| Summary: | <i>Pediococcus acidilactici</i> HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of <i>P. acidilactici</i> HN9 were characterized to provide insights into its potential probiotic activity. Specifically, this work sought to report the complete genome of <i>P. acidilactici</i> HN9 and perform a comparative genome analysis with other bacterial strains belonging to the genus <i>Pediococcus</i>. Genomic features of HN9 were compared with those of all other bacterial <i>Pediococcus</i> strains to examine the adaptation, evolutionary relationships, and diversity within this genus. Additionally, several bioinformatic approaches were used to investigate phylogenetic relationships, genome stability, virulence factors, bacteriocin production, and antimicrobial resistance genes of the HN9 strain, as well as to ensure its safety as a potential starter culture in food applications. A 2,034,522 bp circular chromosome and two circular plasmids, designated pHN9-1 (42,239-bp) and pHN9-2 (30,711-bp), were detected, and used for pan-genome analysis, as well as for identification of bacteriocin-encoding genes in 129 strains belonging to all <i>Pediococcus</i> species. Two CRISPR regions were identified in <i>P. acidilactici</i> HN9, including type II-A CRISPR/CRISPR-associated (Cas). This study provides an in-depth analysis on <i>P. acidilactici</i> HN9, facilitating a better understanding of its adaptability to different environments and its mechanism to maintain genome stability over time.
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