Complete genome sequence and functional characterization of Bacillus amyloliquefaciens NJF-55: a sheep-derived probiotic candidate

Bacillus amyloliquefaciens strain NJF-55, which was isolated from the distal colon of a healthy ram, was investigated as a probiotic candidate. We produced a high-quality assembly comprising a single circular chromosome (3,854,703 bp; 46.1% GC) and a small plasmid (6033 bp), and reconciled multi pipeline annotations to derive a consensus feature set. Functional profiling mapped 2334 genes to 2027 KEGG orthologs (1835 unique), indicating complete central metabolism, broad transport capacity, and stress-adaptation pathways; 94 CAZymes supported glycan turnover and cell-envelope remodeling. Secondary-metabolite mining revealed hallmark Bacillus BGCs—surfactin, fengycin, bacillaene, and macrolactin—and flagged putative novel compounds (a PKS-like region with ~ 7% similarity to the butirosin A/B reference); Five bacteriocin/RiPP regions were identified (class IV lanthipeptide, amylocyclicin, ComX2 pheromone, UviB-like and colicin-like). Genome-safety screening detected no classical virulence determinants or acquired clinically relevant AMR genes; four intact prophages lacked toxin/AMR cargo, and the plasmid encoded no risk loci. Comparative genomics with four reference bacilli yielded a 5,398-cluster pangenome; NJF-55 retained 325 probiotic-associated clusters (largely core) and showed 30 copy-number expansions, notably in the NRPS/PKS and DNA replication/repair families, consistent with a “core-driven, dosage-tuned” architecture. These features suggest that NJF-55 may represent a safe and robust candidate for ruminant gut applications, while underscoring the need for targeted metabolomics and controlled in vivo validation.