Genomic and Phenotypic Characterization of the Probiotic Potential and Safety of Bacillus velezensis CH3-2 Isolated from Chahua Chicken
摘要
Bacillus velezensis has emerged as a promising probiotic alternative to antibiotics in the livestock industry. This study aimed to comprehensively evaluate the probiotic potential and safety of B. velezensis CH3-2, a strain isolated from the feces of Chahua chicken, using a combined phenotypic and genomic strategy. Whole-genome sequencing yielded a 3.91 Mb circular chromosome with no plasmids. Strain CH3-2 exhibited high tolerance to simulated gastrointestinal fluids, after sequential exposure to simulated gastric fluid (4 h) and intestinal fluid (4 h), the viable cell count remained at 6.69 log CFU/mL. These phenotypes were corroborated by the genomic identification of acid tolerance genes (e.g., atpA-atpH) and bile salt efflux transporter genes (e.g., dppB1-E). The strain demonstrated high cell surface hydrophobicity (> 79%) and time-dependent auto-aggregation (77.68% at 20 h), indicating strong adhesion potential supported by genes encoding moonlighting proteins and lipoteichoic acid synthase. Furthermore, CH3-2 displayed significant broad-spectrum antimicrobial activity against Escherichia coli K88, Shigella sonnei CMCC51592, and Listeria monocytogenes BNCC33687. Genome mining revealed 13 secondary metabolite biosynthetic gene clusters, such as those for macrolactin H and fengycin, providing a molecular basis for its antagonism. Additionally, the strain produced exopolysaccharides (0.70 mg/mL at 30 h) and exhibited strong extracellular antioxidant activity. Safety assessments confirmed that CH3-2 is non-hemolytic, does not produce biogenic amines, and lacks virulence genes. Six intrinsic, chromosomally encoded antibiotic resistance genes were identified, posing no risk of horizontal transfer. Acute oral toxicity tests in mice further indicated its preliminary in vivo safety, with no adverse effects on growth or histopathology. Collectively, these findings confirm that B. velezensis CH3-2 is a safe and robust candidate for development as a functional probiotic.