2018

Mining Red Sea bacteria for industrial potential

10/7/2018

Similarity between the genomes of Bac48 and Bac84. Developed using data visualisation software, this figure shows synteny blocks between B. paralicheniformis Bac48 and B. paralicheniformis Bac84. Regions I, II and III are regions in B. paralicheniformis Bac48 that are missing in B. paralicheniformis Bac84.


Analyses of two bacterial strains in the Red Sea show they are enriched with gene clusters with potential to activate the synthesis of a wide range of industrially useful compounds, from novel antibiotics, anticancer agents and pigments to those useful for crop protection and the food industry.

Bacteria are a rich resource for bioactive chemical compounds and Magbubah Essack, of KAUST’s Computational Bioscience Research Center, explains that bacterial strains able to withstand the Red Sea’s highly saline, warm waters were anticipated to produce sturdy enzymes suited for industrial applications.


The research team 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. (Front from l-r: Professor Takashi Gojobori, Professor Vladimir Bajic, Professor Heribert Hirt; Back from l-r: Dr. Magbubah Essack, Ameerah Bokhari, Dr. Salim Bougouffa, Associate Professor Xin Gao, Professor Stefan Arold.) © 2018 KAUST


The team sequenced the genomes of two Bacillus species: B. paralicheniformis Bac48 collected from mangrove mud and B. paralicheniformis Bac84 collected from a microbial mat in the Rabigh Harbor Lagoon on Saudi Arabia’s west coast. These two were compared with the documented genomes of three other B. paralicheniformis and nine B. licheniformis strains. The Red Sea strains had a higher number of gene clusters associated with bioactive compound synthesis compared to the other Bacillus strains.

“The findings affirm the premise that the Red Sea is a metabolically unique environment worthy of exploration for efficient microbes that can be used as biotechnological hosts,” says computational bioscientist Ghofran Othoum, the first author of the study. “Also, our computational exploratory approach showed the strength of computer modeling methods in applications that require ranking biological systems for biotechnological use.”The team also report the first use of a computer program to identify a gene cluster in strains of the B. paralicheniformis species, in this case B. paralicheniformis Bac48, called trans-acyltransferase nonribosomal peptide synthetase/polyketide synthase, which is associated with the production of a specific group of compounds.

Future research will focus on seeking out which bioactive compounds are produced by the two Red Sea strains.

References

Othoum, G., Bougouffa, S., Razali, R., Bokhari, A., Alamoudi, S., Autunes, A., Xao., G., Hoehndorf, R., Arold, S.T., Gojobori, T., Hirt, H., Mijakovic, I., Bajic, V.B. Lafi., F.F. & Essack, M. In silico exploration of Red Sea Bacillusgenomes for natural product biosynthetic gene clusters. BMC Genomics 19, 382 (2018).| article​

ABOUT THE FIRST AUTHOR

Ghofran Othoum

Ph.D. Graduate

Ghofran enrolled at KAUST in 2011 and has since completed both her Master's and Ph.D. degrees under the supervision of Professor Vladimir Bajic. Her research is focused on using computational methods to mine large sets of omics data from biological systems for the purpose