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<p>This study describes the genomic features of <i>Bacillus subtilis</i> B13 (= VTCC 910231) to elucidate the genetic basis underlying its reported antimicrobial activity, metabolic versatility, and environmental adaptability. The draft genome comprised 4,349,051&#xa0;bp with a GC content of 43.5% and 4436 predicted coding sequences. Genome-based analyses assigned B13 to <i>B. subtilis</i> subsp. <i>subtilis</i>, supported by high average nucleotide identity (98.3%) and digital DNA-DNA hybridization (99.7–99.8%) values. Genome mining identified one gene cluster encoding an unidentified sactipeptide along with seven biosynthetic clusters involved in the production of compounds with potential antibacterial activity, including fengycin, surfactin, bacillaene, bacillibactin, bacilysin, subtilosin A, and sporulation-killing factor. These clusters may contribute to its observed bioactive properties. Comparative pan-genome analysis suggested an open genomic architecture dominated by accessory genes, with B13 harboring 67 unique gene clusters at the species level and 336 strain-specific gene clusters in a niche-focused dataset, most of which remain functionally uncharacterised. The annotated genes are associated with environmental adaptation. The genome revealed mobile elements, indicating genome plasticity and potential horizontal gene transfer, but no plasmids were detected. Three high-confidence genomic islands (251&#xa0;kb, 5.8% of the genome) contained mobility-related genes but lacked a virulence gene cluster and antibiotic resistance genes. Functional profiling explored a collection of genes associated with stress response, signal transduction, transport, motility, chemotaxis, and DNA repair. These findings provide insights into genomic features related to the biosynthetic potential, genomic plasticity, and safety profile of B13, and suggest putative determinants of environmental adaptation, while reflecting pan-genome diversity in strain-specific traits.</p>

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Genomic and pan-genomic analyses of Bacillus subtilis B13 provide insights into biosynthetic potential and genetic traits associated with environmental adaptation

  • 期刊论文

  • 发表日期：

    2026年7月29日

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  • Co Thi Kim Nguyen,
  • Hung Tan Dinh,
  • Dat Quoc Bui Dang,
  • Hoang Huy Le,
  • Hoang Duc Nguyen

摘要

This study describes the genomic features of Bacillus subtilis B13 (= VTCC 910231) to elucidate the genetic basis underlying its reported antimicrobial activity, metabolic versatility, and environmental adaptability. The draft genome comprised 4,349,051 bp with a GC content of 43.5% and 4436 predicted coding sequences. Genome-based analyses assigned B13 to B. subtilis subsp. subtilis, supported by high average nucleotide identity (98.3%) and digital DNA-DNA hybridization (99.7–99.8%) values. Genome mining identified one gene cluster encoding an unidentified sactipeptide along with seven biosynthetic clusters involved in the production of compounds with potential antibacterial activity, including fengycin, surfactin, bacillaene, bacillibactin, bacilysin, subtilosin A, and sporulation-killing factor. These clusters may contribute to its observed bioactive properties. Comparative pan-genome analysis suggested an open genomic architecture dominated by accessory genes, with B13 harboring 67 unique gene clusters at the species level and 336 strain-specific gene clusters in a niche-focused dataset, most of which remain functionally uncharacterised. The annotated genes are associated with environmental adaptation. The genome revealed mobile elements, indicating genome plasticity and potential horizontal gene transfer, but no plasmids were detected. Three high-confidence genomic islands (251 kb, 5.8% of the genome) contained mobility-related genes but lacked a virulence gene cluster and antibiotic resistance genes. Functional profiling explored a collection of genes associated with stress response, signal transduction, transport, motility, chemotaxis, and DNA repair. These findings provide insights into genomic features related to the biosynthetic potential, genomic plasticity, and safety profile of B13, and suggest putative determinants of environmental adaptation, while reflecting pan-genome diversity in strain-specific traits.