Multi-omics characterization of a rhizosphere-derived Bacillus cereus CBS-B5 strain reveals genomic stability, metabolic versatility, and biosafety-related genomic features for agricultural applications

Abstract

Introduction Bacillus cereus strains have potential plant growth-promoting properties but may harbor virulence and antimicrobial resistance (AMR) determinants. This study characterized the rhizosphere-derived B. cereus CBS-B5 strain to assess its functional potential and biosafety-related features. Methods CBS-B5, isolated from sugar beet rhizosphere, was characterized using an integrated multi-omics approach combining phenotypic assays, whole-genome sequencing, phylogenomic and comparative genomic analyses, and metabolomic profiling. Results CBS-B5 exhibited visible growth under elevated salinity conditions, demonstrated recovery following heat stress exposure, and strong biofilm formation, but no detectable phosphate solubilization. Whole-genome sequencing revealed a 5.02 Mb genome with 35% GC content, 100% completeness, and 0.03% contamination. Phylogenomic analysis placed CBS-B5 within the B. cereus group. Comparative genomic and functional analyses indicated genomic stability, metabolic versatility, stress-adaptation potential, and diverse biosynthetic gene clusters. Genome plasticity was supported by the presence of mobile genetic elements and horizontal gene transfer events affecting approximately 16% of the proteome. Metabolomic analysis confirmed active metabolic processes, including nitrogen recycling, osmoprotection, and transformation of plant-derived compounds under laboratory conditions. Although virulence-associated genes, including nheABC, cytK , and inhA , and β-hemolytic activity were detected, AMR and virulence determinants showed limited potential for horizontal dissemination. Similarly, AMR genes exhibited low mobility potential and minimal phenotypic resistance beyond intrinsic traits. Discussion Overall, CBS-B5 combines genomic stability, metabolic flexibility, and ecological adaptability. From a One Health perspective, the genomic analyses suggest a limited potential for horizontal dissemination of antimicrobial resistance and virulence determinants. However, the presence of chromosomally encoded toxin-associated genes and β-hemolytic activity indicates that additional biosafety evaluation is required before agricultural application.