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Draft Genome Sequence of an Endophytic Micromonospora sp. Strain, ANENR4, Isolated from the Root of a Peanut Plant (Arachis hypogaea). Microbiol Resour Announc 2022; 11:e0065522. [PMID: 36264266 PMCID: PMC9671019 DOI: 10.1128/mra.00655-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The genus Micromonospora was found to occur in a diverse range of habitats. Here, we report the genome sequence of an endophytic strain of Micromonospora sp., ANENR4. ANENR4 was isolated from the healthy roots of a peanut (Arachis hypogaea) plant from Egra, West Bengal, India.
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Alam AA, Goda DA, Soliman NA, Abdel-Meguid DI, El-Sharouny EE, Sabry SA. Production and statistical optimization of cholesterol-oxidase generated by Streptomyces sp. AN strain. J Genet Eng Biotechnol 2022; 20:156. [DOI: 10.1186/s43141-022-00433-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/23/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Background
Cholesterol oxidases (CHOs) have attracted enormous attention because of their wide biotechnological potential. The present study explores the production of CHOs by Streptomyces sp. AN. Evaluation of culture conditions affecting enzyme production, medium optimization and released metabolite characteristics were also investigated.
Results
The current work reports the isolation of 37 colonies (bacteria/actinobacteria) with different morphotypes from different soil/water samples. The isolate-coded AN was selected for its high potency for CHO production. Morphological characteristics and the obtained partial sequence of 16srRNA of AN showed 99.38% identity to Streptomyces sp. strain P12–37. Factors affecting CHO production were evaluated using Plackett-Burman (PB) and Box-Behnken (BB) statistical designs to find out the optimum level of the most effective variables, namely, pH, starch, NH4NO3 and FeSO4.7H2O with a predicted activity of 6.56 U/mL. According to this optimization, the following medium composition was considered to be optimum (g/L): cholesterol 1, starch 6, MgSO4.7H2O 0.1, CaCl2 0.01, FeSO4.7H2O 0.1, NH4NO3 23.97, yeast extract (YE) 0.2, K2HPO4 0.01, KH2PO4 0.1, NaCl 0.01, Tween 20 0.01, pH 6.36 and incubation temperature (30 °C) for 9 days. Spectophotometric analysis for released metabolites against cholesterol (standard) via Fourier-transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC) was carried out. FTIR spectrum showed the appearance of new absorption peaks at 1644 and 1725cm−1; this confirmed the presence of the Keto group (C=O) stretch bond. Besides, fermentation caused changes in thermal properties such as melting temperature peak (99.26; 148.77 °C), heat flow (− 8; − 3.6 Mw/mg), capacity (− 924.69; − 209.77 mJ) and heat enthalpy (− 385.29; 69.83 J/g) by comparison to the standard cholesterol as recognized through DSC thermogram. These changes are attributed to the action of the CHO enzyme and the release of keto derivatives of cholesterol with different properties.
Conclusion
Streptomyces sp. AN was endowed with the capability to produce CHO. Enzyme maximization was followed using a statistical experimental approach, leading to a 2.6-fold increase in the overall activity compared to the basal condition. CHO catalyzed the oxidation of cholesterol; this was verified by the appearance of a new keto group (C=O) peak at 1644 and 1725 cm−1 observed by FTIR spectroscopic analysis. Also, DSC thermogram demonstrates the alteration of cholesterol triggered by CHO.
