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12 results on '"Dziewit, Lukasz"'

1. Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle

Author

Miłobedzka, Aleksandra (author), Ferreira, Catarina (author), Vaz-Moreira, Ivone (author), Calderon Franco, D. (author), Gorecki, Adrian (author), Purkrtova, Sabina (author), Bartacek, Jan (author), Dziewit, Lukasz (author), Weissbrodt, D.G. (author), Miłobedzka, Aleksandra (author), Ferreira, Catarina (author), Vaz-Moreira, Ivone (author), Calderon Franco, D. (author), Gorecki, Adrian (author), Purkrtova, Sabina (author), Bartacek, Jan (author), Dziewit, Lukasz (author), and Weissbrodt, D.G. (author)

Abstract

Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion., BT/Environmental Biotechnology

Published
2022
Full Text
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2. Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle

Author

Miłobedzka, Aleksandra (author), Ferreira, Catarina (author), Vaz-Moreira, Ivone (author), Calderon Franco, D. (author), Gorecki, Adrian (author), Purkrtova, Sabina (author), Bartacek, Jan (author), Dziewit, Lukasz (author), Weissbrodt, D.G. (author), Miłobedzka, Aleksandra (author), Ferreira, Catarina (author), Vaz-Moreira, Ivone (author), Calderon Franco, D. (author), Gorecki, Adrian (author), Purkrtova, Sabina (author), Bartacek, Jan (author), Dziewit, Lukasz (author), and Weissbrodt, D.G. (author)

Abstract

Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion., BT/Environmental Biotechnology

Published
2022
Full Text
View/download PDF

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

Author

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 Ii, 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, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, Dutilh, Bas E, 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 Ii, 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, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, and Dutilh, Bas E

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'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.

Published
2019

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

Author

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, Diaz Munoz, Samuel L., Fineran, Peter C., Kurilshikov, Alexander, Lavigne, Rob, Mazankova, Karla, McCarthy, David T., Nobrega, Franklin L., Reyes Munoz, Alejandro, Tapia, German, Trefault, Nicole, Tyakht, Alexander, 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, Cortes, Pilar, Cranfield, Mike, Cuevas, Daniel A., De la Iglesia, Rodrigo, Decewicz, Przemyslaw, Doane, Michael P., Dominy, Nathaniel J., Dziewit, Lukasz, Elwasila, Bashir Mukhtar, Murat Eren, A., Franz, Charles, Fu, Jingyuan, Garcia-Aljaro, Cristina, Ghedin, Elodie, Gulino, Kristen M., Haggerty, John M., Head, Steven R., Hendriksen, Rene S., Hill, Colin, Hyoty, Heikki, Ilina, Elena N., Irwin, Mitchell T., Jeffries, Thomas C., Jofre, Juan, Junge, Randall E., Kelley, Scott T., Mirzaei, Mohammadali Khan, 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, Nam-phuong, Nguyen, 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, Ramirez-Rojas, Adan, 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, Ibekwe, MaryAnn Ugochi, Villagra, Nicolas, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, Dutilh, Bas E., 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, Diaz Munoz, Samuel L., Fineran, Peter C., Kurilshikov, Alexander, Lavigne, Rob, Mazankova, Karla, McCarthy, David T., Nobrega, Franklin L., Reyes Munoz, Alejandro, Tapia, German, Trefault, Nicole, Tyakht, Alexander, 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, Cortes, Pilar, Cranfield, Mike, Cuevas, Daniel A., De la Iglesia, Rodrigo, Decewicz, Przemyslaw, Doane, Michael P., Dominy, Nathaniel J., Dziewit, Lukasz, Elwasila, Bashir Mukhtar, Murat Eren, A., Franz, Charles, Fu, Jingyuan, Garcia-Aljaro, Cristina, Ghedin, Elodie, Gulino, Kristen M., Haggerty, John M., Head, Steven R., Hendriksen, Rene S., Hill, Colin, Hyoty, Heikki, Ilina, Elena N., Irwin, Mitchell T., Jeffries, Thomas C., Jofre, Juan, Junge, Randall E., Kelley, Scott T., Mirzaei, Mohammadali Khan, 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, Nam-phuong, Nguyen, 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, Ramirez-Rojas, Adan, 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, Ibekwe, MaryAnn Ugochi, Villagra, Nicolas, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, and Dutilh, Bas E.

