Phages with a broad host range are common across ecosystems
Resumen:
Phages are diverse and abundant within microbial communities, where they play major roles in their evolution and adaptation. Phage replication, and multiplication, is generally thought to be restricted within a single or narrow host range. Here we use published and newly generated proximity-ligation-based metagenomic Hi-C (metaHiC) data from various environments to explore virus–host interactions. We reconstructed 4,975 microbial and 6,572 phage genomes of medium quality or higher. MetaHiC yielded a contact network between genomes and enabled assignment of approximately half of phage genomes to their hosts, revealing that a substantial proportion of these phages interact with multiple species in environments as diverse as the oceanic water column or the human gut. This observation challenges the traditional view of a narrow host spectrum of phages by unveiling that multihost associations are common across ecosystems, with implications for how they might impact ecology and evolution and phage therapy approaches.
| 2025 | |
| ANII: FSGSK_1_2019_1_15973 | |
|
Environmental microbiology Software Virology |
|
| Inglés | |
| Universidad de la República | |
| COLIBRI | |
| https://hdl.handle.net/20.500.12008/54527 | |
| Acceso abierto | |
| Licencia Creative Commons Atribución (CC - By 4.0) |
| _version_ | 1872864704419856384 |
|---|---|
| author | Bignaud, Amaury |
| author2 | Conti, Devon Thierry, Agnès Serizay, Jacques Labadie, Karine Poulain, Julie Cheny, Olivia Colón-González, Maritrini Debarbieux, Laurent Guerrero-Osornio, Marianna Helaine, Sophie Hill, Peter Le Tinier, Gwenaelle Millot, Gael A. Morales, Lucía Parada, Andrés Riera Faraone, Nadia Iraola, Gregorio Koszul, Roman Marbouty, Martial |
| author2_role | author author author author author author author author author author author author author author author author author author author |
| author_facet | Bignaud, Amaury Conti, Devon Thierry, Agnès Serizay, Jacques Labadie, Karine Poulain, Julie Cheny, Olivia Colón-González, Maritrini Debarbieux, Laurent Guerrero-Osornio, Marianna Helaine, Sophie Hill, Peter Le Tinier, Gwenaelle Millot, Gael A. Morales, Lucía Parada, Andrés Riera Faraone, Nadia Iraola, Gregorio Koszul, Roman Marbouty, Martial |
| author_role | author |
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| collection | COLIBRI |
| dc.contributor.filiacion.none.fl_str_mv | Bignaud Amaury Conti Devon Thierry Agnès Serizay Jacques Labadie Karine Poulain Julie Cheny Olivia Colón-González Maritrini Debarbieux Laurent Guerrero-Osornio Marianna Helaine Sophie Hill Peter Le Tinier Gwenaelle Millot Gael A. Morales Lucía Parada Andrés, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Riera Faraone Nadia, Instituto Pasteur (Montevideo). Iraola Gregorio, Instituto Pasteur (Montevideo). Koszul Roman Marbouty Martial |
| dc.creator.none.fl_str_mv | Bignaud, Amaury Conti, Devon Thierry, Agnès Serizay, Jacques Labadie, Karine Poulain, Julie Cheny, Olivia Colón-González, Maritrini Debarbieux, Laurent Guerrero-Osornio, Marianna Helaine, Sophie Hill, Peter Le Tinier, Gwenaelle Millot, Gael A. Morales, Lucía Parada, Andrés Riera Faraone, Nadia Iraola, Gregorio Koszul, Roman Marbouty, Martial |
| dc.date.accessioned.none.fl_str_mv | 2026-04-22T12:47:29Z |
| dc.date.available.none.fl_str_mv | 2026-04-22T12:47:29Z |
| dc.date.issued.none.fl_str_mv | 2025 |
