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
King Abdullah University of Science and Technology (KAUST)
Zayed University
Jens B Nielsen
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Royal Institute of Technology (KTH)
Novo Nordisk Foundation
Vladimir B. Bajic
King Abdullah University of Science and Technology (KAUST)
Ivan Mijakovic
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Novo Nordisk Foundation
M. Essack
King Abdullah University of Science and Technology (KAUST)
Scientific Reports
2045-2322 (ISSN) 20452322 (eISSN)
Vol. 9 1 19254Subject Categories
Evolutionary Biology
Botany
Microbiology
DOI
10.1038/s41598-019-55726-2