Whole-Genome analysis of Bacillus subtilis MBBL2 genomic characterization and comparative genomics

Abstract

This study presents the whole-genome sequencing and comprehensive analysis of Bacillus subtilis MBBL2, a strain isolated from soil samples in Lahore, Pakistan. The genome consists of 4,574,405 base pairs, with a GC content of 42.99%, and is assembled into 908 contigs. Using a range of bioinformatics tools, we performed genome assembly, functional annotation, secondary metabolite biosynthesis prediction, antimicrobial resistance (AMR) gene identification, and CRISPR array detection. The genome was initially assembled, achieving an average coverage of 126.534x, and its quality was also assessed to ensure completeness. Prokka was used to annotate 5,392 genes, including 5,033 protein-coding sequences, tRNAs, and rRNAs. Secondary metabolite biosynthesis clusters were identified revealing several important clusters involved in riboflavin, vitamin B6 biosynthesis, and antimicrobial peptide production via non-ribosomal peptide synthetase (NRPS). Notably, a novel bacteriocin gene cluster was detected, suggesting the strain’s potential as a source of antimicrobial peptides. AMR genes were identified highlighting resistance to various antibiotics. CRISPR arrays were also analyzed indicating the strain’s adaptive immune system. Genomic comparisons provided insights into the genetic diversity and evolutionary relationships of Bacillus subtilis strains. This study reveals the potential of B. subtilis MBBL2 as a probiotic in aquaculture, with applications in sustainable practices such as biocontrol. The findings contribute valuable genomic resources to the B. subtilis research community and open avenues for future biotechnological applications.