Diverse phages found from food metagenomes reveal hidden diversity and potential associations with the human microbiome

Foods harbor a rich diversity of viruses alongside bacteria and fungi. By analyzing 3,013 food metagenomic data sets from, we identified 2,325 high-quality viral sequences, 93.7% of which were bacteriophages belonging to the class Caudoviricetes. Notably, a substantial proportion of these represent novel viral lineages. Only ~50% could be taxonomically resolved to the genus level, and only 36.3% of predicted genes had known functions. Using 10,112 food-derived prokaryotic metagenome-assembled genomes (MAGs), we assigned putative hosts to 62.4% of the foodborne phages. Bacillota was the predominant phylum (>50%), followed by Pseudomonadota, with Lactobacillales and Enterobacterales as the dominant orders. Comparative analysis against 4,709 oral and 58,661 gut phages revealed that 335 foodborne phages shared viral operational taxonomic unit (vOTUs) with gut phages, whereas only 2 overlapped with oral phages. Furthermore, 566 and 656 foodborne phages were predicted to target oral and gut microbial communities, respectively, based on 3,426 oral and 4,744 gut MAGs. Collectively, our findings demonstrate that food contains a vast repertoire of viral sequences, predominantly bacteriophages, which exhibit remarkable diversity and are largely unclassified. Foodborne phages show greater genomic overlap with gut phages than with oral phages, and possess the capacity to target both oral and gut microbiota. These findings highlight the significant potential of foodborne phages to influence human commensal microorganisms.