| dc.description.abstract.none.fl_txt_mv | Phages are diverse and abundant within microbial communities, where they play major roles in their evolution and adaptation. Phage replication, and multiplication, is generally thought to be restricted within a single or narrow host range. Here we use published and newly generated proximity-ligation-based metagenomic Hi-C (metaHiC) data from various environments to explore virus–host interactions. We reconstructed 4,975 microbial and 6,572 phage genomes of medium quality or higher. MetaHiC yielded a contact network between genomes and enabled assignment of approximately half of phage genomes to their hosts, revealing that a substantial proportion of these phages interact with multiple species in environments as diverse as the oceanic water column or the human gut. This observation challenges the traditional view of a narrow host spectrum of phages by unveiling that multihost associations are common across ecosystems, with implications for how they might impact ecology and evolution and phage therapy approaches. |
| dc.description.es.fl_txt_mv | Publicado también en: Nature Microbiology, 2025, 10: 2537–2549. DOI: 10.1038/s41564-025-02108-2 |
| dc.description.sponsorship.none.fl_txt_mv | ANII: FSGSK_1_2019_1_15973 |
| dc.format.extent.es.fl_str_mv | 42 h |
| dc.format.mimetype.es.fl_str_mv | application/pdf |
| dc.identifier.citation.es.fl_str_mv | Bignaud, A, Conti, D, Thierry, A [y otros autores]. "Phages with a broad host range are common across ecosystems" [Preprint]. Publicado en: HAL. 2025: pasteur-05269627. 42 h. |
| dc.identifier.other.none.fl_str_mv | pasteur.hal.science/pasteur-05269627v1 |
| dc.identifier.uri.none.fl_str_mv | https://hdl.handle.net/20.500.12008/54527 |
| dc.language.iso.none.fl_str_mv | en eng |
| dc.publisher.es.fl_str_mv | HAL |
| dc.relation.none.fl_str_mv | HAL, 2025: pasteur-05269627. |
| dc.rights.license.none.fl_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
| dc.subject.es.fl_str_mv | Environmental microbiology Software Virology |
| dc.title.none.fl_str_mv | Phages with a broad host range are common across ecosystems |
| dc.type.es.fl_str_mv | Preprint |
| dc.type.none.fl_str_mv | info:eu-repo/semantics/preprint |
| dc.type.version.none.fl_str_mv | info:eu-repo/semantics/submittedVersion |
| description | Publicado también en: Nature Microbiology, 2025, 10: 2537–2549. DOI: 10.1038/s41564-025-02108-2 |
| eu_rights_str_mv | openAccess |
| format | preprint |
| id | COLIBRI_0f3ad3301a8f9e81e770c079e92dd6ec |
| identifier_str_mv | Bignaud, A, Conti, D, Thierry, A [y otros autores]. "Phages with a broad host range are common across ecosystems" [Preprint]. Publicado en: HAL. 2025: pasteur-05269627. 42 h. pasteur.hal.science/pasteur-05269627v1 |
| instacron_str | Universidad de la República |
| institution | Universidad de la República |
| instname_str | Universidad de la República |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | COLIBRI |
| network_name_str | COLIBRI |
| oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/54527 |
| publishDate | 2025 |
| reponame_str | COLIBRI |
| repository.mail.fl_str_mv | karina.camps@seciu.edu.uy |
| repository.name.fl_str_mv | COLIBRI - Universidad de la República |
| repository_id_str | 4771 |
| rights_invalid_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
| spelling | Bignaud AmauryConti DevonThierry AgnèsSerizay JacquesLabadie KarinePoulain JulieCheny OliviaColón-González MaritriniDebarbieux LaurentGuerrero-Osornio MariannaHelaine SophieHill PeterLe Tinier GwenaelleMillot Gael A.Morales LucíaParada Andrés, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Riera Faraone Nadia, Instituto Pasteur (Montevideo).Iraola Gregorio, Instituto Pasteur (Montevideo).Koszul RomanMarbouty Martial2026-04-22T12:47:29Z2026-04-22T12:47:29Z2025Bignaud, A, Conti, D, Thierry, A [y otros autores]. "Phages with a broad host range are common across ecosystems" [Preprint]. Publicado en: HAL. 2025: pasteur-05269627. 