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'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.

Published
2019
Full Text
View/download PDF

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

Author

Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, 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, Shimashita, John, Stachler, Elyse N., Stene, Lars C., Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J., Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, Brouns, Stan J.J., White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, Dutilh, Bas E., Cazares, Adrian, Jonge, Patrick A. de, 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., Mirzaei, Mohammadali Khan, 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 II, Aaron J., Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A.O., Rossi, Alessandro, Santos, Ricardo, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, 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, Shimashita, John, Stachler, Elyse N., Stene, Lars C., Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J., Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, Brouns, Stan J.J., White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, Dutilh, Bas E., Cazares, Adrian, Jonge, Patrick A. de, 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., Mirzaei, Mohammadali Khan, 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 II, Aaron J., Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A.O., Rossi, Alessandro, and Santos, Ricardo

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’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.

Published
2019

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

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, 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 Ii, 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, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, Dutilh, Bas E, Theoretical Biology and Bioinformatics, Sub Bioinformatics, 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 Ii, 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, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, and Dutilh, Bas E

Published
2019

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

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, 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 Ii, 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, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, Dutilh, Bas E, Theoretical Biology and Bioinformatics, Sub Bioinformatics, 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 Ii, 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, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, and Dutilh, Bas E

Published
2019

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

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, 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 Ii, 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, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, Dutilh, Bas E, Theoretical Biology and Bioinformatics, Sub Bioinformatics, 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 Ii, 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, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, and Dutilh, Bas E

Published
2019

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

Author

Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, 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, Shimashita, John, Stachler, Elyse N., Stene, Lars C., Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J., Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, Brouns, Stan J.J., White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, Dutilh, Bas E., Cazares, Adrian, Jonge, Patrick A. de, 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., Mirzaei, Mohammadali Khan, 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 II, Aaron J., Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A.O., Rossi, Alessandro, Santos, Ricardo, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, 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, Shimashita, John, Stachler, Elyse N., Stene, Lars C., Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J., Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, Brouns, Stan J.J., White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, Dutilh, Bas E., Cazares, Adrian, Jonge, Patrick A. de, 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., Mirzaei, Mohammadali Khan, 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 II, Aaron J., Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A.O., Rossi, Alessandro, and Santos, Ricardo

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’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.

Published
2019

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

Author

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., 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, and Dutilh, Bas E.

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’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.

Published
2019

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

Author

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, Møller Aarestrup, Frank, 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., 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, Møller Aarestrup, Frank, 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, and Dutilh, Bas E.

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’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.

Published
2019

12. Nanostructured silver-gold bimetallic SERS substrates for selective identification of bacteria in human blood

Author

Arumugam, Sivanesan, Witkowska, Evelin, Adamkiewicz, Witold, Dziewit, Lukasz, Kaminska, Agnieszka, Waluk, Jacek, Arumugam, Sivanesan, Witkowska, Evelin, Adamkiewicz, Witold, Dziewit, Lukasz, Kaminska, Agnieszka, and Waluk, Jacek

Abstract

Surface-enhanced Raman spectroscopy (SERS) is a potentially important tool in the rapid and accurate detection of pathogenic bacteria in biological fluids. However, for diagnostic application of this technique, it is necessary to develop a highly sensitive, stable, biocompatible and reproducible SERS-active substrate. In this work, we have developed a silver–gold bimetallic SERS surface by a simple potentiostatic electrodeposition of a thin gold layer on an electrochemically roughened nanoscopic silver substrate. The resultant substrate was very stable under atmospheric conditions and exhibited the strong Raman enhancement with the high reproducibility of the recorded SERS spectra of bacteria (E. coli, S. enterica, S. epidermidis, and B. megaterium). The coating of the antibiotic over the SERS substrate selectively captured bacteria from blood samples and also increased the Raman signal in contrast to the bare surface. Finally, we have utilized the antibiotic-coated hybrid surface to selectively identify different pathogenic bacteria, namely E. coli, S. enterica and S. epidermidis from blood samples.

Published
2014

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