Functional Microbes from Traditional Fermented Food: Genomics, Lipopeptide Profiling and Antimicrobial Potential of Bacillus velezensis R125

Traditional fermented foods harbor functional microorganisms with antimicrobial potential. This study isolated strain Bacillus velezensis R125 GDMCC 67536 from sour porridge in Guangxi, China, which uniquely exhibited broad-spectrum activity against Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 25923, and Fusarium oxysporum f. sp. cubense race 1 201 among 24 isolates. The strain was identified through phenotypic analysis, 16S rRNA gene sequencing (99.59% identity to the type strain), and whole-genome OrthoANI comparison (97.78% similarity to strain B. amyloliquefaciens subsp. plantarum FZB42 ^T , and 99.59% identity to the type strain B. velezensis NRRL B-41580 ^T ). Hybrid sequencing (Illumina HiSeq and PacBio) yielded a complete genome consisting of a circular chromosome (3,970,649 bp, 46.56% GC content) and a circular plasmid (5,981 bp, 52.88% GC content), harboring 3,808 protein-coding genes. Functional annotation using GO, COG, and KEGG databases revealed considerable metabolic versatility, including 51 genes encoding carbohydrate-active enzymes (CAZymes). AntiSMASH analysis predicted 13 biosynthetic gene clusters (BGCs) for secondary metabolites, such as surfactin, fengycin, bacilysin, and macrolactin H. Comparative genomic analysis with strain B. amyloliquefaciens subsp. plantarum FZB42 ^T , strain B. amyloliquefaciens DSM 7, and strain B. subtilis 168 ^T indicated that eight BGCs are conserved within the core genome, while five BGCs with low similarity to known clusters appear to be strain-specific, suggesting adaptive divergence. Notably, strain R125 possesses a significantly higher abundance of GH5 family cellulase genes—a genomic feature potentially reflective of adaptation to a plant-derived fermentation substrate. High-performance liquid chromatography-mass spectrometry (HPLC-MS) confirmed the production of three principal lipopeptides: iturin (30.31%), fengycin (22.42%), and surfactin (14.8%). This study elucidates the genomic and metabolomic basis of antimicrobial activity in strain B. velezensis R125 GDMCC 67536, and identifies three strain-specific novel BGCs and a unique GH5 cellulase gene enrichment characteristic associated with fermentation substrate adaptation; the quantitative synergy pattern of its lipopeptides (Iturin > Fengycin > Surfactin) is first reported to mediate broad-spectrum antimicrobial activity, providing experimental basis for the directional utilization of B. velezensis in food preservation and biocontrol.