Exploration of Natural Product Repository by Combined Genomics and Metabolomics Profiling of Mangrove-Derived <i>Streptomyces murinus</i> THV12 Strain
<i>Streptomyces</i>, one of the largest genera belonging to the phylum Actinobacteria, contribute to more than 60% of the clinically relevant antibiotics. The present study outlined the genomics and the metabolomics of a mangrove-derived <i>Streptomyces murinus</i> THV12 stra...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Fermentation |
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| Online Access: | https://www.mdpi.com/2311-5637/9/6/576 |
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| author | Vineetha Das Niladri Sekhar Chatterjee Prinetha Uruparambil Pushpakaran Kuttanappilly V. Lalitha Toms C. Joseph |
| author_facet | Vineetha Das Niladri Sekhar Chatterjee Prinetha Uruparambil Pushpakaran Kuttanappilly V. Lalitha Toms C. Joseph |
| author_sort | Vineetha Das |
| collection | DOAJ |
| description | <i>Streptomyces</i>, one of the largest genera belonging to the phylum Actinobacteria, contribute to more than 60% of the clinically relevant antibiotics. The present study outlined the genomics and the metabolomics of a mangrove-derived <i>Streptomyces murinus</i> THV12 strain. The Illumina Hiseq 2500 platform-based whole-genome sequencing of the <i>Streptomyces</i> strain generated a consensus sequence of 8,363,247 bp with 107 contigs and 7345 protein-coding genes, which shared significant homology with genes from <i>Streptomyces murinus</i>. The detection of secondary metabolite biosynthetic gene clusters (smBGCs) in the genome performed using the pipeline antiSMASH v6.1.1 revealed that the strain harbored 47 secondary metabolite clusters, which represented 17.9% of the 8.3 Mb genome. The smBGCs belonged to the metabolite categories: PKS, NRPS, ectoine, lassopeptides, lantipeptides, melanin, siderophores, terpenes and other putative products. The strain showed broad-spectrum antimicrobial activity with a inhibition zone of 30 mm against Gram-positive bacteria and <i>Candida albicans</i>. The secondary metabolite profiling of the crude extracts from the fermentation broth of THV12 was performed with the HPLC system coupled with an Orbitrap Exploris120 high-resolution mass spectrometer. As revealed by in silico analysis, compounds such as actinomycin D, pentamycin, desferrioxamine E and cinnabaramide A were detected with MS/MS analysis. Apart from this, compounds belonging to different chemical scaffolds, such as cyclic and linear peptides, bacterial alkaloids, linear polyketides and terpenoids, were also present in the fermentation broth of the strain when cultivated under the OSMAC (One Strain Many Compounds) approach. Thus, the combined strategy of genome mining and metabolomics of the mangrove-derived strain aided in exploring the chemical diversity of BGCs and new chemical entities, which can contribute to drug leads. |
| first_indexed | 2024-03-11T02:29:06Z |
| format | Article |
| id | doaj.art-bdcecdae7a494bb6905691c2f0f253b0 |
| institution | Directory Open Access Journal |
| issn | 2311-5637 |
| language | English |
| last_indexed | 2024-03-11T02:29:06Z |
| publishDate | 2023-06-01 |
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| series | Fermentation |
| spelling | doaj.art-bdcecdae7a494bb6905691c2f0f253b02023-11-18T10:21:40ZengMDPI AGFermentation2311-56372023-06-019657610.3390/fermentation9060576Exploration of Natural Product Repository by Combined Genomics and Metabolomics Profiling of Mangrove-Derived <i>Streptomyces murinus</i> THV12 StrainVineetha Das0Niladri Sekhar Chatterjee1Prinetha Uruparambil Pushpakaran2Kuttanappilly V. Lalitha3Toms C. Joseph4Microbiology Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Kochi 682029, Kerala, IndiaMicrobiology Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Kochi 682029, Kerala, IndiaMicrobiology Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Kochi 