Members of the Lactococcus-Pseudolactococcus clade exhibit extensive genomic diversity in features associated with phage-host co-adaptation.

Lactococcus lactis and Lactococcus cremoris are widely exploited in global dairy fermentations. Consequently, strains of these species are extensively studied, as are their interactions with their infecting bacteriophages. In recent years, the number of lactococcal species has increased significantly and the ecology of these species extends far beyond the dairy niche. Furthermore, this expansion has also warranted the reassignment of several former lactococcal species to the genus Pseudolactococcus. In the present study, we explored the bacteriophage-relevant features of 495 genomes within the Lactococcus-Pseudolactococcus clade, including regions associated with (1) cell wall polysaccharides (CWPS) and exopolysaccharides (EPS) as possible bacteriophage receptors, (2) prophages and phage satellites and (3) anti-phage systems. This analysis revealed the universal presence and consistent genomic location of cwps loci, with extensive relationships between the loci of distinct species of both genera. It was also established that EPS-associated gene clusters are present in approximately half of the evaluated species and occur in a strain-dependent manner, suggesting that they are associated with niche adaptation rather than a core biological function of these organisms. Significant diversity and phylogenetic overlap of prophages across several species of both genera were observed. While prophages were widespread, phage satellites were especially prevalent among dairy-associated species. At the strain level, prophage, satellite and defence-system abundances were positively correlated. Restriction-modification systems appeared to form the core defence strategy of the Lactococcus-Pseudolactococcus taxon, complemented by species- and strain-level tailoring of the anti-phage repertoire to respond to phage pressure in diverse ecological niches. Niche-associated differences observed within L. lactis underscored that greater apparent phage exposure was not uniformly reflected across all phage-relevant features: dairy-associated strains carried more prophages, satellites and defence systems than plant-associated strains, whereas plant isolates exhibited greater rarefied polysaccharide pellicle richness. Overall, this represents the most comprehensive genome-based analysis of members of the Lactococcus-Pseudolactococcus clade, guiding our current understanding of the evolutionary pathways underlying phage-host co-adaptation followed by these micro-organisms.