Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)
Journal article, 2019

Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment. © 2019, The Author(s).

Author

Ghofran Othoum

King Abdullah University of Science and Technology (KAUST)

Sylvain Prigent

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Abderahmane Derouiche

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Lei Shi

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Ameerah Bokhari

King Abdullah University of Science and Technology (KAUST)

Soha Alamoudi

King Abdulaziz University

Salim Bougouffa

King Abdullah University of Science and Technology (KAUST)

X. Gao

King Abdullah University of Science and Technology (KAUST)

Robert Hoehndorf

King Abdullah University of Science and Technology (KAUST)

Stefan T. Arold

King Abdullah University of Science and Technology (KAUST)

T. Gojobori

King Abdullah University of Science and Technology (KAUST)

H. Hirt

King Abdullah University of Science and Technology (KAUST)

Feras F. Lafi

Zayed University

King Abdullah University of Science and Technology (KAUST)

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Novo Nordisk Foundation Center for Biosustainability

Royal Institute of Technology (KTH)

Vladimir B. Bajic

King Abdullah University of Science and Technology (KAUST)

Ivan Mijakovic

Novo Nordisk Foundation Center for Biosustainability

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

M. Essack

King Abdullah University of Science and Technology (KAUST)

Scientific Reports

2045-2322 (ISSN)

Vol. 9 1 19254

Subject Categories

Evolutionary Biology

Botany

Microbiology

DOI

10.1038/s41598-019-55726-2

More information

Latest update

1/9/2020 1