Whole-Genome Sequencing Elucidates the Superior Fermentation Performance, Flavor Formation, and Nutritional Remodeling Mechanisms of Lactococcus garvieae DZ for Fermented Butter Production

Lactococcus garvieae DZ is a specialized fermentation strain isolated from raw water buffalo milk, previously shown to exhibit excellent fermentation performance and significantly enhance the flavor and nutritional quality of butter. To elucidate the molecular basis of these properties, this study employed a combination of second- and third-generation sequencing technologies to complete whole-genome sequencing and functional annotation. The genome consists of one circular chromosome (2.15 Mb, GC content 38.81%) and three plasmids, encoding a total of 2123 genes. Through annotation against KEGG, CAZy, and other databases, this study systematically identified flavor-forming pathways including lactose degradation, glycolysis, diacetyl synthesis, and short- and medium-chain fatty acid accumulation, providing a molecular explanation for the explosive accumulation of characteristic flavor compounds (2,3-butanedione reached 6188 μg·kg−1). The presence of oleate hydratase is consistent with the decrease in oleic acid proportion. Lipolytic enzymes and the antioxidant system may facilitate the release and oxidative protection of unsaturated fatty acids, thereby contributing to the overall increase in PUFAs and MUFAs such as CLA. Genes identified in the genome—including those encoding Na+/H+ antiporters, bile salt hydrolase, and molecular chaperone systems—are consistent with the strain’s excellent gastrointestinal tolerance (94.75% survival at pH 3.0 and 40.43% survival in 0.3% bile salts); the annotation of the β-galactosidase gene also corresponded to its measured enzymatic activity (0.271 U·mL−1). From a safety perspective, no transferable antibiotic resistance genes or typical virulence factors were identified in the genome. Although a hemolysin III gene was annotated, its encoded product is annotated only as a predicted membrane protein and lacks a known toxin catalytic domain; blood agar plate assays confirmed that strain DZ exhibits γ-hemolysis (non-hemolytic), with phenotype consistent with genotype, ruling out the risk of hemolytic virulence. This study elucidates, at the genomic level, the genetic basis underlying the superior fermentation performance, probiotic properties, and safety of strain DZ, providing a theoretical foundation for its industrial application.