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296 results on '"Dziewit, Lukasz"'

7. Landscape of the metaplasmidome of deep-sea hydrothermal vents located at Arctic Mid-Ocean Ridges in the Norwegian–Greenland Sea: ecological insights from comparative analysis of plasmid identification tools.

Author

Ciuchcinski, Karol, Stokke, Runar, Steen, Ida Helene, and Dziewit, Lukasz

Subjects
HYDROTHERMAL vents, MID-ocean ridges, PLURALITY voting, MICROBIAL communities, PLASMIDS
Abstract

Plasmids are one of the key drivers of microbial adaptation and evolution. However, their diversity and role in adaptation, especially in extreme environments, remains largely unexplored. In this study, we aimed to identify, characterize, and compare plasmid sequences originating from samples collected from deep-sea hydrothermal vents located in Arctic Mid-Ocean Ridges. To achieve this, we employed, and benchmarked three recently developed plasmid identification tools—PlasX, GeNomad, and PLASMe—on metagenomic data from this unique ecosystem. To date, this is the first direct comparison of these computational methods in the context of data from extreme environments. Upon recovery of plasmid contigs, we performed a multiapproach analysis, focusing on identifying taxonomic and functional biases within datasets originating from each tool. Next, we implemented a majority voting system to identify high-confidence plasmid contigs, enhancing the reliability of our findings. By analysing the consensus plasmid sequences, we gained insights into their diversity, ecological roles, and adaptive significance. Within the high-confidence sequences, we identified a high abundance of Pseudomonadota and Campylobacterota , as well as multiple toxin–antitoxin systems. Our findings ensure a deeper understanding of how plasmids contribute to shaping microbial communities living under extreme conditions of hydrothermal vents, potentially uncovering novel adaptive mechanisms. [ABSTRACT FROM AUTHOR]

Published
2024
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14. 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, and Dutilh, Bas E.

Published
2019
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18. Diversity of antibiotic resistance gene variants at subsequent stages of the wastewater treatment process revealed by a metagenomic analysis of PCR amplicons.

Author

Gorecki, Adrian, Ostapczuk, Piotr, and Dziewit, Lukasz

Subjects
DRUG resistance in bacteria, GENETIC variation, WASTEWATER treatment, SEWAGE disposal plants, EMERGING contaminants, ANTIBIOTIC residues
Abstract

Wastewater treatment plants have been recognised as point sources of various antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG) which are considered recently emerging biological contaminants. So far, culture-based and molecular-based methods have been successfully applied to monitor antimicrobial resistance (AMR) in WWTPs. However, the methods applied do not permit the comprehensive identification of the true diversity of ARGs. In this study we applied next-generation sequencing for a metagenomic analysis of PCR amplicons of ARGs from the subsequent stages of the analysed WWTP. The presence of 14 genes conferring resistance to different antibiotic families was screened by PCR. In the next step, three genes were selected for detailed analysis of changes of the profile of ARG variants along the process. A relative abundance of 79 variants was analysed. The highest diversity was revealed in the ermF gene, with 52 variants. The relative abundance of some variants changed along the purification process, and some ARG variants might be present in novel hosts for which they were currently unassigned. Additionally, we identified a pool of novel ARG variants present in the studied WWTP. Overall, the results obtained indicated that the applied method is sufficient for analysing ARG variant diversity. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Phenotypic plasticity of Escherichia coli upon exposure to physical stress induced by ZnO nanorods

Author

Matuła, Kinga, Richter, Łukasz, Janczuk-Richter, Marta, Nogala, Wojciech, Grzeszkowiak, Mikołaj, Peplińska, Barbara, Jurga, Stefan, Wyroba, Elżbieta, Suski, Szymon, Bilski, Henryk, Silesian, Adrian, Bluyssen, Hans A. R., Derebecka, Natalia, Wesoły, Joanna, Łoś, Joanna M., Łoś, Marcin, Decewicz, Przemyslaw, Dziewit, Lukasz, Paczesny, Jan, and Hołyst, Robert

Published
2019
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26. 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
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37. Structure and functions of a multireplicon genome of Antarctic Psychrobactersp. ANT_H3: characterization of the genetic modules suitable for the construction of the plasmid-vectors for cold-active bacteria

Author

Decewicz, Przemyslaw, Romaniuk, Krzysztof, Gorecki, Adrian, Radlinska, Monika, Dabrowska, Maria, Wyszynska, Agnieszka, and Dziewit, Lukasz

