Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

Abstract

Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment.

Super protective anti-bacterial coating development with silica–titania nano core–shells

“…Bacillus species frequently occur in chains and cause skin infection. 10,11 As such, antibacterial coatings are needed for dened surfaces.…”

Hemicellulosic biomass conversion by Moroccan hot spring Bacillus paralicheniformis CCMM B940 evidenced by glycoside hydrolase activities and whole genome sequencing

“…gov) using the BLAST service deployed on local servers with the genome obtained sequences and fastANI (Jain et al 2018). The draft genome was most closely related to B. paralicheniformis Bac84 (accession number ASM299392v1) living in sea environment (Othoum et al 2019) (Fan et al 2017). Taxonomic identity of the CCMM B940 strain was also confirmed using the GTDB-Tk tool for genome classification (Chaumeil et al 2020) with 98.95% identity to the B. paralicheniformis KJ-16 genome (accession number ASM104248v2).…”

“…Species identity was confirmed by comparing the genome reference sequences of B. licheniformis and Bacillus paralicheniformis available in the NCBI database ( https://www.ncbi.nlm.nih.gov ) using the BLAST service deployed on local servers with the genome obtained sequences and fastANI (Jain et al 2018 ). The draft genome was most closely related to B. paralicheniform is Bac84 (accession number ASM299392v1) living in sea environment (Othoum et al 2019 ) with an ANI value of 98.94%, and shared only 94.36% identity with B. licheniformis DSM 13 T (NC_006270.3). B. aerius CCMM B940 was, therefore, reclassified as B. paralicheniformis CCMM B940, placing it in the B. subtilis group; a group known for its wide array of uses in biotechnology mainly through species like B. subtilis and B. licheniformis (Fan et al 2017 ).…”

Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives

“…In another study, ref. [82] demonstrated the potential of two more Red Sea strains B. paralicheniformis (Bac48) and B. halosaccharovorans (Bac94), which are capable of secreting twice as much protein as the model strain B. subtilis 168. The strain Bac94 was shown to be enriched with genes associated with the Tat and Sec protein secretion system, hence making it a promising system for recombinant protein expression work.…”