In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

Othoum, Ghofran; Bougouffa, Salim; Razali, Rozaimi Mohamad; Bokhari, Ameerah; Alamoudi, Soha A.; Antunes, André; Gao, Xin; Hoehndorf, Robert; Arold, Stefan T.; Gojobori, Takashi; Hirt, Heribert; Mijaković, Ivan; Bajic, Vladimir B.; Lafi, Feras F.; Essack, Magbubah

doi:10.1186/s12864-018-4796-5

Cited by 19 publications

(26 citation statements)

References 72 publications

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“…The close relationship between their genomes suggests that some aspects of the metabolism of the newly sequenced species have occurred that enable them to colonize this specific environment. Thus, the B. paralicheniformis (Bac84) and B. paralicheniformis (Bac48) strains were also used in a separate study focused on the differences in the closely-related licheniformis and paralicheniformis strains based on predicted biosynthetic capabilities 70 .…”

Section: Resultsmentioning

confidence: 99%

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

Othoum

Prigent

Derouiche

et al. 2019

Sci Rep

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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.

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Section: Resultsmentioning

confidence: 99%

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

Othoum

Prigent

Derouiche

et al. 2019

Sci Rep

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“…Despite the availability of a total of 30 publicly available Virgibacillus genomes (at the time of the study), the biosynthetic potential of these strains has not been sufficiently explored. Species from marine environments, such as the Red Sea [25], were shown to harbor a number of promising clusters for the biosynthesis of modular antimicrobial clusters with unique structural properties. Here, we are analyzing Virgibacillus strains isolated from the Red Sea, along with publicly available Virgibacillus genomes, for their biosynthetic capabilities, leveraging the availability of complete genomes of the Red Sea isolates.…”

Section: Discussionmentioning

confidence: 99%

“…Prodigal [26] was used as the gene prediction method and genome annotation was completed using the Automatic Annotation of Microbial Genomes pipeline (AAMG) [27] with default parameters. A detailed description of sequencing, assembly, and annotation are available in [25].…”

Section: Methodsmentioning

confidence: 99%

Mining biosynthetic gene clusters in Virgibacillus genomes

et al. 2019

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Background Biosynthetic gene clusters produce a wide range of metabolites with activities that are of interest to the pharmaceutical industry. Specific interest is shown towards those metabolites that exhibit antimicrobial activities against multidrug-resistant bacteria that have become a global health threat. Genera of the phylum Firmicutes are frequently identified as sources of such metabolites, but the biosynthetic potential of its Virgibacillus genus is not known. Here, we used comparative genomic analysis to determine whether Virgibacillus strains isolated from the Red Sea mangrove mud in Rabigh Harbor Lagoon, Saudi Arabia, may be an attractive source of such novel antimicrobial agents. Results A comparative genomics analysis based on Virgibacillus dokdonensis Bac330, Virgibacillus sp. Bac332 and Virgibacillus halodenitrificans Bac324 (isolated from the Red Sea) and six other previously reported Virgibacillus strains was performed. Orthology analysis was used to determine the core genomes as well as the accessory genome of the nine Virgibacillus strains. The analysis shows that the Red Sea strain Virgibacillus sp. Bac332 has the highest number of unique genes and genomic islands compared to other genomes included in this study. Focusing on biosynthetic gene clusters, we show how marine isolates, including those from the Red Sea, are more enriched with nonribosomal peptides compared to the other Virgibacillus species. We also found that most nonribosomal peptide synthases identified in the Virgibacillus strains are part of genomic regions that are potentially horizontally transferred. Conclusions The Red Sea Virgibacillus strains have a large number of biosynthetic genes in clusters that are not assigned to known products, indicating significant potential for the discovery of novel bioactive compounds. Also, having more modular synthetase units suggests that these strains are good candidates for experimental characterization of previously identified bioactive compounds as well. Future efforts will be directed towards establishing the properties of the potentially novel compounds encoded by the Red Sea specific trans -AT PKS/NRPS cluster and the type III PKS/NRPS cluster. Electronic supplementary material The online version of this article (10.1186/s12864-019-6065-7) contains supplementary material, which is available to authorized users.

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“…Although B. paralicheniformis was isolated from fermented foods 18,40 , there was no record of thermophilic B. paralicheniformis and its enzyme production. B. paralicheniformis in this study could able to produce amylase, lipase, protease and…”

Section: Enzyme Production Capacities Of Thermophilesmentioning

confidence: 99%

Presence of Different Bacterial Species in Thermal Sources and Novelty in Their Industrial Enzyme Productions

Albayrak¹,

Genç²,

Özkan³

et al. 2019

J Pure Appl Microbiol

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In this study, one hundred and thirty isolates were isolated from water and sludge samples taken from hot springs located in different regions of Turkey. Among them, eleven isolates were chosen according to conventional (morphological, physiological and biochemical tests) and molecular methods (rep-PCR and 16S rRNA sequencing). These bacteria were then tested for their capability to produce valuable enzymes. As a result; species belonging to Bacillus, Anoxybacillus, Aeribacillus, Enterococcus, Exiguobacterium and Paenibacillus were identified. Test strains were found to have optimum reproductive potential at pH 5.0-9.0 and 15-65°C, usually at a concentration of 1.0-10.0% (w/v) NaCl. In addition, all thermotolerant bacteria were Gram, endospore (except E. profundum), catalase and oxidase (except E. faecium and E. profundum) positive, and rod-shaped (except E. faecium). It was observed that all isolates had a 99% similarity percentage as a result of 16S rRNA sequence analysis. All of the isolates were capable of producing industrially important enzymes moreover, eight of them could produce at least two of these enzymes. Test strains had high potential of industrial enzyme production, and the enzymes from these thermo-tolerant isolates will be widely used in biotechnological processes.

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In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

Cited by 19 publications

References 72 publications

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

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

Mining biosynthetic gene clusters in Virgibacillus genomes

Presence of Different Bacterial Species in Thermal Sources and Novelty in Their Industrial Enzyme Productions

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