Metagenomics as a preliminary screen for antimicrobial bioprospecting

Handle URI:
http://hdl.handle.net/10754/622014
Title:
Metagenomics as a preliminary screen for antimicrobial bioprospecting
Authors:
Al Amoudi, Soha ( 0000-0003-1028-7634 ) ; Razali, Rozaimi; Essack, Magbubah ( 0000-0003-2709-5356 ) ; Amini, Mohammad Shoaib; Bougouffa, Salim ( 0000-0001-9218-6452 ) ; Archer, John A.C. ( 0000-0002-3302-3933 ) ; Lafi, Feras Fawzi; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
Since the composition of soil directs the diversity of the contained microbiome and its potential to produce bioactive compounds, many studies has been focused on sediment types with unique features characteristic of extreme environments. However, not much is known about the potential of microbiomes that inhabit the highly saline and hot Red Sea lagoons. This case study explores mangrove mud and the microbial mat of sediments collected from the Rabigh harbor lagoon and Al Kharrar lagoon for antimicrobial bioprospecting. Rabigh harbor lagoon appears the better location, and the best sediment type for this purpose is mangrove mud. On the other hand, Al Kharrar lagoon displayed increased anaerobic hydrocarbon degradation and an abundance of bacterial DNA associated with antibiotic resistance. Moreover, our findings show an identical shift in phyla associated with historic hydrocarbon contamination exposure reported in previous studies (that is, enrichment of Gamma-and Delta-proteobacteria), but we also report that bacterial DNA sequences associated with antibiotic synthesis enzymes are derived from Gamma-, Delta-and Alpha-proteobacteria. This suggests that selection pressure associated with hydrocarbon contamination tend to enrich the bacterial classes DNA associated with antibiotic synthesis enzymes. Although Actinobacteria tends to be the common target for research when it comes to antimicrobial bioprospecting, our study suggests that Firmicutes (Bacilli and Clostridia), Bacteroidetes, Cyanobacteria, and Proteobacteria should be antimicrobial bioprospecting targets as well. To the best of our knowledge, this is the first metagenomic study that analyzed the microbiomes in Red Sea lagoons for antimicrobial bioprospecting. (C) 2016 The Authors. Published by Elsevier B.V.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Al-Amoudi S, Razali R, Essack M, Amini MS, Bougouffa S, et al. (2016) Metagenomics as a preliminary screen for antimicrobial bioprospecting. Gene 594: 248–258. Available: http://dx.doi.org/10.1016/j.gene.2016.09.021.
Publisher:
Elsevier BV
Journal:
Gene
KAUST Grant Number:
URF/1/1976-02; FCS/1/2448-01
Issue Date:
16-Sep-2016
DOI:
10.1016/j.gene.2016.09.021
Type:
Article
ISSN:
0378-1119
Sponsors:
This publication is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Awards No URF/1/1976-02 and FCS/1/2448-01.
Additional Links:
http://www.sciencedirect.com/science/article/pii/S037811191630748X
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorAl Amoudi, Sohaen
dc.contributor.authorRazali, Rozaimien
dc.contributor.authorEssack, Magbubahen
dc.contributor.authorAmini, Mohammad Shoaiben
dc.contributor.authorBougouffa, Salimen
dc.contributor.authorArcher, John A.C.en
dc.contributor.authorLafi, Feras Fawzien
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2016-12-13T13:46:39Z-
dc.date.available2016-12-13T13:46:39Z-
dc.date.issued2016-09-16en
dc.identifier.citationAl-Amoudi S, Razali R, Essack M, Amini MS, Bougouffa S, et al. (2016) Metagenomics as a preliminary screen for antimicrobial bioprospecting. Gene 594: 248–258. Available: http://dx.doi.org/10.1016/j.gene.2016.09.021.en
dc.identifier.issn0378-1119en
dc.identifier.doi10.1016/j.gene.2016.09.021en
dc.identifier.urihttp://hdl.handle.net/10754/622014-
dc.description.abstractSince the composition of soil directs the diversity of the contained microbiome and its potential to produce bioactive compounds, many studies has been focused on sediment types with unique features characteristic of extreme environments. However, not much is known about the potential of microbiomes that inhabit the highly saline and hot Red Sea lagoons. This case study explores mangrove mud and the microbial mat of sediments collected from the Rabigh harbor lagoon and Al Kharrar lagoon for antimicrobial bioprospecting. Rabigh harbor lagoon appears the better location, and the best sediment type for this purpose is mangrove mud. On the other hand, Al Kharrar lagoon displayed increased anaerobic hydrocarbon degradation and an abundance of bacterial DNA associated with antibiotic resistance. Moreover, our findings show an identical shift in phyla associated with historic hydrocarbon contamination exposure reported in previous studies (that is, enrichment of Gamma-and Delta-proteobacteria), but we also report that bacterial DNA sequences associated with antibiotic synthesis enzymes are derived from Gamma-, Delta-and Alpha-proteobacteria. This suggests that selection pressure associated with hydrocarbon contamination tend to enrich the bacterial classes DNA associated with antibiotic synthesis enzymes. Although Actinobacteria tends to be the common target for research when it comes to antimicrobial bioprospecting, our study suggests that Firmicutes (Bacilli and Clostridia), Bacteroidetes, Cyanobacteria, and Proteobacteria should be antimicrobial bioprospecting targets as well. To the best of our knowledge, this is the first metagenomic study that analyzed the microbiomes in Red Sea lagoons for antimicrobial bioprospecting. (C) 2016 The Authors. Published by Elsevier B.V.en
dc.description.sponsorshipThis publication is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Awards No URF/1/1976-02 and FCS/1/2448-01.en
dc.publisherElsevier BVen
dc.relation.urlhttp://www.sciencedirect.com/science/article/pii/S037811191630748Xen
dc.rightsArchived with thanks to Gene. Under a Creative Commons license http://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectRed Seaen
dc.subjectLagoonen
dc.subjectMangroveen
dc.subjectMicrobial maten
dc.subjectBiodiversityen
dc.subjectMetagenomeen
dc.subjectAntimicrobialen
dc.subjectAntibioticen
dc.subjectBioactivityen
dc.subjectBioprospectingen
dc.subjectBiosynthetic genesen
dc.subjectEnvironmenten
dc.subjectBioinformaticsen
dc.titleMetagenomics as a preliminary screen for antimicrobial bioprospectingen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalGeneen
dc.eprint.versionPublisher's Version/PDFen
kaust.authorAl Amoudi, Sohaen
kaust.authorRazali, Rozaimien
kaust.authorEssack, Magbubahen
kaust.authorAmini, Mohammad Shoaiben
kaust.authorBougouffa, Salimen
kaust.authorArcher, John A.C.en
kaust.authorLafi, Feras Fawzien
kaust.authorBajic, Vladimir B.en
kaust.grant.numberURF/1/1976-02en
kaust.grant.numberFCS/1/2448-01en
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