Genomic analysis of probiotics from breast milk Limosilactobacillus fermentum UP-1 and application in fermented milk

Limosilactobacillus fermentum is a promising probiotic species. Limosilactobacillus fermentum UP-1 was isolated from human milk by our research team; however, its genetic background and fermentation characteristics remain unclear. In this study, the whole genome of UP-1 was sequenced, assembled, and analyzed through comparative analysis with 61 publicly available L. fermentum genomes. Subsequently, it was combined with a basic starter culture to investigate its fermentation characteristics and storage stability in fermented milk. Phylogenetic analysis indicated that UP-1 is closely related to strain EFEL6800, which was isolated from human saliva, and the human isolates exhibited a clear clustering trend. The UP-1 genome contains a 4,221-bp exopolysaccharide (EPS) gene cluster that encodes genes involved in EPS production, regulation, and transport. When co-applied with starter cultures in fermented milk, UP-1 significantly enhanced the water-holding capacity, texture, and viscosity and improved the sensory attributes in the early stages of storage. Furthermore, UP-1 significantly increased the crude EPS content of the fermented dairy products. This study provides a comprehensive genomic characterization of the breast milk-isolated probiotic UP-1, highlighting its functional genomic features and substantiating its potential as a probiotic for applications in fermented dairy products.