Profiling phage-host interactions between Skunavirus receptor binding proteins and lactococcal cell wall polysaccharide structures

Mesophilic starter cultures rely on the activity of lactic acid bacteria such as Lactococcus lactis and Lactococcus cremoris for the acidification of milk. This biotechnological process can be affected by bacteriophage infection of bacterial starter strains resulting in failed or delayed fermentations. The majority of studied lactococcal phages commence infection with the binding of a tail-associated receptor binding protein (RBP) to a host surface-exposed cell wall polysaccharide (CWPS). In the present study, phage prevalence and phage diversity in whey samples originating from fermentations performed in various European countries and employing mesophilic undefined, complex starter cultures were investigated using phageome analysis. The range of Skunavirus RBP genotypes and associated RBP-CWPS binding abilities of the isolated phages was evaluated, resulting in the identification of several novel Skunavirus RBP (sub)groups. These findings vastly improve our knowledge on lactococcal Skunavirus RBP diversity and their specificity towards CWPS receptor structures, thereby improving the predictability of fermentation outcomes and robustness of starter culture rotations or blends.