Lactococcal phage–host profiling through binding studies between cell wall polysaccharide types and Skunavirus receptor-binding proteins

Dairy fermentations using mesophilic starter cultures rely on the activity of specific lactic acid bacteria (LAB) such as <i>Lactococcus lactis</i> and <i>Lactococcus cremoris</i> for the acidification of milk. This biotechnological process can be affected by bacteriophage infection of LAB starter strains, which may result in delayed or even failed fermentations. Most studied lactococcal phages commence infection with the binding of a tail-associated receptor-binding protein (RBP) to a host cell surface-exposed cell wall polysaccharide (CWPS). In the present study, phage prevalence and diversity in whey samples originating from fermentations performed in various European countries employing undefined mesophilic starter cultures were investigated using phageome analysis. The range of <i>Skunavirus</i> RBP genotypes present in the phageomes and associated RBP-CWPS binding abilities were evaluated, resulting in the refinement and expansion of the <i>Skunavirus</i> RBP grouping system and the identification of several heretofore unknown <i>Skunavirus</i> RBP (sub)groups. These findings substantially expand our knowledge on lactococcal <i>Skunavirus</i> RBP diversity and their binding specificity towards CWPS receptor structures, thereby improving the predictability of fermentation outcomes and robustness of starter culture rotations and blends.