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Zamora-Quintero AY, Torres-Beltrán M, Guillén Matus DG, Oroz-Parra I, Millán-Aguiñaga N. Rare actinobacteria isolated from the hypersaline Ojo de Liebre Lagoon as a source of novel bioactive compounds with biotechnological potential. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35213299 PMCID: PMC8941997 DOI: 10.1099/mic.0.001144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Ojo de Liebre Lagoon is a Marine Protected Area that lies within a UNESCO World Heritage Site and is a critical habitat for important migratory species such as the grey whale and bird species. Unique hypersaline environments, such as the Ojo de Liebre Lagoon, are underexplored in terms of their bacterial and chemical diversity, representing a potential source for new bioactive compounds with pharmacological properties. Actinobacteria are one of the most diverse and prolific taxonomic bacterial groups in terms of marine bioactive compounds. This study aimed to identify the culturable actinobacterial community inhabiting the Lagoon, as well as to test their potential as new sources of anticancer compounds with pharmacological potential. A selective isolation approach focused on spore-forming bacteria from 40 sediment samples generated a culture collection of 64 strains. The 16S rRNA gene analyses identified three phyla in this study, the Actinobacteria, Firmicutes and Proteobacteria, where the phylum Actinobacteria dominated (57%) the microbial community profiles. Within the Actinobacteria, nine different genera were isolated including the Actinomadura, Micromonospora, Nocardiopsis, Plantactinospora and Streptomyces sp. We observed seasonal differences on actinobacteria recovery. For instance, Micromonospora strains were recovered during the four sampling seasons, while Arthrobacter and Pseudokineococcus were only isolated in February 2018, and Blastococcus, Rhodococcus and Streptomyces were uniquely isolated in June 2018. Ethyl acetate crude extracts derived from actinobacterial cultures were generated and screened for cytotoxic activity against six cancer cell lines. Strains showed promising low percentages of viability on lung (H1299), cervical (SiHa), colon (Caco-2) and liver (HepG2) cancer lines. Molecular networking results suggest many of the metabolites produced by these strains are unknown and they might harbour novel chemistry. Our results showed the Ojo de Liebre Lagoon is a novel source for isolating diverse marine actinobacteria which produce promising bioactive compounds for potential biotechnological use as anticancer agents.
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Affiliation(s)
- Andrea Y Zamora-Quintero
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Mónica Torres-Beltrán
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Dulce G Guillén Matus
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Irasema Oroz-Parra
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Natalie Millán-Aguiñaga
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
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Fu G, Wang R, Ding J, Qi H, Zhao Z, Chen C, Zhang H, Xue Z, Wang J, Wu M. Micromonospora zhangzhouensis sp. nov., a Novel Actinobacterium Isolated from Mangrove Soil, Exerts a Cytotoxic Activity in vitro. Sci Rep 2020; 10:3889. [PMID: 32127574 PMCID: PMC7054543 DOI: 10.1038/s41598-020-60677-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/13/2020] [Indexed: 11/21/2022] Open
Abstract
A new bacterial strain, designated HM134T, was isolated from a sample of soil collected from a Chinese mangrove Avicennia marina forest. Assessed by a polyphasic approach, the taxonomy of strain HM134T was found to be associated with a range of phylogenetic and chemotaxonomic properties consistent with the genus Micromonospora. Phylogenetic analysis based on the 16s rRNA gene sequence indicated that strain HM134T formed a distinct lineage with the most closely related species, including M. rifamycinica AM105T, M. wenchangensis CCTCC AA 2012002T and M. mangrovi 2803GPT1-18T. The ANI values between strain HM134T and the reference strains ranged from 82.6% to 95.2%, which was below the standard criteria for classifying strains as the same species (96.5%). Strain HM134T and related species shared in silico dDDH similarities values below the recommended 70% cut-off for the delineation of species (range from 25.7–62.6%). The DNA G+C content of strain HM134T was 73.2 mol%. Analysis of phylogenetic, genomic, phenotypic and chemotaxonomic characteristics revealed that strain HM134T is considered to represent a novel species of the genus Micromonospora, for which the name M. zhangzhouensis sp. nov. is proposed. The extract of strain HM134T was demonstrated to exhibit cytotoxic activity against the human cancer cell lines HepG2, HCT-116 and A549. Active substance presented in the fermentation broth of strain HM134T was isolated by bioassay-guided analysis and purified afterwards. A new derivative of diterpenoid was identified through electrospray ionizing mass spectrometry (MS) and nuclear magnetic resonance (NMR). The compound showed different cytotoxic activities against cancer cells, with the highest cytotoxicity against HCT-116, corresponding to IC50 value of 38.4 μg/mL.
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Affiliation(s)
- Geyi Fu
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ruijun Wang
- Ocean College, Zhejiang University, Zhoushan, China
| | - Jinglin Ding
- Zhoushan Tourism & Health College, Zhoushan, China
| | - Huan Qi
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China
| | - Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Can Chen
- Ocean College, Zhejiang University, Zhoushan, China
| | - Hui Zhang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China.,College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Zhenglian Xue
- College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Jidong Wang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China. .,College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China.
| | - Min Wu
- Ocean College, Zhejiang University, Zhoushan, China. .,College of Life Sciences, Zhejiang University, Hangzhou, China.
