The average content of casein in yak milk is 40.2 g/L. Casein can be degraded by enzymatic digestion or food processing to produce abundant degradation peptides. International researchers have studied the degradation peptides of yak milk casein by using multiple techniques and methods, such as in vitro activity tests, cellular experiments, proteomics, bioinformatics, etc., and found that the degradation peptides have a wide range of functional activities that are beneficial to the human body, such as angiotensin-converting enzyme (ACE) inhibitory, antioxidant, anti-inflammatory, antidiabetic, antimicrobial, anticancer, and immunomodulatory activities, etc., and it has been proved that the types and strengths of functional activities are closely related to the structural characteristics of the peptides. This paper describes the characteristics of yak milk proteins, the functional activities, and mechanism of action of degraded peptides. Based on the types of functional activities of yak milk casein degradation peptides, we classified and elucidated the effects of structural factors, such as peptide molecular weight, peptide length, amino acid sequence, physicochemical properties, electrical charge, hydrophobicity, spatial conformation, chain length, and the type of enzyme on these activities. It reveals the great potential of yak milk casein degradation peptides as functional active peptide resources and as auxiliary treatments for diseases. It also provides important insights for analyzing yak casein degradation peptide activity and exploring high-value utilization.

Lactiplantibacillus plantarum MS11, isolated from traditionally fermented yak milk in the high-altitude Gannan region of the eastern Tibetan Plateau, was investigated for its technological and functional potential in food applications. Using whole-genome sequencing combined with targeted experimental verification, this study clarified the genetic determinants and metabolic capacity associated with its production of folate, lactic acid, bacteriocin, and exopolysaccharides (EPS). The MS11 genome consists of one circular chromosome and three plasmids, totaling 3,318,231 bp with a GC content of 44.48%, and encodes 3155 predicted open reading frames. Complete biosynthetic gene clusters were identified for folate (7 genes), L-lactic acid (13 genes), bacteriocin (14 genes), and EPS (17 genes). Phenotypic assays confirmed the strain’s high metabolite productivity, including folate (0.6043 μg/mL), L-lactic acid (76.24 mg/mL), and EPS (544.2 mg/L). The cell-free fermented supernatant exhibited strong antibacterial activity against Escherichia coli, supporting the functional relevance of its bacteriocin-associated gene cluster. To the best of our knowledge, this is the integrated genomic and experimental characterization demonstrating that a L. plantarum strain originating from a unique high-altitude fermented dairy niche can concurrently synthesize high levels of folate together with multiple beneficial metabolites. The multifunctional attributes of MS11—including nutrient fortification, acidification capacity, EPS formation, and antimicrobial activity—indicate substantial promise for its application as a composite starter culture, natural bio-preservative, and nutritionally enhanced probiotic in fermented food systems.