42 h.pasteur.hal.science/pasteur-05269627v1https://hdl.handle.net/20.500.12008/54527Publicado también en: Nature Microbiology, 2025, 10: 2537–2549. DOI: 10.1038/s41564-025-02108-2Phages are diverse and abundant within microbial communities, where they play major roles in their evolution and adaptation. Phage replication, and multiplication, is generally thought to be restricted within a single or narrow host range. Here we use published and newly generated proximity-ligation-based metagenomic Hi-C (metaHiC) data from various environments to explore virus–host interactions. We reconstructed 4,975 microbial and 6,572 phage genomes of medium quality or higher. MetaHiC yielded a contact network between genomes and enabled assignment of approximately half of phage genomes to their hosts, revealing that a substantial proportion of these phages interact with multiple species in environments as diverse as the oceanic water column or the human gut. This observation challenges the traditional view of a narrow host spectrum of phages by unveiling that multihost associations are common across ecosystems, with implications for how they might impact ecology and evolution and phage therapy approaches.Submitted by Pintos Natalia (nataliapintosmvd@gmail.com) on 2026-04-17T14:26:32Z No. of bitstreams: 2 license_rdf: 25630 bytes, checksum: e7132498e7c1fe99f7096667baa99b25 (MD5) pp.hal.science.pasteur-05269627.pdf: 12134660 bytes, checksum: eeb8ab28ec01c94ec70efe99df06721f (MD5)Approved for entry into archive by Faget Cecilia (lfaget@fcien.edu.uy) on 2026-04-21T17:36:59Z (GMT) No. of bitstreams: 2 license_rdf: 25630 bytes, checksum: e7132498e7c1fe99f7096667baa99b25 (MD5) pp.hal.science.pasteur-05269627.pdf: 12134660 bytes, checksum: eeb8ab28ec01c94ec70efe99df06721f (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2026-04-22T12:47:29Z (GMT). No. of bitstreams: 2 license_rdf: 25630 bytes, checksum: e7132498e7c1fe99f7096667baa99b25 (MD5) pp.hal.science.pasteur-05269627.pdf: 12134660 bytes, checksum: eeb8ab28ec01c94ec70efe99df06721f (MD5) Previous issue date: 2025ANII: FSGSK_1_2019_1_1597342 happlication/pdfenengHALHAL, 2025: pasteur-05269627.Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)Environmental microbiologySoftwareVirologyPhages with a broad host range are common across ecosystemsPreprintinfo:eu-repo/semantics/preprintinfo:eu-repo/semantics/submittedVersionreponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaBignaud, AmauryConti, DevonThierry, AgnèsSerizay, JacquesLabadie, KarinePoulain, JulieCheny, OliviaColón-González, MaritriniDebarbieux, LaurentGuerrero-Osornio, MariannaHelaine, SophieHill, PeterLe Tinier, GwenaelleMillot, Gael A.Morales, LucíaParada, AndrésRiera Faraone, NadiaIraola, GregorioKoszul, RomanMarbouty, MartialLICENSElicense.txtlicense.txttext/plain; charset=utf-84267http://localhost:8080/xmlui/bitstream/20.500.12008/54527/5/license.txt6429389a7df7277b72b7924fdc7d47a9MD55CC-LICENSElicense_urllicense_urltext/plain; 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públicahttps://udelar.edu.uy/https://www.colibri.udelar.edu.uy/oai/requestkarina.camps@seciu.edu.uyUruguayopendoar:47712026-04-22T12:47:29COLIBRI - Universidad de la Repúblicafalse |
| spellingShingle | Phages with a broad host range are common across ecosystems Bignaud, Amaury Environmental microbiology Software Virology |
| status_str | submittedVersion |
| title | Phages with a broad host range are common across ecosystems |
| title_full | Phages with a broad host range are common across ecosystems |
| title_fullStr | Phages with a broad host range are common across ecosystems |
| title_full_unstemmed | Phages with a broad host range are common across ecosystems |
| title_short | Phages with a broad host range are common across ecosystems |
| title_sort | Phages with a broad host range are common across ecosystems |
| topic | Environmental microbiology Software Virology |
| url | https://hdl.handle.net/20.500.12008/54527 |
