Soy Sauce Fermentation metagenome Raw sequence reads

The composition and function of phages in fermented foods have garnered increasing attention; however, their ecological roles and underlying mechanisms during the fermentation of high-salt soy sauce remain largely unclear. In this study, phage communities, functional potentials, phage and host interactions, and defense mechanisms were systematically investigated across two distinct soy sauce fermentation processes (Cantonese type, CP; Japanese type, JP) using shotgun metagenomics. A total of 823 phage species (vOTUs) were identified, with most phages associated with temperate lifestyle. Although phage compositions varied between the two processes, the number of vOTUs was significantly positively correlated with the abundance of prokaryotes, fungi, total acidity, and amino acid nitrogen content. Comparative genomic analysis revealed that 91 phages were associated with 26 bacterial genomes (metagenomic associated genomes, MAGs). Host defense mechanisms analysis showed that all 45 bacterial metagenome-assembled genomes (MAGs) had CRISPRsystems, followed by restriction modification systems. Functional annotation revealed that phages predominantly encoded genes involved in cell growth, replication, and metabolism of amino acids, carbohydrates, and nucleotides.