. de Jonge, Christelle Desnues, Samuel L. Díaz Muñoz, Peter C. Fineran, Alexander Kurilshikov, Rob Lavigne, Karla MazankovaDavid 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, et al

Western Sydney University

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	1727-1736
Number of pages	46
Journal	Nature Microbiology
Volume	4
Issue number	10
DOIs	https://doi.org/10.1038/s41564-019-0494-6
Publication status	Published - 2019

Keywords

genomes
nucleotide sequence
phylogeography
viruses

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10.1038/s41564-019-0494-6

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Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K., Barr, J. J., Bibby, K., Brouns, S. J. J., Cazares, A., de Jonge, P. A., Desnues, C., Díaz Muñoz, S. L., Fineran, P. C., Kurilshikov, A., Lavigne, R., ... et al (2019). Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nature Microbiology, 4(10), 1727-1736. https://doi.org/10.1038/s41564-019-0494-6

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title = "Global phylogeography and ancient evolution of the widespread human gut virus crAssphage",

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.",

keywords = "genomes, nucleotide sequence, phylogeography, viruses",

author = "Edwards, {Robert A.} and Vega, {Alejandro A.} and Norman, {Holly M.} and Maria Ohaeri and Kyle Levi and Dinsdale, {Elizabeth A.} and Ondrej Cinek and Aziz, {Ramy K.} and Katelyn McNair and Barr, {Jeremy J.} and Kyle Bibby and Brouns, {Stan J. J.} and Adrian Cazares and {de Jonge}, {Patrick A.} and Christelle Desnues and {D{\'i}az Mu{\~n}oz}, {Samuel L.} and Fineran, {Peter C.} and Alexander Kurilshikov and Rob Lavigne and Karla Mazankova and McCarthy, {David T.} and Nobrega, {Franklin L.} and {Reyes Mu{\~n}oz}, Alejandro and German Tapia and Nicole Trefault and Tyakht, {Alexander V.} and Pablo Vinuesa and Jeroen Wagemans and Alexandra Zhernakova and Aarestrup, {Frank M.} and Gunduz Ahmadov and Abeer Alassaf and Josefa Anton and Abigail Asangba and Emma Billings and Cantu, {Vito Adrian} and Carlton, {Jane M.} and Daniel Cazares and Gyu-Sung Cho and Tess Condeff and Pilar Cort{\'e}s and Mike Cranfield and Cuevas, {Daniel A..} and {De la Iglesia}, Rodrigo and Przemyslaw Decewicz and Doane, {Michael P.} and Dominy, {Nathaniel J.} and Lukasz Dziewit and Elwasila, {Bashir Mukhtar} and Eren, {A. Murat} and Charles Franz and Jingyuan Fu and Cristina Garcia-Aljaro and Elodie Ghedin and Gulino, {Kristen M..} and Haggerty, {John M.} and Head, {Steven R.} and Hendriksen, {Rene S.} and Colin Hill and Heikki Hy{\"o}ty and Ilina, {Elena N.} and Irwin, {Mitchell T.} and Thomas Jeffries and {et al}",

year = "2019",

doi = "10.1038/s41564-019-0494-6",

language = "English",

volume = "4",

pages = "1727--1736",

journal = "Nature Microbiology",

issn = "2058-5276",

publisher = "Nature Publishing Group",

number = "10",

}

Edwards, RA, Vega, AA, Norman, HM, Ohaeri, M, Levi, K, Dinsdale, EA, Cinek, O, Aziz, RK, McNair, K, Barr, JJ, Bibby, K, Brouns, SJJ, Cazares, A, de Jonge, PA, Desnues, C, Díaz Muñoz, SL, Fineran, PC, Kurilshikov, A, Lavigne, R, Mazankova, K, McCarthy, DT, Nobrega, FL, Reyes Muñoz, A, Tapia, G, Trefault, N, Tyakht, AV, Vinuesa, P, Wagemans, J, Zhernakova, A, Aarestrup, FM, Ahmadov, G, Alassaf, A, Anton, J, Asangba, A, Billings, E, Cantu, VA, Carlton, JM, Cazares, D, Cho, G-S, Condeff, T, Cortés, P, Cranfield, M, Cuevas, DA, De la Iglesia, R, Decewicz, P, Doane, MP, Dominy, NJ, Dziewit, L, Elwasila, BM, Eren, AM, Franz, C, Fu, J, Garcia-Aljaro, C, Ghedin, E, Gulino, KM, Haggerty, JM, Head, SR, Hendriksen, RS, Hill, C, Hyöty, H, Ilina, EN, Irwin, MT, Jeffries, T & et al 2019, 'Global phylogeography and ancient evolution of the widespread human gut virus crAssphage', Nature Microbiology, vol. 4, no. 10, pp. 1727-1736. https://doi.org/10.1038/s41564-019-0494-6

TY - JOUR

T1 - Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

AU - Edwards, Robert A.

AU - Vega, Alejandro A.

AU - Norman, Holly M.

AU - Ohaeri, Maria

AU - Levi, Kyle

AU - Dinsdale, Elizabeth A.

AU - Cinek, Ondrej

AU - Aziz, Ramy K.

AU - McNair, Katelyn

AU - Barr, Jeremy J.

AU - Bibby, Kyle

AU - Brouns, Stan J. J.

AU - Cazares, Adrian

AU - de Jonge, Patrick A.

AU - Desnues, Christelle

AU - Díaz Muñoz, Samuel L.

AU - Fineran, Peter C.

AU - Kurilshikov, Alexander

AU - Lavigne, Rob

AU - Mazankova, Karla

AU - McCarthy, David T.

AU - Nobrega, Franklin L.

AU - Reyes Muñoz, Alejandro

AU - Tapia, German

AU - Trefault, Nicole

AU - Tyakht, Alexander V.

AU - Vinuesa, Pablo

AU - Wagemans, Jeroen

AU - Zhernakova, Alexandra

AU - Aarestrup, Frank M.

AU - Ahmadov, Gunduz

AU - Alassaf, Abeer

AU - Anton, Josefa

AU - Asangba, Abigail

AU - Billings, Emma

AU - Cantu, Vito Adrian

AU - Carlton, Jane M.

AU - Cazares, Daniel

AU - Cho, Gyu-Sung

AU - Condeff, Tess

AU - Cortés, Pilar

AU - Cranfield, Mike

AU - Cuevas, Daniel A..

AU - De la Iglesia, Rodrigo

AU - Decewicz, Przemyslaw

AU - Doane, Michael P.

AU - Dominy, Nathaniel J.

AU - Dziewit, Lukasz

AU - Elwasila, Bashir Mukhtar

AU - Eren, A. Murat

AU - Franz, Charles

AU - Fu, Jingyuan

AU - Garcia-Aljaro, Cristina

AU - Ghedin, Elodie

AU - Gulino, Kristen M..

AU - Haggerty, John M.

AU - Head, Steven R.

AU - Hendriksen, Rene S.

AU - Hill, Colin

AU - Hyöty, Heikki

AU - Ilina, Elena N.

AU - Irwin, Mitchell T.

AU - Jeffries, Thomas

AU - et al, null

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - genomes

KW - nucleotide sequence

KW - phylogeography

KW - viruses

UR - http://handle.westernsydney.edu.au:8081/1959.7/uws:52620

U2 - 10.1038/s41564-019-0494-6

DO - 10.1038/s41564-019-0494-6

M3 - Article

SN - 2058-5276

VL - 4

SP - 1727

EP - 1736

JO - Nature Microbiology

JF - Nature Microbiology

IS - 10

ER -

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

Abstract

Keywords

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