Comparative genomics and phenotypic assessment of lactic acid bacteria isolated from artisanal cheese as potential starter cultures

Novel starter cultures are coveted by the dairy industry for enhancing the sensory, quality, and safety attributes of fermented dairy products. In this study, artisanal cheeses were investigated as a source of novel starter cultures. Lactic acid bacteria (LAB) were isolated from the cheese and underwent an antimicrobial activity screening. Six potential antimicrobial producers were selected for whole genome sequencing and were confirmed to be new LAB strains belonging to the genera Lacticaseibacillus , Lactococcus , Leuconostoc , and Enterococcus . Genes associated with carbohydrate utilization, proteolytic enzyme production, and exopolysaccharide synthesis were identified. Additionally, in silico analysis revealed safety-related traits including absence of antibiotic resistance genes, intact prophage regions, and biogenic amine production genes. Genome-guided phenotypic confirmation of important identified traits was completed, which included utilization of multiple carbohydrates, hydrolysis of casein, coagulation of milk, and susceptibility to antibiotic. Among these LAB strains, Lactococcus lactis OSY-92 contained and expressed the necessary genes for a dairy starter culture. The strain displayed anti-Gram-positive antimicrobial activity, a strong preference for lactose and galactose, limited casein hydrolysis, and ability to coagulate milk in 7.5 h. When all these findings were considered, L. lactis OSY-92 qualified as a potential novel and safe starter culture for dairy fermentations. • Market artisanal cheeses were screened for beneficial lactic acid bacteria (LAB). • Using genomic and phenotypic analyses, superior starter cultures were selected. • Analyses allowed for cultures with enhanced safety characteristics to be discovered. • High-throughput methods allowed for rapid and accurate isolation of novel starters. • Study findings revealed a potential candidate for commercial starter development.