VIRE: a metagenome-derived, planetary-scale virome resource with environmental context

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dc.contributor.authorNishijima, Suguru
dc.contributor.authorFullam, Anthony
dc.contributor.authorSchmidt, Thomas S B
dc.contributor.authorKuhn, Michael
dc.contributor.authorBork, Peer
dc.contributor.funderTakeda Science Foundation
dc.contributor.funderUehara Memorial Foundation
dc.contributor.funderTaighde Éireann - Research Ireland, 12/RC/2273-P2
dc.date.accessioned2026-10-21T15:37:01Z
dc.date.available2026-10-21T15:37:01Z
dc.date.issued2026-01-06
dc.description.abstractViruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.en
dc.description.sponsorshipTakeda Science Foundation, Uehara Memorial Foundation, and Research Ireland [12/RC/2273-P2]. Funding to pay the Open Access publication charges for this article was provided by Internal EMBL funding for publication.
dc.description.versionPublished Version
dc.format.extent10
dc.format.mimetypeapplication/pdfen
dc.identifier.articleidgkaf1225
dc.identifier.authororcidNishijima, Suguru
dc.identifier.authororcidFullam, Anthony
dc.identifier.authororcidSchmidt, Thomas S B§0000-0001-8587-4177
dc.identifier.authororcidKuhn, Michael
dc.identifier.authororcidBork, Peer
dc.identifier.citationNishijima, S, Fullam, A, Schmidt, T S B, Kuhn, M & Bork, P 2026, 'VIRE: a metagenome-derived, planetary-scale virome resource with environmental context', Nucleic Acids Research, vol. 54, no. 1, gkaf1225, pp. D902-D911. https://doi.org/10.1093/nar/gkaf1225
dc.identifier.doi10.1093/nar/gkaf1225
dc.identifier.endpageD911
dc.identifier.issn0305-1048
dc.identifier.issued1
dc.identifier.journaltitleNucleic Acids Research
dc.identifier.otherORCID: /0000-0001-8587-4177/work/198283366
dc.identifier.startpageD902
dc.identifier.urihttps://hdl.handle.net/10468/19490
dc.identifier.volume54
dc.language.isoen
dc.publisherOxford University Press
dc.relation.urihttps://www.scopus.com/pages/publications/105027737644
dc.rights© The Author(s) 2025. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.accessrightsopen access
dc.rights.licensenameAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.statusPeer reviewed
dc.subjectVIRE
dc.subjectViral genomes
dc.subjectViruses
dc.titleVIRE: a metagenome-derived, planetary-scale virome resource with environmental contexten
dc.typeArticle (peer-reviewed)
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