Genomic and Phenotypic Characterization of <i>Streptomyces sirii</i> sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil
In our large-scale search for antimicrobial-producing bacteria, we isolated an actinomycete strain from rhizospheric soil of <i>Bambusa vulgaris</i>. The strain designated BP-8 showed noticeable antibacterial activity. BP-8 was subjected to a whole-genome analysis via a polyphasic taxono...
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2024-12-01
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| author | Yuliya V. Zakalyukina Vera A. Alferova Arina A. Nikandrova Albina R. Kiriy Alisa P. Chernyshova Marsel R. Kabilov Olga A. Baturina Mikhail V. Biryukov Petr V. Sergiev Dmitrii A. Lukianov |
| author_facet | Yuliya V. Zakalyukina Vera A. Alferova Arina A. Nikandrova Albina R. Kiriy Alisa P. Chernyshova Marsel R. Kabilov Olga A. Baturina Mikhail V. Biryukov Petr V. Sergiev Dmitrii A. Lukianov |
| author_sort | Yuliya V. Zakalyukina |
| collection | DOAJ |
| description | In our large-scale search for antimicrobial-producing bacteria, we isolated an actinomycete strain from rhizospheric soil of <i>Bambusa vulgaris</i>. The strain designated BP-8 showed noticeable antibacterial activity. BP-8 was subjected to a whole-genome analysis via a polyphasic taxonomy approach, and its antibacterial metabolite was identified by HRLS-MS. The results of the physiological and morphological analyses indicated that BP-8 is an aerobic, neutrophilic, mesophilic organism that is tolerant to 8% NaCl and can use a wide range of carbohydrates. It forms curly sporophores with a warty surface. The results of the phylogenetic and average nucleotide identity analyses and in silico DNA–DNA hybridization calculation indicated that BP-8 represents the type strain of a novel <i>Streptomyces</i> species. A comparative in silico analysis of the genome sequences of BP-8 and its closest related strains revealed the presence of genes encoding chemotaxonomic markers characteristic of <i>Streptomyces</i>. The antibacterial compound was identified as amicetin. Genomic mining also revealed more than 10 biosynthetic gene clusters that have not been described previously and may lead to the discovery of new valuable compounds. On the basis of these results, strain BP-8<sup>T</sup> (=VKM Ac-3066<sup>T</sup> = CCTCC AA 2024094<sup>T</sup>) is proposed as the type strain of the novel species <i>Streptomyces sirii</i> sp. nov. |
| format | Article |
| id | doaj-art-246fbb3dde2a4c2d9219ce8674d75993 |
| institution | Kabale University |
| issn | 2076-2607 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj-art-246fbb3dde2a4c2d9219ce8674d759932024-12-27T14:41:47ZengMDPI AGMicroorganisms2076-26072024-12-011212262810.3390/microorganisms12122628Genomic and Phenotypic Characterization of <i>Streptomyces sirii</i> sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric SoilYuliya V. Zakalyukina0Vera A. Alferova1Arina A. Nikandrova2Albina R. Kiriy3Alisa P. Chernyshova4Marsel R. Kabilov5Olga A. Baturina6Mikhail V. Biryukov7Petr V. Sergiev8Dmitrii A. Lukianov9Department of Soil Science, Lomonosov Moscow State University, 119991 Moscow, RussiaBelozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, RussiaCenter for Molecular and Cellular Biology, 121205 Moscow, Skolkovo, RussiaInstitute of Biomedical Problems of the Russian Academy of Sciences, 123007 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Science, 117997 Moscow, RussiaInstitute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, RussiaDepartment of Biology, Lomonosov Moscow State University, 119991 Moscow, RussiaBelozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, RussiaCenter for Molecular and Cellular Biology, 121205 Moscow, Skolkovo, RussiaIn our large-scale search for antimicrobial-producing bacteria, we isolated an actinomycete strain from rhizospheric soil of <i>Bambusa vulgaris</i>. The strain designated BP-8 showed noticeable antibacterial activity. BP-8 was subjected to a whole-genome analysis via a polyphasic taxonomy approach, and its antibacterial metabolite was identified by HRLS-MS. The results of the physiological and morphological analyses indicated that BP-8 is an aerobic, neutrophilic, mesophilic organism that is tolerant to 8% NaCl and can use a wide range of carbohydrates. It forms curly sporophores with a warty surface. The results of the phylogenetic and average nucleotide identity analyses and in silico DNA–DNA hybridization calculation indicated that BP-8 represents the type strain of a novel <i>Streptomyces</i> species. A comparative in silico analysis of the genome sequences of BP-8 and its closest related strains revealed the presence of genes encoding chemotaxonomic markers characteristic of <i>Streptomyces</i>. The antibacterial compound was identified as amicetin. Genomic mining also revealed more than 10 biosynthetic gene clusters that have not been described previously and may lead to the discovery of new valuable compounds. On the basis of these results, strain BP-8<sup>T</sup> (=VKM Ac-3066<sup>T</sup> = CCTCC AA 2024094<sup>T</sup>) is proposed as the type strain of the novel species <i>Streptomyces sirii</i> sp. nov.https://www.mdpi.com/2076-2607/12/12/2628amicetinBGCspolyphasic taxonomyrhizosphere soil<i>Streptomyces</i> |
| spellingShingle | Yuliya V. Zakalyukina Vera A. Alferova Arina A. Nikandrova Albina R. Kiriy Alisa P. Chernyshova Marsel R. Kabilov Olga A. Baturina Mikhail V. Biryukov Petr V. Sergiev Dmitrii A. Lukianov Genomic and Phenotypic Characterization of <i>Streptomyces sirii</i> sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil Microorganisms amicetin BGCs polyphasic taxonomy rhizosphere soil <i>Streptomyces</i> |
| title | Genomic and Phenotypic Characterization of <i>Streptomyces sirii</i> sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil |
| title_full | Genomic and Phenotypic Characterization of <i>Streptomyces sirii</i> sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil |
| title_fullStr | Genomic and Phenotypic Characterization of <i>Streptomyces sirii</i> sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil |
| title_full_unstemmed | Genomic and Phenotypic Characterization of <i>Streptomyces sirii</i> sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil |
| title_short | Genomic and Phenotypic Characterization of <i>Streptomyces sirii</i> sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil |
| title_sort | genomic and phenotypic characterization of i streptomyces sirii i sp nov amicetin producing actinobacteria isolated from bamboo rhizospheric soil |
| topic | amicetin BGCs polyphasic taxonomy rhizosphere soil <i>Streptomyces</i> |
| url | https://www.mdpi.com/2076-2607/12/12/2628 |
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