Comparative genomics analysis of Pediococcus acidilactici species

Abstract

Pediococcus acidilactici is a probiotic with promising applications in food fermentation and the health industry, garnering significant attention for its bacteriocin-producing capabilities; however, the genetic basis of this species has not yet been systematically elucidated. This study aimed to reveal the intraspecific genetic diversity, core and pan-genome characteristics, and ecological adaptation mechanisms of P. acidilactici using comparative genomics. Whole-genome sequencing and comparative analysis were performed on 41 strains isolated from diverse ecological niches, employing methods such as average nucleotide identity (ANI) calculation, pan-genome analysis, and phylogenetic tree construction. The results demonstrated high genetic diversity and an open pan-genome structure, characterized by a substantial accessory genome—including mobile genetic elements and hypothetical proteins—acquired through horizontal gene transfer. Bacteriocin genes encoding pediocin PA-1, enterolysin A, and colicin-B were identified across 11 strains. Comparative genomic analysis unveiled the genetic mechanisms underlying the species' adaptation to host environments, including CRISPR/Cas systems for defense against exogenous DNA invasion and diverse carbohydrate fermentation capabilities. The ability of these 41 strains to metabolize a wide range of carbon sources enhances their adaptability and survival across different environments. These findings provide a genetic perspective on the antimicrobial potential, genomic evolution, and ecological flexibility of P. acidilactici , offering robust genomic support for its industrial development and application.