Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages
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Date
2026-03-27
Authors
Walsh, Liam H.
Soni, Viyal
Ancla, Joseph
Somerville, Vincent
Segata, Nicola
Joyce, Susan
Sinderen, Douwe van
Mahony, Jennifer
Shkoporov, Andrey N.
Kenny, John G.
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Research
Published Version
Abstract
Bacteriophages 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.
Description
Keywords
Food metagenomes , dsDNA bacteriophages , Microbial ecology , [BiochemistryCellBiology]
Citation
Walsh, 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