Comprehensive genome-based characterization and pan-genome analysis of Bacillus paranthracis SM02 isolated from a...

Fermented foods represent complex microbial ecosystems in which spore-forming Bacillus species persist due to their stress tolerance and metabolic versatility. In the present study, whole-genome sequencing was applied to characterize Bacillus paranthracis SM02, a strain isolated from a traditional fermented sword bean food, with the aim of resolving its taxonomic position and genomic features related to adaptation and biosafety. Whole genome sequencing generated a 5.50 Mb draft genome assembled into 65 contigs with an N50 of 257,567 bp and a GC content of 35.13%, comprising 5,567 predicted protein-coding genes. Average nucleotide identity values exceeding 95% with reference genomes and phylogenomic analysis based on conserved orthologs confirmed the placement of SM02 within the B. paranthracis lineage. Genome annotation identified 35 AMR genes, including putative resistance determinants such as fosB and bcrA-C, along with conserved antibiotic target-associated genes such as gyrA, gyrB, rpoB, and mprF. These findings represent genomic predictions and do not by themselves establish phenotypic antimicrobial resistance. Virulence-associated genes such as nheA, nheB, nheC, alo, inhA, codY, and sigB, along with oxidative stress response genes (sodA, sodC), were detected. Genes linked to biofilm-associated lifestyles, including luxS, lsrR, rpoN, hfq, and polysaccharide metabolism genes (glgA, glgC), were also present. Pan-genome analysis of sixteen B. paranthracis genomes revealed an open pan-genome comprising approximately 7,500-8,000 gene families with a conserved core of nearly 3,900 gene families, while SM02 contained 1,086 accessory and 133 strain-specific genes. Overall, the results revealed a conserved genomic backbone coupled with a flexible accessory genome, suggesting genomic features that may contribute to adaptation within the fermented food environment.