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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. / Edwards, Robert A.; Vega, Alejandro A.; Norman, Holly M.; Ohaeri, Maria; Levi, Kyle; Dinsdale, Elizabeth A.; Cinek, Ondrej; Aziz, Ramy K.; McNair, Katelyn; Barr, Jeremy J.; Bibby, Kyle; Brouns, Stan J.J.; Cazares, Adrian; de Jonge, Patrick A.; Desnues, Christelle; Díaz Muñoz, Samuel L.; Fineran, Peter C.; Kurilshikov, Alexander; Lavigne, Rob; Mazankova, Karla; McCarthy, David T.; Nobrega, Franklin L.; Reyes Muñoz, Alejandro; Tapia, German; Trefault, Nicole; Tyakht, Alexander V.; Vinuesa, Pablo; Wagemans, Jeroen; Zhernakova, Alexandra; Aarestrup, Frank M.; Ahmadov, Gunduz; Alassaf, Abeer; Anton, Josefa; Asangba, Abigail; Billings, Emma K.; Cantu, Vito Adrian; Carlton, Jane M.; Cazares, Daniel; Cho, Gyu-Sung; Condeff, Tess; Cortés, Pilar; Cranfield, Mike; Cuevas, Daniel A.; De la Iglesia, Rodrigo; Decewicz, Przemyslaw; Doane, Michael P.; Dominy, Nathaniel J.; Dziewit, Lukasz; Elwasila, Bashir Mukhtar; Eren, A. Murat; Franz, Charles; Fu, Jingyuan; Garcia-Aljaro, Cristina; Ghedin, Elodie; Gulino, Kristen M.; Haggerty, John M.; Head, Steven R.; Hendriksen, Rene S.; Hill, Colin; Hyöty, Heikki; Ilina, Elena N.; Irwin, Mitchell T.; Jeffries, Thomas C.; Jofre, Juan; Junge, Randall E.; Kelley, Scott T.; Khan Mirzaei, Mohammadali; Kowalewski, Martin; Kumaresan, Deepak; Leigh, Steven R.; Lipson, David; Lisitsyna, Eugenia S.; Llagostera, Montserrat; Maritz, Julia M.; Marr, Linsey C.; McCann, Angela; Molshanski-Mor, Shahar; Monteiro, Silvia; Moreira-Grez, Benjamin; Morris, Megan; Mugisha, Lawrence; Muniesa, Maite; Neve, Horst; Nguyen, Nam phuong; Nigro, Olivia D.; Nilsson, Anders S.; O’Connell, Taylor; Odeh, Rasha; Oliver, Andrew; Piuri, Mariana; Prussin, Aaron J.; Qimron, Udi; Quan, Zhe Xue; Rainetova, Petra; Ramírez-Rojas, Adán; Raya, Raul; Reasor, Kim; Rice, Gillian A.O.; Rossi, Alessandro; Santos, Ricardo; Shimashita, John; Stachler, Elyse N.; Stene, Lars C.; Strain, Ronan; Stumpf, Rebecca; Torres, Pedro J.; Twaddle, Alan; Ugochi Ibekwe, Mary Ann; Villagra, Nicolás; Wandro, Stephen; White, Bryan; Whiteley, Andy; Whiteson, Katrine L.; Wijmenga, Cisca; Zambrano, Maria M.; Zschach, Henrike; Dutilh, Bas E.
I:
Nature Microbiology, Bind 4, 2019, s. 1727-1736.
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Harvard
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, EK, 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, TC, Jofre, J, Junge, RE, Kelley, ST, Khan Mirzaei, M, Kowalewski, M, Kumaresan, D, Leigh, SR, Lipson, D, Lisitsyna, ES, Llagostera, M, Maritz, JM, Marr, LC, McCann, A, Molshanski-Mor, S, Monteiro, S, Moreira-Grez, B, Morris, M, Mugisha, L, Muniesa, M, Neve, H, Nguyen, NP, Nigro, OD, Nilsson, AS, O’Connell, T, Odeh, R, Oliver, A, Piuri, M, Prussin, AJ, Qimron, U, Quan, ZX, Rainetova, P, Ramírez-Rojas, A, Raya, R, Reasor, K, Rice, GAO, Rossi, A, Santos, R, Shimashita, J, Stachler, EN, Stene, LC, Strain, R, Stumpf, R, Torres, PJ, Twaddle, A, Ugochi Ibekwe, MA, Villagra, N, Wandro, S, White, B, Whiteley, A, Whiteson, KL, Wijmenga, C, Zambrano, MM
, Zschach, H & Dutilh, BE 2019, '
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage',
Nature Microbiology, bind 4, s. 1727-1736.
https://doi.org/10.1038/s41564-019-0494-6APA
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., ... Dutilh, B. E. (2019).