682029, Kerala, IndiaMicrobiology Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Kochi 682029, Kerala, IndiaMicrobiology Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Kochi 682029, Kerala, India<i>Streptomyces</i>, one of the largest genera belonging to the phylum Actinobacteria, contribute to more than 60% of the clinically relevant antibiotics. The present study outlined the genomics and the metabolomics of a mangrove-derived <i>Streptomyces murinus</i> THV12 strain. The Illumina Hiseq 2500 platform-based whole-genome sequencing of the <i>Streptomyces</i> strain generated a consensus sequence of 8,363,247 bp with 107 contigs and 7345 protein-coding genes, which shared significant homology with genes from <i>Streptomyces murinus</i>. The detection of secondary metabolite biosynthetic gene clusters (smBGCs) in the genome performed using the pipeline antiSMASH v6.1.1 revealed that the strain harbored 47 secondary metabolite clusters, which represented 17.9% of the 8.3 Mb genome. The smBGCs belonged to the metabolite categories: PKS, NRPS, ectoine, lassopeptides, lantipeptides, melanin, siderophores, terpenes and other putative products. The strain showed broad-spectrum antimicrobial activity with a inhibition zone of 30 mm against Gram-positive bacteria and <i>Candida albicans</i>. The secondary metabolite profiling of the crude extracts from the fermentation broth of THV12 was performed with the HPLC system coupled with an Orbitrap Exploris120 high-resolution mass spectrometer. As revealed by in silico analysis, compounds such as actinomycin D, pentamycin, desferrioxamine E and cinnabaramide A were detected with MS/MS analysis. Apart from this, compounds belonging to different chemical scaffolds, such as cyclic and linear peptides, bacterial alkaloids, linear polyketides and terpenoids, were also present in the fermentation broth of the strain when cultivated under the OSMAC (One Strain Many Compounds) approach. Thus, the combined strategy of genome mining and metabolomics of the mangrove-derived strain aided in exploring the chemical diversity of BGCs and new chemical entities, which can contribute to drug leads.https://www.mdpi.com/2311-5637/9/6/576<i>Streptomyces</i>genomebiosynthetic gene clustermolecular annotationmetabolome |
| spellingShingle | Vineetha Das Niladri Sekhar Chatterjee Prinetha Uruparambil Pushpakaran Kuttanappilly V. Lalitha Toms C. Joseph Exploration of Natural Product Repository by Combined Genomics and Metabolomics Profiling of Mangrove-Derived <i>Streptomyces murinus</i> THV12 Strain Fermentation <i>Streptomyces</i> genome biosynthetic gene cluster molecular annotation metabolome |
| title | Exploration of Natural Product Repository by Combined Genomics and Metabolomics Profiling of Mangrove-Derived <i>Streptomyces murinus</i> THV12 Strain |
| title_full | Exploration of Natural Product Repository by Combined Genomics and Metabolomics Profiling of Mangrove-Derived <i>Streptomyces murinus</i> THV12 Strain |
| title_fullStr | Exploration of Natural Product Repository by Combined Genomics and Metabolomics Profiling of Mangrove-Derived <i>Streptomyces murinus</i> THV12 Strain |
| title_full_unstemmed | Exploration of Natural Product Repository by Combined Genomics and Metabolomics Profiling of Mangrove-Derived <i>Streptomyces murinus</i> THV12 Strain |
| title_short | Exploration of Natural Product Repository by Combined Genomics and Metabolomics Profiling of Mangrove-Derived <i>Streptomyces murinus</i> THV12 Strain |
| title_sort | exploration of natural product repository by combined genomics and metabolomics profiling of mangrove derived i streptomyces murinus i thv12 strain |
| topic | <i>Streptomyces</i> genome biosynthetic gene cluster molecular annotation metabolome |
| url | https://www.mdpi.com/2311-5637/9/6/576 |
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