Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil

Abstract

One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison and analysis of orthologous genes carried out between B. subtilis MJ01, reference strain B. subtilis subsp. subtilis str. 168, and close relative spizizenii TU-B-10 by microscope platform and various bioinformatics tools. More than 88% of 4269 predicted coding sequences in MJ01 had at least one similar sequence in genome of reference strain and spizizenii TU-B-10. Despite this high similarity, some differences were detected among encoding sequences of non-ribosome protein and bacteriocins in MJ01 and spizizenii TU-B-10. MJ01 has unique nucleotide sequences and a novel predicted lasso-peptide bacteriocin; it also has not any similar nucleotide sequence in non-redundant nucleotide data base.

Companion Animals Are Spillover Hosts of the Multidrug-Resistant Human Extraintestinal Escherichia coli Pandemic Clones ST131 and ST1193

“…The resulting FASTQ files were trimmed using CLC Genomics Workbench (QIAGEN Version 12), with a quality limit of 0.01, and reads with an ambiguous base were trimmed (ambiguous limit = 1). De novo assembly for each isolate was also performed using the CLC Genomics Workbench, using the default settings ( Rahimi et al, 2018 ). WGS analysis was undertaken using web-based tools available at the Centre for Genome Epidemiology (CGE) and custom BLAST databases implemented in the CLC Genomics Workbench (see Supplementary Material B ).…”

Comparative Genome Characterization of a Petroleum-Degrading Bacillus subtilis Strain DM2

“…B. subtilis B-1 is a petroleum-degrading and biofilm-producing strain isolated from the oil field biofilms [21]. B. subtilis MJ01 is also a petroleum-degrading strain isolated from oil-contaminated soil [12]. B. subtilis TO-A JPC is a probiotic strain isolated from a probiotic drug Vibact® [13].…”

“…Bacillus subtilis , an extensively studied gram-positive model bacterial species in the Bacillus genus, has been isolated from a variety of distinct environments, such as diverse soils and waters [2, 3], fermented foods [4], marine sand [5], rumen and intestinal tract [6], and plant endophytic bacteria [7, 8]. The versatile physiological functions of this bacterium have been explored for industrial production [9], bioremediation of polluted environment [10–12], plant growth promotion and pathogen control [7], and even for use as probiotics for humans [13]. The diverse habitats of these strains reflect versatile metabolic pathways and a robust capacity of environmental adaptation of a widely distributed species [3, 14].…”

“…The B-1 genome displays 50% sequence homology with that of the model laboratory strain B. subtilis 168. Another B. subtilis strain, MJ01, was isolated from oil-contaminated soil and evaluated as a new biosurfactant-producing strain [12]. Digital DNA-DNA hybridization showed the most similarity (94.7%) with the genome of B. subtilis subsp .…”

Comprehensive genomic analysis of Bacillus subtilis 9407 reveals its biocontrol potential against bacterial fruit blotch

“…The development of genome sequencing technology and bioinformatic analysis have made it convenient to obtain genomic information on B. subtilis, allowing us to comprehensively understand its life activities (Moszer 1998). Genomic comparison of different B. subtilis strains can elucidate the genetic variation, evolutionary classification, and genomic diversity of this species (Rahimi et al 2018). To date, the genome sequences of 389 strains of B. subtilis have been deposited in the National Center for Biotechnology Information (NCBI) genome assembly database.…”