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Comparative Study
. 2019 Dec 17;9(1):19254.
doi: 10.1038/s41598-019-55726-2.

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

G Othoum  1 , S Prigent  2 , A Derouiche  2 , L Shi  2 , A Bokhari  3 , S Alamoudi  4 , S Bougouffa  1 , X Gao  1 , R Hoehndorf  1 , S T Arold  1 , T Gojobori  1   3 , H Hirt  3 , F F Lafi  1   5 , J Nielsen  2   6   7 , V B Bajic  1 , I Mijakovic  8   9 , M Essack  10
Affiliations
Comparative Study

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

G Othoum et al. Sci Rep. .

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.

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Conflict of interest statement

V.B.B. is an editorial board member of the Scientific Reports journal. All other authors declare no competing interests.

Figures

Figure 1
Figure 1
Phylogenetic tree of the ten Red Sea strains and 30 other species. The Red Sea species are displayed in grey while other previously sequenced strains are displayed in black.
Figure 2
Figure 2
Evaluation of sporulation (A) and protein secretion (B) in the Red Sea strains through gene prediction and in vitro measurements. Strains with the third TatA subunit missing, are indicated with *.
Figure 3
Figure 3
Metabolic networks reconstruction. The left part of the figure corresponds to the number of reactions present in the metabolic networks. The right part of the figure corresponds to a clustering performed on the 32 species based on the presence and absence of reactions. The 32 species have been divided into seven metabolic clades based on this clustering.
Figure 4
Figure 4
Number of predicted secondary metabolic gene clusters in the genomes of the Red Sea strains (red) and 22 other Bacillus genomes (blue).
Figure 5
Figure 5
Co-localization of gene clusters using the normalized position for each SMGC based on the length of the chromosome and the position of the middle of the SMGC. Plain lines join co-localized SMGCs, dotted lines join SMGCs that are not co-localized.
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