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    In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

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    Type
    Article
    Authors
    Othoum, Ghofran K. cc
    Bougouffa, Salim cc
    Mohamad Razali, Rozaimi cc
    Bokhari, Ameerah cc
    Alamoudi, Soha
    Antunes, André
    Gao, Xin cc
    Hoehndorf, Robert cc
    Arold, Stefan T. cc
    Gojobori, Takashi cc
    Hirt, Heribert cc
    Mijakovic, Ivan
    Bajic, Vladimir B. cc
    Lafi, Feras Fawzi
    Essack, Magbubah cc
    KAUST Department
    Applied Mathematics and Computational Science Program
    Bio-Ontology Research Group (BORG)
    Bioinformatics
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Chemical Engineering Program
    Competitive Research Funds
    Computational Bioscience Research Center (CBRC)
    Computer Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Desert Agriculture Initiative
    Hirt Lab
    OCRF- Special Academic Partnership
    Physical Science and Engineering (PSE) Division
    Plant Science
    Structural Biology and Engineering
    Structural and Functional Bioinformatics Group
    KAUST Grant Number
    FCC/1/1976–02-01
    FCS/1/2911–01-01
    BAS/1/1606–01-01
    URF/1/1976–06-01
    BAS/1/1624–01-01
    BAS/1/1659–01-01
    BAS/1/1059–01-01
    Date
    2018-05-22
    Online Publication Date
    2018-05-22
    Print Publication Date
    2018-12
    Permanent link to this record
    http://hdl.handle.net/10754/627974
    
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    Abstract
    BackgroundThe increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions.ResultsWe report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species.ConclusionsB. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems.
    Citation
    Othoum G, Bougouffa S, Razali R, Bokhari A, Alamoudi S, et al. (2018) In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters. BMC Genomics 19. Available: http://dx.doi.org/10.1186/s12864-018-4796-5.
    Sponsors
    The authors wish to acknowledge the experimental support from the King Abdullah University of Science and Technology (KAUST) Bioscience Core Laboratory. The research reported in this publication was supported by King Abdullah University of Science and Technology (KAUST) through the Awards Nos. FCC/1/1976–02-01, FCS/1/2911–01-01, BAS/1/1606–01-01, URF/1/1976–06-01, BAS/1/1624–01-01, BAS/1/1659–01-01, BAS/1/1059–01-01 from the Office of Sponsored Research (OSR).
    Publisher
    Springer Nature
    Journal
    BMC Genomics
    DOI
    10.1186/s12864-018-4796-5
    Additional Links
    https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4796-5
    Relations
    Is Supplemented By:
    • [Dataset]
      . DOI: 10.6084/m9.figshare.6319310 HANDLE: 10754/664123
    Is Supplemented By:
    • [Dataset]
      . DOI: 10.6084/m9.figshare.c.4108970 HANDLE: 10754/664135
    ae974a485f413a2113503eed53cd6c53
    10.1186/s12864-018-4796-5
    Scopus Count
    Collections
    Articles; Bio-Ontology Research Group (BORG); Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Applied Mathematics and Computational Science Program; Physical Science and Engineering (PSE) Division; Structural and Functional Bioinformatics Group; Computer Science Program; Chemical Engineering Program; Computational Bioscience Research Center (CBRC); Desert Agriculture Initiative; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

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