Whole Genome Sequencing-based Genetic Characterization and Safety Assessment of Probiotic Bacillus subtilis strain PLSSC

Abstract

Varieties of microbes are beneficial to humans. Probiotic microbes act by balancing the microbial flora in the gut. Whole genome sequencing (WGS) technique has been used to identify and characterize novel microbes. In the present study, genetic characterization of probiotic Bacillus subtilis (B. subtilis) strain PLSSC was carried out by WGS. A single scaffold of 4,204,670 bp size having 43.58 mol% G+C was derived by using both short reads and long reads generated by Illumina and Nano-pore respectively. Gene annotation by Prokaryotic Genome annotation pipeline (PGAP) resulted in identification of 4296 coding sequences (CDS), 86 tRNAs, 30 rRNAs and 5 ncRNA. BLASTN of assembled genome revealed that B. subtilis KCTC 3135 is the closest strain showing ~99% identity. Analysis of assembled PLSSC genome for the genes related to safety such as antibiotic resistance, virulence factors and toxins revealed that none of the identified genes pose risk to human health. Presence of clustered regularly interspaced short palindromic repeats (CRISPR) and lack of functional prophage sequences appeared to be advantageous in maintaining the genome stability. Additionally, presence of genes contributing to probiotic properties such as acid and bile salt tolerance, anchoring to the gut mucosa and anti-microbial activity in the PLSSC genome ensure strain survivability thereby increasing their colonization and reducing pathogenic adherence in the gut. Overall, genomic analysis strongly suggests that B. subtilis strain PLSSC is a safe strain and can be used as a probiotic.