Comprehensive Genome Characterization of Carnobacterium divergens UFJF 3.2 Reveals Adaptative Traits and Antimicrobial Potential

Abstract

Lactic acid bacteria (LAB) are widely recognized for their antimicrobial activity and health-promoting effects. However, the genomic potential of underexplored species, such as Carnobacterium divergens, remains insufficiently characterized. This study aimed to perform a comprehensive genomic characterization of C. divergens UFJF 3.2, isolated from tilapia fillet, to identify functional and safety-related attributes supporting its probiotic potential. Whole-genome sequencing on the Illumina platform yielded a high-quality assembly (2.72 Mb) with 99.45% completeness and low contamination (0.55%). Taxonomic assignment was confirmed by ANIb (98.82%) and digital DNA–DNA hybridization (dDDH, 91.9%), supporting its classification within the species. Functional annotation identified 90 genes associated with probiotic-related traits, including coordinated stress response systems such as the complete arcABC operon (arginine deiminase pathway), dltABCD (cell wall modification), and the chaperone systems groESL and dnaK. In addition, genes associated with acid and bile tolerance, as well as exopolysaccharide biosynthesis and short-chain fatty acid (SCFA) production, were identified. Notably, a gene encoding a Zoocin A-like bacteriocin was identified in strain UFJF 3.2, a feature shared with only three other genomes within the species. Altogether, these genomic traits underscore the promising probiotic potential of C. divergens UFJF 3.2. This study provides a theoretical framework for future in vitro and in vivo investigations into its probiotic properties and prospective applications in food biotechnology.