Metagenomics as a preliminary screen for antimicrobial bioprospecting

• Published in: Gene 2016-12, Vol.594 (2), p.248-258
• Main Authors: Al-Amoudi, Soha, Razali, Rozaimi, Essack, Magbubah, Amini, Mohammad Shoaib, Bougouffa, Salim, Archer, John A.C., Lafi, Feras F., Bajic, Vladimir B.
• Format: Article
• Language: English
• Subjects: Actinobacteria; Antibiotic; Antimicrobial; Bacteria - genetics; Bacteria - metabolism; Bioactivity; Biodiversity; Bioinformatics; Bioprospecting; Biosynthetic genes; Cyanobacteria; Environment; Firmicutes; Indian Ocean; Lagoon; Mangrove; Metagenome; Microbial mat; Microbiota - genetics; Proteobacteria; Red Sea; Water Microbiology
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2016.09.021

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. •Although Actinobacteria tends to be the common target for antimicrobial bioprospecting, our study suggest that Firmicutes (Bacilli and Clostridia) should be a target plylum for antimicrobial bioprospecting in all locations.•In hydrocarbon contaminated sites Bacteroidetes, Proteobacteria, Cyanobacteria and Firmicutes frequently appear to be better targets for antimicrobial bioprospecting than Actinobacteria.•Selection pressure associated with hydrocarbon-contamination enriched the bacterial classes linked to DNA associated with antibiotic synthesis enzymes.•Our study suggests that is will be beneficial to use metagenomics as a preliminary screen to comprehensively identify target phyla for this type of bioprospecting.