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Ay H, Nouioui I, Klenk HP, Cetin D, Igual JM, Sahin N, Isik K. Genome-based classification of Micromonospora craterilacus sp. nov., a novel actinobacterium isolated from Nemrut Lake. Antonie Van Leeuwenhoek 2020; 113:791-801. [PMID: 32060815 DOI: 10.1007/s10482-020-01390-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/28/2020] [Indexed: 11/28/2022]
Abstract
A novel actinobacterial strain, designated NA12T, was isolated from coastal sediment sample of Nemrut Lake, a crater lake in eastern Anatolia, Turkey. The taxonomic position of the strain was established using a polyphasic approach. Cultural and chemotaxonomic characteristics of the strain were consistent with its classification within the family Micromonosporaceae. The 16S rRNA gene sequence analysis of strain NA12T showed that the strain closely related to M. radicis AZ1-13T, M. zingiberis PLAI 1-1T, M. craniella LHW63014T and M. endophytica 202201T with pairwise sequence identity values ranging from 99.4 to 99.3%. Digital DNA-DNA hybridization values between strain NA12T and the closely related type strains were ranged from 41.0 to 18.3% while the average nucleotide identity values were between 87.3 and 86.5%, which are well below the designed cut-off points of 70 and 95%, respectively. The G + C content of genomic DNA was 71.5%. Whole-cell hydrolysates of strain NA12T contained 3-hydroxydiaminopimelic acid and meso-diaminopimelic acid. Cell-wall sugars were composed of arabinose, fucose, glucose, mannose, rhamnose and xylose. The polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, glycophospholipid, amino-phospholipid and two unidentified phospholipids. The predominant menaquinones were MK-9(H6) and MK-9(H4). Major fatty acids were iso-C16:0 and C17:1ω8c. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain NA12T (DSM 100982T = KCTC 39647T) is proposed to represent the type strain of a novel species, Micromonospora craterilacus sp. nov.
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Affiliation(s)
- Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey.
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Demet Cetin
- Division of Science Education, Department of Mathematics and Science Education, Gazi Faculty of Education, Gazi University, 06500, Ankara, Turkey
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiologia de Salamanca, Consejo Superior de Investigaciones Cientificas (IRNASA-CSIC), Salamanca, Spain
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey
| | - Kamil Isik
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey
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Kuncharoen N, Kudo T, Yuki M, Okuma M, Booncharoen A, Tanasupawat S. Micromonospora musae sp. nov., an endophytic actinomycete isolated from roots of Musa species. Syst Appl Microbiol 2019; 42:126020. [DOI: 10.1016/j.syapm.2019.126020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 08/06/2019] [Accepted: 08/20/2019] [Indexed: 10/25/2022]
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Veyisoglu A, Carro L, Cetin D, Igual JM, Klenk HP, Sahin N. Micromonospora orduensis sp. nov., isolated from deep marine sediment. Antonie van Leeuwenhoek 2019; 113:397-405. [DOI: 10.1007/s10482-019-01349-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/10/2019] [Indexed: 11/28/2022]
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Kuncharoen N, Kudo T, Yuki M, Okuma M, Pittayakhajonwut P, Tanasupawat S. Micromonospora radicis sp. nov., isolated from roots of Azadirachta indica var. siamensis Valenton, and reclassification of Jishengella zingiberis as Micromonospora zingiberis comb. nov. Int J Syst Evol Microbiol 2019; 69:2884-2891. [PMID: 31310194 DOI: 10.1099/ijsem.0.003574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel endophytic actinomycete strain AZ1-13T was isolated from roots of Azadirachta indica, and its taxonomic position was investigated using a polyphasic approach. Pairwise 16S rRNA gene sequence similarities of strain AZ1-13T and its closest species, Jishegella zingiberis PLAI1-1T and Micromonospora endophytica 202201T, were 99.7 and 99.2 %, respectively. Phylogenetic analyses of the family Micromonosporaceae based on 16S rRNA gene sequences indicated strains AZ1-13T and J. zingiberis PLAI1-1Tare located within the genus Micromonospora. The approximate genome size of the strain was 5.96 Mb with 71.9 mol% of G+C content. The strain AZ1-13T exhibited ANIb values of 87.4 % with J. zingiberis PLAI1-1T and 85.1 % with M. endophytica 202201T. Chemotaxonomic characteristics of strain AZ1-13T were consistent within the genus Micromonospora: cell-wall peptidoglycan of the strain contained meso-diaminopimelic acid; glucose, mannose, ribose and xylose are presented as the whole-cell sugars; the predominant menaquinones were MK-9(H4) and MK-9(H6); major cellular fatty acids were iso-C15 : 0, 10-methyl C17 : 0, C17 : 0, anteiso-C17 : 0 and iso-C17 : 1ω8c; diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were detected as distinguished phospholipids. Based on phenotypic properties, phylogeny and genomic data, the strain AZ1-13T could be distinguished from its closest neighbours, representing a novel species of the genus Micromonospora, for which the name Micromonospora radicis sp. nov. is proposed. The type strain is AZ1-13T (=KCTC 39786T=NBRC 112324T=JCM 32147T = TISTR 2404T). This study also proposed that J. zingiberisis transferred to the genus Micromonospora as Micromonospora zingiberis comb. nov. (type strain PLAI1-1T=TBRC 7644T=NBRC 113144T=JCM 32592T).