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.
Nature Microbiology,
4, 1727-1736.
https://doi.org/10.1038/s41564-019-0494-6Vancouver
Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA o.a.
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.
Nature Microbiology. 2019;4:1727-1736.
https://doi.org/10.1038/s41564-019-0494-6Author
Edwards, Robert A. ; Vega, Alejandro A. ; Norman, Holly M. ; Ohaeri, Maria ; Levi, Kyle ; Dinsdale, Elizabeth A. ; Cinek, Ondrej ; Aziz, Ramy K. ; McNair, Katelyn ; Barr, Jeremy J. ; Bibby, Kyle ; Brouns, Stan J.J. ; Cazares, Adrian ; de Jonge, Patrick A. ; Desnues, Christelle ; Díaz Muñoz, Samuel L. ; Fineran, Peter C. ; Kurilshikov, Alexander ; Lavigne, Rob ; Mazankova, Karla ; McCarthy, David T. ; Nobrega, Franklin L. ; Reyes Muñoz, Alejandro ; Tapia, German ; Trefault, Nicole ; Tyakht, Alexander V. ; Vinuesa, Pablo ; Wagemans, Jeroen ; Zhernakova, Alexandra ; Aarestrup, Frank M. ; Ahmadov, Gunduz ; Alassaf, Abeer ; Anton, Josefa ; Asangba, Abigail ; Billings, Emma K. ; Cantu, Vito Adrian ; Carlton, Jane M. ; Cazares, Daniel ; Cho, Gyu-Sung ; Condeff, Tess ; Cortés, Pilar ; Cranfield, Mike ; Cuevas, Daniel A. ; De la Iglesia, Rodrigo ; Decewicz, Przemyslaw ; Doane, Michael P. ; Dominy, Nathaniel J. ; Dziewit, Lukasz ; Elwasila, Bashir Mukhtar ; Eren, A. Murat ; Franz, Charles ; Fu, Jingyuan ; Garcia-Aljaro, Cristina ; Ghedin, Elodie ; Gulino, Kristen M. ; Haggerty, John M. ; Head, Steven R. ; Hendriksen, Rene S. ; Hill, Colin ; Hyöty, Heikki ; Ilina, Elena N. ; Irwin, Mitchell T. ; Jeffries, Thomas C. ; Jofre, Juan ; Junge, Randall E. ; Kelley, Scott T. ; Khan Mirzaei, Mohammadali ; Kowalewski, Martin ; Kumaresan, Deepak ; Leigh, Steven R. ; Lipson, David ; Lisitsyna, Eugenia S. ; Llagostera, Montserrat ; Maritz, Julia M. ; Marr, Linsey C. ; McCann, Angela ; Molshanski-Mor, Shahar ; Monteiro, Silvia ; Moreira-Grez, Benjamin ; Morris, Megan ; Mugisha, Lawrence ; Muniesa, Maite ; Neve, Horst ; Nguyen, Nam phuong ; Nigro, Olivia D. ; Nilsson, Anders S. ; O’Connell, Taylor ; Odeh, Rasha ; Oliver, Andrew ; Piuri, Mariana ; Prussin, Aaron J. ; Qimron, Udi ; Quan, Zhe Xue ; Rainetova, Petra ; Ramírez-Rojas, Adán ; Raya, Raul ; Reasor, Kim ; Rice, Gillian A.O. ; Rossi, Alessandro ; Santos, Ricardo ; Shimashita, John ; Stachler, Elyse N. ; Stene, Lars C. ; Strain, Ronan ; Stumpf, Rebecca ; Torres, Pedro J. ; Twaddle, Alan ; Ugochi Ibekwe, Mary Ann ; Villagra, Nicolás ; Wandro, Stephen ; White, Bryan ; Whiteley, Andy ; Whiteson, Katrine L. ; Wijmenga, Cisca ; Zambrano, Maria M. ; Zschach, Henrike ; Dutilh, Bas E. / Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. I: Nature Microbiology. 2019 ; Bind 4. s. 1727-1736.
