Temporal dynamics of the S. thermophilus phage population in a yogurt production facility

Starter cultures are essential for milk fermentation, but phage infections can disrupt production, compromising product quality and causing economic losses. In this study, we investigated the dynamics, diversity, and persistence of 25 S. thermophilus phages isolated over a 15-year period from a large yogurt manufacturing plant. Phages were classified into Moineauvirus (16) and Brussowvirus (9), comprising ten distinct restriction profiles. Host range, genomic features, and resistance to thermal and chemical treatments were analyzed to identify factors underlying their long-term persistence. No significant differences in thermal resistance between the two groups were observed at 63 °C (30 min), 72 °C (5 min), or 90 °C (5 min). However, Brussowvirus phages exhibited greater stability during storage at 25 °C and 8 °C over eight months and tolerated sodium hypochlorite concentrations up to 500 ppm. All phages were effectively inactivated by 2.0% Lysoform™, below the manufacturer's recommended concentration (2.8%). Most phages displayed at least one resistance trait, contributing to their persistence in industrial environments. Genomic analysis revealed double-stranded DNA genomes ranging from 33.2 to 39.8 kb, encoding 40-58 predicted ORFs. Several phages carried genes coding for anti-CRISPR proteins (AcrIIA3, AcrIIA5, AcrIIA6, AcrIIA21, AcrIIA25, and truncated AcrIIA36), enabling evasion of the main defense systems in S. thermophilus. Notably, infectivity was not always linked to Acr presence or protospacer matches, indicating alternative bacterial resistance mechanisms. These findings underscore the complexity of phage-host interactions and highlight the need for continuous monitoring and improved control strategies in dairy processing environments.