Genomic and Functional Characterization of Bacillus siamensis B01 with Antimicrobial Activity Against Vibrio spp.

Abstract

This study reports the first investigation of the biological, genomic, and anti-Vibrio properties of Bacillus siamensis B01 (= VTCC 910229) isolated from a mangrove forest in Vietnam. Comparative genomic analysis revealed a significant similarity between the genomes of strain B01 and B. siamensis KCTC 13613^T, as indicated by average nucleotide identity and digital DNA-DNA hybridization values of 98.8% and 97.5%, respectively. The draft genome comprised 3,823,156 bp, showed a GC composition of 46.2%, and encompassed 112 tRNAs and 3,738 coding sequences (CDSs), with key functional groups related to biological processes, amino acid transport, and metabolism. Within the genome, an 80,406 bp plasmid with a GC content of 38.5% was identified, carrying 105 CDSs, one tRNA, and seven mobile genetic elements without virulence and antibiotic resistance genes. Gene clusters for antibacterial compounds, including bacillaene, fengycin, difficidin, and bacillibactin, showed 100% similarity to known biosynthetic pathways. Pan-genome analysis revealed that strain B01 shares 2,433 core genes with 23 other B. siamensis genomes, whereas this isolate possesses 160 unique genes, accounting for 4.28% of its genome. The isolate grew optimally in neutral environments, tolerated alkaline pH and 10% NaCl, formed biofilms, showed no hemolysis, and secreted proteases, lipases, cellulases, and amylases. The ethyl acetate extract demonstrated antibacterial activity against Vibrio azureus, Vibrio sinaloensis, Vibrio neocaledonicus, Vibrio alginolyticus, and Vibrio parahaemolyticus with inhibition zones measuring 15.7-24.3 mm in diameter. These results underscore the promise of this Bacillus strain as a probiotic against pathogenic Vibrio in aquaculture.