Comparative genomics reveals population structure and ecological adaptation in Lactobacillus helveticus

Lactobacillus helveticus (L. helveticus) is an important starter culture in fermented dairy production and is valued for its pronounced proteolytic activity. However, the genetic basis of its functional diversity and ecological adaptation warrants further investigation. This study presents a comparative genomic analysis of 284 L. helveticus isolated from diverse geographical regions and ecological niches. This investigation identified a core genome of 490 genes and a pan-genome encompassing 15,105 genes, revealing an open pan-genome structure for this species. Phylogenetic analysis classified the strains into six distinct evolutionary clades, indicating that their genetic evolution was likely driven by selective pressure associated with ecological niches. Statistically significant functional metabolic differences (P < 0.05) were observed among the different phylogenetic and ecological clades, whereas the intracellular peptidases were highly conserved. Assessment of angiotensin-converting enzyme (ACE) inhibitory activity among the strains revealed no significant differences across the phylogenetic clades. These findings demonstrate that L. helveticus has evolved evolutionary genomic mechanisms that facilitate its adaptation to diverse ecological environments. This study highlights the functional diversity of this species and provides a critical theoretical foundation for future industrial strain selection and development.