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Affiliation(s)
- Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Okuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani 12120, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Genomic Insight into Three Marine Micromonospora sp. Strains from the Gulf of California. Microbiol Resour Announc 2019; 8:8/28/e01673-18. [PMID: 31296693 PMCID: PMC6624776 DOI: 10.1128/mra.01673-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Three actinomycete strains, designated BL1, BL4, and CV4, were isolated from sediment samples from the Gulf of California in 2009 together with nearly 300 other actinobacteria. Genome mining and analysis of their ∼6.4-Mb sequences confirmed the bioprospecting potential of these three bacteria belonging to the genus Micromonospora. Three actinomycete strains, designated BL1, BL4, and CV4, were isolated from sediment samples from the Gulf of California in 2009 together with nearly 300 other actinobacteria. Genome mining and analysis of their ∼6.4-Mb sequences confirmed the bioprospecting potential of these three bacteria belonging to the genus Micromonospora.
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Subramani R, Sipkema D. Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products. Mar Drugs 2019; 17:E249. [PMID: 31035452 PMCID: PMC6562664 DOI: 10.3390/md17050249] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
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Affiliation(s)
- Ramesh Subramani
- School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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A study of three bacteria isolated from marine sediment and description of Micromonospora globispora sp. nov. Syst Appl Microbiol 2018; 42:190-197. [PMID: 30528275 DOI: 10.1016/j.syapm.2018.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 11/23/2022]
Abstract
During a study looking for the isolation of new actinobacteria strains with potential for antibiotic production from deep marine sediment, three strains were collected with a morphology similar to the one described for the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of the strains S2901T, S2903, and S2904. All the strains showed chemotaxonomic properties in line with their classification in the genus Micromonospora, meso-diaminopimelic acid in the wall peptidoglycan, a tetrahydrogenated menaquinone with nine isoprene units as major respiratory quinone, iso-C15:0 and iso-C16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The 16S rRNA gene sequences of strain S2901T, S2903, and S2904 showed the highest similarity (99.2%) with the type strain of Micromonospora halophytica DSM 43171T, forming an independent branch in the phylogenetic gene tree. Their independent position was confirmed with gyrB gene and MLSA phylogenies. Whole genome sequences confirmed by digital DNA-DNA hybridization analysis that the isolates should be assigned to a new species within the genus Micromonospora for which the name Micromonospora globispora sp. nov. (S2901T, S2903 and S2904) is proposed.
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Micromonospora azadirachtae sp. nov., isolated from roots of Azadirachta indica A. Juss. var. siamensis Valeton. Antonie van Leeuwenhoek 2018; 112:253-262. [DOI: 10.1007/s10482-018-1152-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/25/2018] [Indexed: 10/28/2022]
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Kuncharoen N, Pittayakhajonwut P, Tanasupawat S. Micromonospora globbae sp. nov., an endophytic actinomycete isolated from roots of Globba winitii C. H. Wright. Int J Syst Evol Microbiol 2018; 68:1073-1077. [PMID: 29458491 DOI: 10.1099/ijsem.0.002625] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel endophytic actinomycete, strain WPS1-2T, isolated from a root of Globba winitii C. H. Wright, was characterized taxonomically by using a polyphasic approach. Strain WPS1-2T exhibited identical characteristics to the members of the genus Micromonospora. Single spores were observed directly on substrate mycelia. The cell-wall peptidoglycan of the strain contained meso-diaminopimelic acid and 3-OH-meso-diaminopimelic acid. Whole-cell hydrolysates contained glucose, ribose, arabinose and xylose. The predominant menaquinones were MK-10(H8) and MK-10(H10). The major cellular fatty acids consisted of iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. According to the 16S rRNA gene sequence of the strain, WPS1-2T showed highest similarity to Micromonospora costi CS1-12T (99.02 %). Phylogenetic analysis of the gyrase subunit B (gyrB) gene indicated that the strain was related to M. costi CS1-12T. The DNA G+C content was 73.7 mol%. The strain could be distinguished from closely related type strains by using a combination of morphological, chemotaxonomic, physiological and biochemical data together with DNA-DNA relatedness values. Based on these observations, strain WPS1-2T is considered to represent a novel species of the genus Micromonospora, for which the name Micromonospora globbae sp. nov. is proposed. The type strain is WPS1-2T (=KCTC 39787T=NBRC 112325T=TISTR 2405T).
