Biodiversity of skunaviruses isolated from dairy fermentation facilities employing undefined mesophilic starter cultures

Mesophilic starter cultures rely on the activity of lactic acid bacteria such as Lactococcus lactis and Lactococcus cremoris to acidify milk in dairy fermentations. Bacteriophage infection of starter bacteria remains one of the most significant threats to a successful fermentation, as they may cause costly disruptions and loss of production. The exclusively virulent skunaviruses represent one of the most problematic lactococcal phage genera in dairy fermentation facilities and have consequently been studied extensively in recent decades. In the present study, the diversity of lactococcal phages in whey samples originating from fermentations employing undefined mesophilic starter cultures was assessed by culture-dependent phage screening, targeted isolation based on predicted receptor binding protein specificity, and phage RBP-activated cell sorting (PhRACS). Through these approaches, 26 distinct Skunavirus isolates were characterized and their genomes were sequenced. A comparative genomic analysis and structure predictions of the proteins encoded by these 26 phages identified genes that encode tail-associated proteins with novel carbohydrate-binding domains. Furthermore, host range analysis revealed a clear correlation between specific Skunavirus receptor binding protein phylogroups and the cell wall polysaccharide-associated genotype of the corresponding host strain. Finally, phageome-derived Skunavirus contigs were analysed to determine the diversity of phages present in the dairy fermentation facilities.