Bibtex
@article{f8ec3d4a348c4f9fa7f50addb839c681,
title = "Global phylogeography and ancient evolution of the widespread human gut virus crAssphage",
abstract = "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{\textquoteright}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.",
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 Billings, {Emma K.} 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 Jeffries, {Thomas C.} and Juan Jofre and Junge, {Randall E.} and Kelley, {Scott T.} and {Khan Mirzaei}, Mohammadali and Martin Kowalewski and Deepak Kumaresan and Leigh, {Steven R.} and David Lipson and Lisitsyna, {Eugenia S.} and Montserrat Llagostera and Maritz, {Julia M.} and Marr, {Linsey C.} and Angela McCann and Shahar Molshanski-Mor and Silvia Monteiro and Benjamin Moreira-Grez and Megan Morris and Lawrence Mugisha and Maite Muniesa and Horst Neve and Nguyen, {Nam phuong} and Nigro, {Olivia D.} and Nilsson, {Anders S.} and Taylor O{\textquoteright}Connell and Rasha Odeh and Andrew Oliver and Mariana Piuri and Prussin, {Aaron J.} and Udi Qimron and Quan, {Zhe Xue} and Petra Rainetova and Ad{\'a}n Ram{\'i}rez-Rojas and Raul Raya and Kim Reasor and Rice, {Gillian A.O.} and Alessandro Rossi and Ricardo Santos and John Shimashita and Stachler, {Elyse N.} and Stene, {Lars C.} and Ronan Strain and Rebecca Stumpf and Torres, {Pedro J.} and Alan Twaddle and {Ugochi Ibekwe}, {Mary Ann} and Nicol{\'a}s Villagra and Stephen Wandro and Bryan White and Andy Whiteley and Whiteson, {Katrine L.} and Cisca Wijmenga and Zambrano, {Maria M.} and Henrike Zschach and Dutilh, {Bas E.}",
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",
}
RIS
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 K.
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 C.
AU - Jofre, Juan
AU - Junge, Randall E.
AU - Kelley, Scott T.
AU - Khan Mirzaei, Mohammadali
AU - Kowalewski, Martin
AU - Kumaresan, Deepak
AU - Leigh, Steven R.
AU - Lipson, David
AU - Lisitsyna, Eugenia S.
AU - Llagostera, Montserrat
AU - Maritz, Julia M.
AU - Marr, Linsey C.
AU - McCann, Angela
AU - Molshanski-Mor, Shahar
AU - Monteiro, Silvia
AU - Moreira-Grez, Benjamin
AU - Morris, Megan
AU - Mugisha, Lawrence
AU - Muniesa, Maite
AU - Neve, Horst
AU - Nguyen, Nam phuong
AU - Nigro, Olivia D.
AU - Nilsson, Anders S.
AU - O’Connell, Taylor
AU - Odeh, Rasha
AU - Oliver, Andrew
AU - Piuri, Mariana
AU - Prussin, Aaron J.
AU - Qimron, Udi
AU - Quan, Zhe Xue
AU - Rainetova, Petra
AU - Ramírez-Rojas, Adán
AU - Raya, Raul
AU - Reasor, Kim
AU - Rice, Gillian A.O.
AU - Rossi, Alessandro
AU - Santos, Ricardo
AU - Shimashita, John
AU - Stachler, Elyse N.
AU - Stene, Lars C.
AU - Strain, Ronan
AU - Stumpf, Rebecca
AU - Torres, Pedro J.
AU - Twaddle, Alan
AU - Ugochi Ibekwe, Mary Ann
AU - Villagra, Nicolás
AU - Wandro, Stephen
AU - White, Bryan
AU - Whiteley, Andy
AU - Whiteson, Katrine L.
AU - Wijmenga, Cisca
AU - Zambrano, Maria M.
AU - Zschach, Henrike
AU - Dutilh, Bas E.
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
U2 - 10.1038/s41564-019-0494-6
DO - 10.1038/s41564-019-0494-6
M3 - Journal article
C2 - 31285584
AN - SCOPUS:85068899860
VL - 4
SP - 1727
EP - 1736
JO - Nature Microbiology
JF - Nature Microbiology
SN - 2058-5276
ER -