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Affiliation(s)
- Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani 12120, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz MDC, Sahin N, Smith DL, Kim KE, Peluso P, Deshpande S, Woyke T, Shapiro N, Kyrpides NC, Klenk HP, Göker M, Goodfellow M. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 2018; 8:525. [PMID: 29323202 PMCID: PMC5765111 DOI: 10.1038/s41598-017-17392-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022] Open
Abstract
There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Vartul Sangal
- Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Martha E Trujillo
- Departamento de Microbiologia y Genetica, Lab 214, Universidad de Salamanca, Salamanca, Spain
| | | | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, Kurupelit-Samsun, Turkey
| | - Darren Lee Smith
- Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Kristi E Kim
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA
| | - Paul Peluso
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
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Abstract
A novel actinobacterium, designated strain UDF-1T, was isolated from forest soil in Chungnam, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain UDF-1T formed a branched brownish-orange substrate mycelium with spherical or oval spores. No aerial mycelium was formed. Comparative 16S rRNA gene sequence analysis indicated that strain UDF-1T belongs to the genus Micromonospora, showing the highest sequence similarity to Micromonospora palomenae NEAU-CX1T (99.2 % 16S rRNA gene sequence similarity), 'Micromonospora maoerensis' NEAU-MES19 (99.0 %), Micromonospora endolithica DSM 44398T (98.8 %) and Micromonospora matsumotoense IMSNU 22003T (98.8 %). The predominant menaquinones of strain UDF-1T were MK-10 (H4) and MK-10 (H6). The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The major polar lipids were phosphatidylinositol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 73.1 mol%. DNA-DNA relatedness between strain UDF-1T and closely related type strains in the genus Micromonospora was below 30 %. On the basis of the polyphasic analysis conducted in this study, strain UDF-1T represents a novel species of the genus Micromonospora, for which the name Micromonospora fulva sp. nov. is proposed. The type strain is UDF-1T (=KACC 18696T=NBRC 111826T).
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Affiliation(s)
- Hyo-Jin Lee
- Institute of Microbial Ecology & Resources, Mokwon University, Daejeon 302-729, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbial & Nano Materials, Mokwon University, Daejeon 302-729, Republic of Korea
- Institute of Microbial Ecology & Resources, Mokwon University, Daejeon 302-729, Republic of Korea
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16
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Zhao S, Liu C, Zheng W, Ma Z, Cao T, Zhao J, Yan K, Xiang W, Wang X. Micromonospora parathelypteridis sp. nov., an endophytic actinomycete with antifungal activity isolated from the root of Parathelypteris beddomei (Bak.) Ching. Int J Syst Evol Microbiol 2017; 67:268-274. [PMID: 27902235 DOI: 10.1099/ijsem.0.001614] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel endophytic actinomycete with antifungal activity, designated strain NEAU-JXY5T, was isolated from the root of Parathelypteris beddomei (Bak.) Ching. Strain NEAU-JXY5T showed closest 16S rRNA gene sequence similarity to Micromonospora luteifusca GUI2T (99.31 %), and phylogenetically clustered with Micromonospora noduli GUI43T (99.24 %), 'Micromonospora lycii' NEAU-gq11 (99.19 %), 'Micromonospora zeae' NEAU-gq9 (99.12 %), Micromonospora saelicesensis Lupac 09T (98.97 %), Micromonospora vinacea GUI63T (98.96 %), 'Micromonospora jinlongensis' NEAU-GRX11 (98.91 %), Micromonospora profundi DS3010T (98.77 %), Micromonospora zamorensis CR38T (98.76 %), Micromonospora chokoriensis 2-19(6)T (98.71 %), Micromonospora lupini Lupac 14NT (98.69 %), Micromonospora ureilytica GUI23T (98.69 %), Micromonospora violae NEAU-zh8T (98.57 %) and Micromonospora taraxaci NEAU-P5T (98.37 %). Phylogenetic analysis based on gyrB gene sequences also indicated that the isolate clustered with the above strains except M. violae NEAU-zh8T. A combination of DNA-DNA hybridization results and some phenotypic characteristics indicated that the strain could be readily distinguished from these closest phylogenetic relatives. Therefore, it is concluded that strain NEAU-JXY5T represents a novel species of the genus Micromonospora, for which the name Micromonospora parathelypteridis sp. nov. is proposed. The type strain is NEAU-JXY5T (=CGMCC 4.7347T=DSM 103125T).
