Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages

Simple item page
dc.contributor.authorWalsh, Liam H.
dc.contributor.authorSoni, Viyal
dc.contributor.authorAncla, Joseph
dc.contributor.authorSomerville, Vincent
dc.contributor.authorSegata, Nicola
dc.contributor.authorJoyce, Susan
dc.contributor.authorSinderen, Douwe van
dc.contributor.authorMahony, Jennifer
dc.contributor.authorShkoporov, Andrey N.
dc.contributor.authorKenny, John G.
dc.contributor.authorCotter, Paul D.
dc.contributor.authorO’Sullivan, Orla
dc.contributor.funderEuropean Union’s Horizon 2020 research and innovation programme
dc.contributor.funderEuropean Union’s Horizon Europe research and innovation programme
dc.contributor.funderItalian Ministry of Foreign Affairs and International Cooperation
dc.contributor.funderEuropean Research Council
dc.contributor.funderEuropean Union's Horizon 2020
dc.contributor.funderTaighde Éireann - Research Ireland
dc.contributor.funderEnterprise Ireland
dc.date.accessioned2026-09-11T15:24:01Z
dc.date.available2026-09-11T15:24:01Z
dc.date.issued2026-03-27
dc.description.abstractBacteriophages are key drivers of microbial ecology, co-existing and co-evolving with bacteria across diverse environments. Limitations in culturing, alongside advances in sequencing and bioinformatics, have driven the use of metagenomics to explore viral diversity. Viral-specific analysis of >3000 food metagenomes from cFMD produced the FVGC, comprising ~3400 metagenome-assembled viruses, most of which belong to novel Caudoviricetes lineages (n = 91), with only ~15% represented in IMG/VR v4. Together, these findings reveal extensive uncharacterized viral diversity in food systems. Beyond serving as a reference, the FVGC facilitates detailed investigation of virus–host interactions. Viral sequences were pervasive across microbial genomes, with several bacterial families exhibiting near-universal associations with viral elements. Bacterial antiviral defence systems were abundant and taxonomically diverse, dominated by restriction–modification systems, while CRISPR–Cas systems showed pronounced lineage-specific distributions; in contrast, viral anti-defence genes were detected at low frequency (<10% of MAVs). Host prediction linked MAVs to clinically relevant taxa, including expanded ESKAPE pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, Staphylococcus aureus, and Enterobacter spp., highlighting the ecological connectivity between food-associated viruses and clinically important bacteria. Antimicrobial resistance signals were scarce, suggesting minimal phage-mediated AMR dissemination in food environments. This new publicly available viral database represents a valuable resource for further exploration of viral diversity.en
dc.description.sponsorshipEuropean Union’s Horizon 2020|818368
dc.description.sponsorshipEuropean Union’s Horizon Europe programme|101060218
dc.description.sponsorshipItalian Ministry of Foreign Affairs and International Cooperation|VN21GR09
dc.description.sponsorshipEuropean Research Council|MetaPG-716575
dc.description.sponsorshipEuropean Research Council|101045015
dc.description.sponsorshipEuropean Union’s Horizon 2020 programme|ONCOBIOME-825410
dc.description.sponsorshipEuropean Union’s Horizon 2020 programme|IHMCSA-964590
dc.description.sponsorshipEuropean Union’s Horizon 2020 programme|101034371
dc.description.sponsorshipTaighde Éireann-Research Ireland|SFI/12/RC/2273_P2
dc.description.sponsorshipTaighde Éireann-Research Ireland|SFI/16/RC/3835 (VistaMilk)
dc.description.sponsorshipEnterprise Ireland|TC/2018/0025
dc.description.versionPublished Version
dc.format.extent14
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid104
dc.identifier.authororcidWalsh, Liam H.
dc.identifier.authororcidSoni, Viyal
dc.identifier.authororcidAncla, Joseph
dc.identifier.authororcidSomerville, Vincent
dc.identifier.authororcidSegata, Nicola
dc.identifier.authororcidJoyce, Susan§0000-0003-4771-3123
dc.identifier.authororcidSinderen, Douwe van§0000-0003-1823-7957
dc.identifier.authororcidMahony, Jennifer§0000-0001-5846-6303
dc.identifier.authororcidShkoporov, Andrey N.
dc.identifier.authororcidKenny, John G.
dc.identifier.authororcidCotter, Paul D.
dc.identifier.authororcidO’Sullivan, Orla
dc.identifier.citationWalsh, L H, Soni, V, Ancla, J, Somerville, V, Segata, N, Joyce, S, Sinderen, D V, Mahony, J, Shkoporov, A N, Kenny, J G, Cotter, P D & O’Sullivan, O 2026, 'Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages', npj Biofilms and Microbiomes, vol. 12, no. 1, 104, pp. 1-14. https://doi.org/10.1038/s41522-026-00941-9
dc.identifier.doi10.1038/s41522-026-00941-9
dc.identifier.endpage14
dc.identifier.issn2055-5008
dc.identifier.issued1
dc.identifier.journaltitlenpj Biofilms and Microbiomes
dc.identifier.otherORCID: /0000-0003-1823-7957/work/226487417
dc.identifier.startpage1
dc.identifier.urihttps://hdl.handle.net/10468/19243
dc.identifier.volume12
dc.language.isoen
dc.publisherNature Research
dc.relation.urihttps://www.scopus.com/pages/publications/105040741512
dc.rights© 2026, the Author(s). This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.accessrightsopen access
dc.rights.licensenameAttribution-NonCommercial-NoDerivatives 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.statusPeer reviewed
dc.subjectFood metagenomes
dc.subjectdsDNA bacteriophages
dc.subjectMicrobial ecology
dc.subject[BiochemistryCellBiology]
dc.titleMining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophagesen
dc.typeArticle (peer-reviewed)
Files
Original bundle
Now showing 1 - 2 of 2
Thumbnail Image
Name:
s41522-026-00941-9.pdf
Size:
3.45 MB
Format:
Adobe Portable Document Format
Download
Thumbnail Image
Name:
41522_2026_941_MOESM1_ESM_1_.docx
Size:
9.86 MB
Format:
Microsoft Word XML
Download
Collections
School of Biochemistry and Cell Biology