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dc.contributor.authorOthoum, Ghofran K.
dc.contributor.authorBougouffa, Salim
dc.contributor.authorBokhari, Ameerah
dc.contributor.authorLafi, Feras Fawzi
dc.contributor.authorGojobori, Takashi
dc.contributor.authorHirt, Heribert
dc.contributor.authorMijakovic, Ivan
dc.contributor.authorBajic, Vladimir B.
dc.contributor.authorEssack, Magbubah
dc.date.accessioned2019-09-10T06:48:02Z
dc.date.available2019-09-10T06:48:02Z
dc.date.issued2019-09-05
dc.identifier.doi10.1186/s12864-019-6065-7
dc.identifier.urihttp://hdl.handle.net/10754/656705
dc.description.abstractBACKGROUND:Biosynthetic gene clusters produce a wide range of metabolites with activities that are of interest to the pharmaceutical industry. Specific interest is shown towards those metabolites that exhibit antimicrobial activities against multidrug-resistant bacteria that have become a global health threat. Genera of the phylum Firmicutes are frequently identified as sources of such metabolites, but the biosynthetic potential of its Virgibacillus genus is not known. Here, we used comparative genomic analysis to determine whether Virgibacillus strains isolated from the Red Sea mangrove mud in Rabigh Harbor Lagoon, Saudi Arabia, may be an attractive source of such novel antimicrobial agents. RESULTS:A comparative genomics analysis based on Virgibacillus dokdonensis Bac330, Virgibacillus sp. Bac332 and Virgibacillus halodenitrificans Bac324 (isolated from the Red Sea) and six other previously reported Virgibacillus strains was performed. Orthology analysis was used to determine the core genomes as well as the accessory genome of the nine Virgibacillus strains. The analysis shows that the Red Sea strain Virgibacillus sp. Bac332 has the highest number of unique genes and genomic islands compared to other genomes included in this study. Focusing on biosynthetic gene clusters, we show how marine isolates, including those from the Red Sea, are more enriched with nonribosomal peptides compared to the other Virgibacillus species. We also found that most nonribosomal peptide synthases identified in the Virgibacillus strains are part of genomic regions that are potentially horizontally transferred. CONCLUSIONS:The Red Sea Virgibacillus strains have a large number of biosynthetic genes in clusters that are not assigned to known products, indicating significant potential for the discovery of novel bioactive compounds. Also, having more modular synthetase units suggests that these strains are good candidates for experimental characterization of previously identified bioactive compounds as well. Future efforts will be directed towards establishing the properties of the potentially novel compounds encoded by the Red Sea specific trans-AT PKS/NRPS cluster and the type III PKS/NRPS cluster.
dc.description.sponsorshipThe authors wish to acknowledge the experimental support from the King Abdullah University of Science and Technology (KAUST) Bioscience Core Laboratory. We would also like to thank L’Oréal - UNESCO for awarding the first author (GO) the ‘For Women in Science fellowship’, as a recognition, partly, for this work.
dc.description.sponsorshipFunding : The authors wish to acknowledge the experimental support from the King Abdullah University of Science and Technology (KAUST) Bioscience Core Laboratory. We would also like to thank L’Oréal - UNESCO for awarding the first author (GO) the ‘For Women in Science fellowship’, as a recognition, partly, for this work.
dc.publisherSpringer Science and Business Media LLC
dc.relation.urlhttps://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6065-7
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/
dc.subjectVirgibacillus
dc.subjectAntimicrobial
dc.subjectBiosynthetic gene clusters
dc.subjectGenome-mining
dc.subjectNonribosomal peptides
dc.subjectPolyketides
dc.subjectBacteriocins
dc.subjectLanthipeptides
dc.subjectBioinformatics
dc.titleMining biosynthetic gene clusters in Virgibacillus genomes.
dc.typeArticle
dc.contributor.departmentChemical and Biological Engineering Program
dc.contributor.departmentBioinformatics
dc.contributor.departmentBioscience Program
dc.contributor.departmentCompetitive Research Funds
dc.contributor.departmentOCRF- Special Academic Partnership
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentDesert Agriculture Initiative
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentPlant Science
dc.contributor.departmentApplied Mathematics and Computational Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalBMC genomics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
dc.contributor.institutionCollege of Natural and Health Sciences, Zayed University, Abu-Dhabi, 144534, United Arab Emirates
dc.contributor.institutionDivision of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.
dc.contributor.institutionNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
kaust.personOthoum, Ghofran K
kaust.personBougouffa, Salim
kaust.personBokhari, Ameerah
kaust.personLafi, Feras Fawzi
kaust.personGojobori, Takashi
kaust.personHirt, Heribert
kaust.personBajic, Vladimir B.
kaust.personEssack, Magbubah
refterms.dateFOA2019-09-10T06:52:06Z
kaust.acknowledged.supportUnitBioscience Core Laboratory


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This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Except where otherwise noted, this item's license is described as This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.