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Affiliation(s)
- Shanshan Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Chongxi Liu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Weiwei Zheng
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Zhaoxu Ma
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Tingting Cao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Kai Yan
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.,Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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17
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Talukdar M, Das D, Bora C, Bora TC, Deka Boruah HP, Singh AK. Complete genome sequencing and comparative analyses of broad-spectrum antimicrobial-producing Micromonospora sp. HK10. Gene 2016; 594:97-107. [PMID: 27609432 DOI: 10.1016/j.gene.2016.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 08/29/2016] [Accepted: 09/02/2016] [Indexed: 01/21/2023]
Abstract
Micromonospora genus produces >700 bioactive compounds of medical relevance. In spite of its ability to produce high number of bioactive compounds, no genome sequence is available with comprehensive secondary metabolite gene clusters analysis for anti-microbial producing Micromonospora strains. Thus, here we contribute the full genome sequence of Micromonospora sp. HK10 strain, which has high antibacterial activity against several important human pathogens like, Mycobacterium abscessus, Mycobacterium smegmatis, Bacillus subtillis, Staphylococcus aureus, Proteus vulgaris, Pseudomonas aeruginosa, Salmonella and Escherichia coli. We have generated whole genome sequence data of Micromonospora sp. HK10 strain using Illumina NexSeq 500 sequencing platform (2×150bp paired end library) and assembled it de novo. The sequencing of HK10 genome enables identification of various genetic clusters associated with known- and probably unknown- antimicrobial compounds, which can pave the way for new antimicrobial scaffolds.
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Affiliation(s)
- Madhumita Talukdar
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Dhrubajyoti Das
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Chiranjeeta Bora
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Tarun Chandra Bora
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Hari Prasanna Deka Boruah
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Anil Kumar Singh
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India; Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India.
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18
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Phongsopitanun W, Kudo T, Ohkuma M, Pittayakhajonwut P, Suwanborirux K, Tanasupawat S. Micromonospora sediminis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2016; 66:3235-3240. [PMID: 27220280 DOI: 10.1099/ijsem.0.001175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The novel actinomycete, strain CH3-3T, was isolated from mangrove sediment collected from Chonburi Province, Thailand. On the basis of its spore morphology and chemotaxonomic characteristics, the strain belonged to the genus Micromonospora. It contained meso-diaminopimelic acid, glucose, mannose, xylose, ribose and rhamnose in the whole-cell hydrolysate, MK-10(H4), MK-10(H6) and MK-10(H8) as major menaquinones, and iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 as major cellular fatty acids. blast analysis of 16S rRNA gene sequences revealed that the strain showed highest similarity with Micromonospora palomenae NEAU-CX1T (98.97 %) and Micromonospora coxensis 2-30-b(28)T (98.97 %). Based on phylogenetic tree analysis of the 16S rRNA gene sequence, the strain formed a cluster with M. palomenae NEAU-CX1T, Micromonospora halophytica DSM 43171T, M. coxensis 2-30-b(28)T and Micromonospora purpureochromogenes DSM 43821T. On the basis of phenotypic differences and DNA-DNA relatedness evidence, strain CH3-3T could be clearly distinguished from the closely related species of the genus Micromonospora and represents a novel species of the genus Micromonospora for which the name Micromonospora sediminis sp. nov. is proposed. The type strain is CH3-3T (=JCM 18523T=PCU 350T=TISTR 2396T).
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Affiliation(s)
- Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Khanit Suwanborirux
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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