Metagenomics as a preliminary screen for antimicrobial bioprospecting

Soha Al-Amoudi, Rozaimi Mohamad Razali, Magbubah Essack, Mohammad Shoaib Amini, Salim Bougouffa, John A.C. Archer, Feras F. Lafi, Vladimir B. Bajic

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)248-258
Number of pages11
JournalGene
Volume594
Issue number2
DOIs
Publication statusPublished - 15 Dec 2016
Externally publishedYes

Fingerprint

Metagenomics
Bacterial DNA
Microbiota
Hydrocarbons
Deltaproteobacteria
Indian Ocean
Bacteroidetes
Anti-Bacterial Agents
Alphaproteobacteria
Gammaproteobacteria
Proteobacteria
Clostridium
Actinobacteria
Cyanobacteria
Enzymes
Microbial Drug Resistance
Bacillus
Soil
Pressure
Bioprospecting

Keywords

  • Antibiotic
  • Antimicrobial
  • Bioactivity
  • Biodiversity
  • Bioinformatics
  • Bioprospecting
  • Biosynthetic genes
  • Environment
  • Lagoon
  • Mangrove
  • Metagenome
  • Microbial mat
  • Red Sea

ASJC Scopus subject areas

  • Genetics

Cite this

Al-Amoudi, S., Mohamad Razali, R., Essack, M., Amini, M. S., Bougouffa, S., Archer, J. A. C., ... Bajic, V. B. (2016). Metagenomics as a preliminary screen for antimicrobial bioprospecting. Gene, 594(2), 248-258. https://doi.org/10.1016/j.gene.2016.09.021

Metagenomics as a preliminary screen for antimicrobial bioprospecting. / Al-Amoudi, Soha; Mohamad Razali, Rozaimi; Essack, Magbubah; Amini, Mohammad Shoaib; Bougouffa, Salim; Archer, John A.C.; Lafi, Feras F.; Bajic, Vladimir B.

In: Gene, Vol. 594, No. 2, 15.12.2016, p. 248-258.

Research output: Contribution to journalArticle

Al-Amoudi, S, Mohamad Razali, R, Essack, M, Amini, MS, Bougouffa, S, Archer, JAC, Lafi, FF & Bajic, VB 2016, 'Metagenomics as a preliminary screen for antimicrobial bioprospecting', Gene, vol. 594, no. 2, pp. 248-258. https://doi.org/10.1016/j.gene.2016.09.021
Al-Amoudi S, Mohamad Razali R, Essack M, Amini MS, Bougouffa S, Archer JAC et al. Metagenomics as a preliminary screen for antimicrobial bioprospecting. Gene. 2016 Dec 15;594(2):248-258. https://doi.org/10.1016/j.gene.2016.09.021
Al-Amoudi, Soha ; Mohamad Razali, Rozaimi ; Essack, Magbubah ; Amini, Mohammad Shoaib ; Bougouffa, Salim ; Archer, John A.C. ; Lafi, Feras F. ; Bajic, Vladimir B. / Metagenomics as a preliminary screen for antimicrobial bioprospecting. In: Gene. 2016 ; Vol. 594, No. 2. pp. 248-258.
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