A phylogenetic perspective on the performance of Lactococcus lactis as starter culture in milk and plant milks

Lactococcus lactis is used as a starter culture in dairy fermentations but also occurs in spontaneous plant fermentations. Phylogenetic analyses have differentiated Lc. lactis into distinct clades. One clade consists exclusively of dairy isolates, which evolved from a more ancestral clade comprising both plant and dairy isolates. However, it remains unclear whether strains from these clades differ in their ability to ferment milk and plant-based milk. This study aimed to compare the fermentative properties of Lc. lactis from a phylogenetic perspective. A core genome phylogenetic tree based on high-quality Lc. lactis genomes revealed distinct ancestral, plant, and dairy lineages which were not congruent with the current subspecies classification. The phylogeny of the dairy lineage and the geographic origin of the isolates supported domestication of the dairy lineage. A phenotypic analysis of 12 representative strains from the lineages (ancestral, plant and dairy) demonstrated that sugar metabolism and acidification profiles aligned with genotypic differences. Dairy-lineage strains acidified bovine milk more effectively and produced higher levels of lactic acid. In contrast, most strains of the plant-lineage were unable to acidify bovine milk below pH 5.4, or to produce lactic acid in milk. These strains, however, exhibited efficient metabolism of raffinose family oligosaccharides and rapidly acidified lupin milk. Lc. lactis FUA3579, classified within the ancestral lineage, effectively acidified both plant-based and dairy matrices and metabolized sugars in both. This study highlights the metabolic divergence among Lc. lactis lineages and provides insights for selection of starter cultures tailored for milk or plant-based dairy alternatives.