Complete genome sequence and comparative analysis of two potential probiotics Bacillus subtilis isolated from honey and honeybee microbiomes

Abstract

Background: We have previously isolated Bacillus subtilis HMNig-2 and MENO2 strains, from honey and the honeybee gut microbiome respectively, and demonstrated these strains to produce levansucrase with potential probiotics characteristics. Here we report their complete genome sequence and comparative analysis with other and other B. subtilis strains.

Results: The complete genome sequences of Bacillus subtilis HMNig-2 and MENO2 were de novo assembled from MiSeq paired-end sequence reads and annotated using the RAST tool. Whole-genome alignments were performed to identify functional differences associated with their potential use as probiotics.

Conclusions: The comparative analysis and the availability of the genome sequence of these two strains will provide comprehensive analysis about the diversity of these valuable Bacillus strains and the possible impact of the environment on bacterial evolution.

Significance and impact of study: We introduce complete genome sequence of two new B. subtilis strains HMNig-2 and MENO2 with probiotic potential and as cell factories for the production of levan and other valuable components for pharmaceutical and industrial applications.

Keywords: Bacillus subtilis; Genome sequence; Honey; Honeybee; Probiotics.

Fig. 1

Neighbor-joining phylogenetic tree of the B. subtilis HMNig-2 and MENO2 genome, their closest neighbors from other B. subtilis strains are shown. Accession numbers are given in parentheses. Phylogenetic analysis was performed using MEGA7

Fig. 2

a Visualizing features, ORFs, start and stop codons of B. subtilis HMNig-2 genome, and comparing the sequence with proteins encoded by other B. subtilis. This map was generated by CGview. The first and second [outermost] rings show the locations of protein coding, tRNA, and rRNA genes on the forward and reverse strands, respectively. All subsequent rings, with the exception of the two innermost plots, display regions of similarity detected using BLAST [E value = 0.1] between the HMNig-2 genome sequence and the genome sequences of several related sequences [n = 100]. Regions of similarity are colored based on the percent identity between the aligned sequence segments. The black plot depicts GC content with the peaks extending towards the outside of the circle representing GC content above the genome average, whereas those extending towards the center mark segments with GC content lower than the genome average. The innermost plot depicts GC skew. Both base composition plots were generated using a sliding window of 50,000 nt. b Visualizing features, ORFs, start and stop codons of B. subtilis MENO2 genome, and comparing the sequence with proteins encoded by other B. subtilis. This map was generated by CGview. The first and second [outermost] rings show the locations of protein coding, tRNA, and rRNA genes on the forward and reverse strands, respectively. All subsequent rings, with the exception of the two innermost plots, display regions of similarity detected using BLAST [E value = 0.1] between the MENO2 genome sequence and the genome sequences of several related sequences [n = 100]. Regions of similarity are colored based on the percent identity between the aligned sequence segments. The black plot depicts GC content with the peaks extending towards the outside of the circle representing GC content above the genome average, whereas those extending towards the center mark segments with GC content lower than the genome average. The innermost plot depicts GC skew. Both base composition plots were generated using a sliding window of 50,000 nt

Fig. 3

Phylogenetic analysis based on the levansucrase encoded by sacB gene, their closest neighbors from other B. subtilis strains are shown. Accession numbers are given in parentheses. Phylogenetic analysis was performed using MEGA7