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<p>Probiotic <i>Bacillus</i> species are being investigated as sustainable interventions to enhance health and disease resilience in aquaculture. However, the functional basis, biosafety profile, and genomic determinants of probiotic suitability in shrimp gut-associated <i>Bacillus</i> strains remain insufficiently characterized. In this study, a <i>Bacillus</i> strain (KNSH39) isolated from the intestine of Pacific white shrimp (<i>Litopenaeus vannamei</i>) was evaluated using integrated phenotypic, functional, and genome-resolved approaches. Classical assays assessed morphology, sporulation, antibiotic susceptibility, gastrointestinal tolerance, storage stability, and antibacterial activity of cell-free supernatant under thermal and pH stress. Hybrid whole-genome sequencing using Oxford Nanopore Technologies and Illumina platforms enabled high-quality assembly, followed by comprehensive functional annotation, mobilome analysis, biosynthetic gene cluster prediction, and comparative genomics. KNSH39 exhibited strong sporulation capacity (98.04%), a non-hemolytic phenotype, high tolerance to acidic and bile conditions, and formulation-dependent storage stability, with gel-bead encapsulation markedly improving viability. Cell-free supernatant inhibited <i>Streptococcus agalactiae</i> and <i>Aeromonas hydrophila</i> in a concentration-, time-, temperature-, and pH-dependent manner, retaining activity after heating to 120&#xa0;°C. Genome analysis revealed a 5.49 Mb <i>Bacillus cereus</i>–group genome with complete central metabolic pathways, extensive quorum sensing systems, diverse secondary metabolite biosynthetic gene clusters, and an open pangenome structure. Collectively, these findings suggest that KNSH39 strain presents as a promising aquaculture probiotic candidate, exhibiting thermally stable antibacterial potential and well-defined genomic attributes.</p>

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Comprehensive characterization and genome-resolved insights into the probiotic potential of Bacillus sp. KNSH39 isolated from Litopenaeus vannamei intestine

  • 期刊论文

  • 发表日期：

    2026年4月27日

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  • Patima Permpoonpattana,
  • Sk Injamamul Islam,
  • Luu Tang Phuc Khang,
  • Orathai Dangsawat,
  • Papungkorn Sangsawad,
  • Shu-Dan Yeh,
  • Kritsada Phetduang,
  • Phatthanaphong Therdtatha,
  • Sarayut Onsanit,
  • Nguyen Vu Linh

摘要

Probiotic Bacillus species are being investigated as sustainable interventions to enhance health and disease resilience in aquaculture. However, the functional basis, biosafety profile, and genomic determinants of probiotic suitability in shrimp gut-associated Bacillus strains remain insufficiently characterized. In this study, a Bacillus strain (KNSH39) isolated from the intestine of Pacific white shrimp (Litopenaeus vannamei) was evaluated using integrated phenotypic, functional, and genome-resolved approaches. Classical assays assessed morphology, sporulation, antibiotic susceptibility, gastrointestinal tolerance, storage stability, and antibacterial activity of cell-free supernatant under thermal and pH stress. Hybrid whole-genome sequencing using Oxford Nanopore Technologies and Illumina platforms enabled high-quality assembly, followed by comprehensive functional annotation, mobilome analysis, biosynthetic gene cluster prediction, and comparative genomics. KNSH39 exhibited strong sporulation capacity (98.04%), a non-hemolytic phenotype, high tolerance to acidic and bile conditions, and formulation-dependent storage stability, with gel-bead encapsulation markedly improving viability. Cell-free supernatant inhibited Streptococcus agalactiae and Aeromonas hydrophila in a concentration-, time-, temperature-, and pH-dependent manner, retaining activity after heating to 120 °C. Genome analysis revealed a 5.49 Mb Bacillus cereus–group genome with complete central metabolic pathways, extensive quorum sensing systems, diverse secondary metabolite biosynthetic gene clusters, and an open pangenome structure. Collectively, these findings suggest that KNSH39 strain presents as a promising aquaculture probiotic candidate, exhibiting thermally stable antibacterial potential and well-defined genomic attributes.