Genomics divergence of Lactococcus lactis subsp. lactis isolated from naturally fermented dairy products

Lactococcus lactis subsp. lactis (L. lactis subsp. lactis) is commonly found in naturally fermented dairy products (NFDPs). This subspecies is of high economic value due to its wide application in dairy industry. However, the genetic background and evolutionary history of L. lactis subsp. lactis are still poorly understood, analysis of its genetic background and functional genome will lay a genetic foundation for its application. This study analyzed the whole genomes of 227 novel L. lactis subsp. lactis isolated from NFDPs and investigated the genetic history of this subspecies from a population genetic perspective. These strains were classified into four phylogenetically distinct groups, which were likely derived from only a few wild ancestors through three divergence events, resulting in genetic and phenotypic divergence. Functional genomic analysis found that the divergence events caused strong lineage-specific selection for carbohydrate utilization and lactic acid production genes. Moreover, the time of the divergence coincided with mass migration of nomads due to climate change and decrease in average annual temperature, suggesting that these drastic environmental changes might be evolutionary drivers of the divergence. Genome-wide association analysis results showed that the single nucleic acid polymorphic loci we associated with pepF and CoiA genes were significantly correlated with fermentation capability, and based on this, a rapid screening model for potential starter strains was constructed. Our findings shed light on the evolutionary history and genomic diversity of NFDP-originated L. lactis subsp. lactis, and provide a new insight for screening strains with excellent characteristics.