Abstract

Among Psychrobacterspp., there are several multireplicon strains, carrying more than two plasmids. Psychrobactersp. ANT_H3 carries as many as 11 extrachromosomal replicons, which is the highest number in Psychrobacterspp. Plasmids of this strain were subjected to detailed genomic analysis, which enables an insight into the structure and functioning of this multireplicon genome. The replication and conjugal transfer modules of ANT_H3 plasmids were analyzed functionally to discover their potential for being used as building blocks for the construction of novel plasmid-vectors for cold-active bacteria. It was shown that two plasmids have a narrow host range as they were not able to replicate in species other than Psychrobacter, while remaining plasmids had a wider host range and were functional in various Alpha- and Gammaproteobacteria. Moreover, it was confirmed that mobilization modules of seven plasmids were functional, i.e., could be mobilized for conjugal transfer by the RK2 conjugation system. Auxiliary genes were also distinguished in ANT_H3 plasmids, including these encoding putative DNA-protecting protein DprA, multidrug efflux SMR transporter of EmrE family, glycine cleavage system T protein, MscS small-conductance mechanosensitive channel protein, and two type II restriction-modification systems. Finally, all genome-retrieved plasmids of Psychrobacterspp. were subjected to complex genome- and proteome-based comparative analyses showing that Antarctic replicons are significantly different from plasmids from other locations.

Published
2023
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38. Transposable modules generated by a single copy of insertion sequence ISPme1 and their influence on structure and evolution of natural plasmids of Paracoccus methylutens DM12

Author

Bartosik, Dariusz, Putyrski, Mateusz, Dziewit, Lukasz, Malewska, Edyta, Szymanik, Michal, Jagiello, Ewa, Lukasik, Jacek, and Baj, Jadwiga

Subjects
Plasmids -- Research, Gram-negative bacteria -- Genetic aspects, Gram-negative bacteria -- Physiological aspects, Biological sciences
Abstract

We demonstrated that a single copy of insertion sequence ISPmel can mobilize adjacent segments of genomic DNA of Paracoccus methylutens DM12, which leads to the generation of diverse transposable elements of various size and DNA contents. All elements (named transposable modules [TMos]) contain ISPmel (placed at the 5' ends of the elements) and have variable 3'-end regions of between 0.5 and 5 kb. ISPmel was shown to encode an outwardly oriented promoter, which may activate the transcription of genes transposed within TMos in evolutionarily distinct hosts. TMos may therefore be considered to be natural systems enabling gene capture, expression, and spread. However, unless these elements have been inserted into a highly conserved genetic context to enable a precise definition of their termini, it is extremely difficult or even impossible to identify them in bacterial genomes by in silico sequence analysis. We showed that TMos are present in the chromosome and plasmids of strain DM12. Sequence analysis of plasmid pMTH1 (32 kb) revealed that four TMos, previously identified with a trap vector, pMEC1, comprise 87% of its genome. Repeated TMos within pMTH1 may stimulate other structural rearrangements resulting from homologous recombination between long repeat sequences. This illustrates that TMos may play a significant role in shaping the structure of natural plasmids, which consequently may have a great impact on the evolution of plasmid genomes.

Published
2008

39. The SXT conjugative element and linear prophage N15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the Paracoccus aminophilus plasmid pAMI2

Author

Dziewit, Lukasz, Jazurek, Magdalena, Drewniak, Lukasz, Baj, Jadwiga, and Bartosik, Dariusz

Subjects
Bacteriophages -- Research, Bacterial genetics -- Research, Bacterial genetics -- Identification and classification, Microbial toxins -- Research, Biological sciences
Abstract

A group of proteic toxin-antitoxin (TA) cassettes whose representatives are widely distributed among bacterial genomes has been identified. These cassettes occur in chromosomes, plasmids, bacteriophages, and noncomposite transposons, as well as in the SXT conjugative element of Vibrio cholerae. The following four homologous loci were subjected to detailed comparative studies: (i) tad-ata from plasmid pAMI2 of Paracoccus aminophilus (the prototype of this group), (ii) gp49-gp48 from the linear bacteriophage N15 of Escherichia coli, (iii) s045-s044 from SXT, and (iv) Z3230-Z3231 from the genomic island of enterohemorrhagic Escherichia coli O157:H7 strain EDL933. Functional analysis revealed that all but one of these loci (Z3230-Z3231) are able to stabilize heterologous replicons, although the host ranges varied. The TA cassettes analyzed have the following common features: (i) the toxins are encoded by the first gene of each operon; (ii) the antitoxins contain a predicted helix-turn-helix motif of the XRE family; and (iii) the cassettes have two promoters that are different strengths, one which is located upstream of the toxin gene and one which is located upstream of the antitoxin gene. All four toxins tested are functional in E. coli; overexpression of the toxins (in the absence of antitoxin) results in a bacteriostatic effect manifested by elongation of bacterial cells and growth arrest. The toxins have various effects on cell viability, which suggests that they may recognize different intracellular targets. Preliminary data suggest that different cellular proteases are involved in degradation of antitoxins encoded by the loci analyzed.

Published
2007

40. Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland

Author

Dyda, Magdalena, primary, Laudy, Agnieszka, additional, Decewicz, Przemyslaw, additional, Romaniuk, Krzysztof, additional, Ciezkowska, Martyna, additional, Szajewska, Anna, additional, Solecka, Danuta, additional, Dziewit, Lukasz, additional, Drewniak, Lukasz, additional, and Skłodowska, Aleksandra, additional

Published
2021
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49. 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

50. 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

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