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Oyuntsetseg B, Lee HB, Kim SB. Amycolatopsis mongoliensis sp. nov., a novel actinobacterium with antifungal activity isolated from a coal mining site in Mongolia. Int J Syst Evol Microbiol 2024; 74. [PMID: 38359091 DOI: 10.1099/ijsem.0.006266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
A novel filamentous actinobacterium designated strain 4-36T showing broad-spectrum antifungal activity was isolated from a coal mining site in Mongolia, and its taxonomic position was determined using polyphasic approach. Optimum growth occurred at 30 °C, pH 7.5 and in the absence of NaCl. Aerial and substrate mycelia were abundantly formed on agar media. The colour of aerial mycelium was white and diffusible pigments were not formed. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain 4-36T formed a distinct clade within the genus Amycolatopsis. The 16S rRNA gene sequence similarity showed that the strain was mostly related to Amycolatopsis lexingtonensis DSM 44544T and Amycolatopsis rifamycinica DSM 46095T with 99.3 % sequence similarity. However, the highest digital DNA-DNA hybridization value to closest species was 44.1 %, and the highest average nucleotide identity value was 90.2 %, both of which were well below the species delineation thresholds. Chemotaxonomic properties were typical of the genus Amycolatopsis, as the major fatty acids were C15 : 0, iso-C16 : 0 and C16 : 0, the cell-wall diamino acid was meso-diaminopimelic acid, the quinone was MK-9(H4), and the main polar lipids were diphosphatidylglycerol, phosphatidylmethanolamine and phosphatidylethanolamine. The in silico prediction of chemotaxonomic markers was also carried out by phylogenetic analysis. The genome mining for biosynthetic gene clusters of secondary metabolites in strain 4-36T revealed the presence of 34 gene clusters involved in the production of polyketide synthase, nonribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, lanthipeptide, terpenes, siderophore and many other unknown clusters. Strain 4-36T showed broad antifungal activity against several filamentous fungi. The phenotypic, biochemical and chemotaxonomic properties indicated that the strain could be clearly distinguished from other species of Amycolatopsis, and thus the name Amycolatopsis mongoliensis sp. nov. is proposed accordingly (type strain, 4-36T=KCTC 39526T=JCM 30565T).
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Affiliation(s)
- Bilguun Oyuntsetseg
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hyang Burm Lee
- Department of Agricultural Biological Chemistry, College of Agriculture & Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
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Looking Back to Amycolatopsis: History of the Antibiotic Discovery and Future Prospects. Antibiotics (Basel) 2021; 10:antibiotics10101254. [PMID: 34680834 PMCID: PMC8532670 DOI: 10.3390/antibiotics10101254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022] Open
Abstract
The emergence of antibiotic-resistant pathogenic bacteria in recent decades leads us to an urgent need for the development of new antibacterial agents. The species of the genus Amycolatopsis are known as producers of secondary metabolites that are used in medicine and agriculture. The complete genome sequences of the Amycolatopsis demonstrate a wide variety of biosynthetic gene clusters, which highlights the potential ability of actinomycetes of this genus to produce new antibiotics. In this review, we summarize information about antibiotics produced by Amycolatopsis species. This knowledge demonstrates the prospects for further study of this genus as an enormous source of antibiotics.
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Jin Y, Aobulikasimu N, Zhang Z, Liu C, Cao B, Lin B, Guan P, Mu Y, Jiang Y, Han L, Huang X. Amycolasporins and Dibenzoyls from Lichen-Associated Amycolatopsis hippodromi and Their Antibacterial and Anti-inflammatory Activities. JOURNAL OF NATURAL PRODUCTS 2020; 83:3545-3553. [PMID: 33216556 DOI: 10.1021/acs.jnatprod.0c00547] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Eleven metabolites, six echinosporins (1-6), four dibenzoyls (7-10), and an aromatic compound (11), were isolated from the fermentation broth of lichen-associated Amycolatopsis hippodromi. The structures of the new compounds (1-5, 8-11) were elucidated by comprehensive spectroscopic analysis including data from experimental and calculated ECD spectra. Amycolasporins A-C (1-3) demonstrated antibacterial activities against Bacillus subtilis, Staphylococcus aureus, and Escherichia coli with MIC values of 25 or 100 μg/mL. Amycolasporin C (3) and the known dibenzoyl (7) attenuated the production of NO due to the suppression of the expression of nitric oxide synthase (iNOS) in LPS-induced RAW 264.7 cells in a dose-dependent manner.
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Affiliation(s)
- Ying Jin
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
| | - Nuerbiye Aobulikasimu
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
| | - Zengguang Zhang
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
| | - Chengbin Liu
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, People's Republic of China
| | - Bixuan Cao
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
| | - Bin Lin
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Peipei Guan
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
| | - Yu Mu
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, People's Republic of China
| | - Li Han
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
| | - Xueshi Huang
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, People's Republic of China
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Niu MM, Ming H, Cheng LJ, Zhao ZL, Ji WL, Li M, Yi BF, Xia TT, Nie GX. Amycolatopsis nivea sp. nov., isolated from a Yellow River sample. Int J Syst Evol Microbiol 2020; 70:3084-3090. [PMID: 32250240 DOI: 10.1099/ijsem.0.004134] [Citation(s) in RCA: 7] [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 actinobacterium, designated strain CFH S0261T, was isolated from a sediment sample of the Yellow River. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of strain CFH S0261T were Gram-reaction-positive, aerobic, non-motile. Growth occurs at 15-37 °C, pH 6.0-8.0 and with 0-9.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CFH S0261T was a member of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain CFH S0261T is most closely related to the type strains of Amycolatopsis niigatensis LC11T (98.95 %), Amycolatopsis echigonensis LC2T (98.81 %) and Amycolatopsis albidoflavus IMSNU 22139T (98.73 %). The whole-genome of CFH S0261T showed a G+C content of 69.5 mol%. The ANI values and in silico DDH values between CFH S0261T and the other species of the genus Amycolatopsis were found to be low (ANIb <90.61 % and DDH <53.40 %). The cell wall diamino acid in the peptidoglycan of strain CFH S0261T was meso-diaminopimelic acid and the whole-cell hydrolysate comprised arabinose, galactose, glucose, rhamnose and ribose. The predominant menaquinone was MK-9(H4). The major cellular fatty acids were C16 : 0, iso-C15 : 0 and iso-C16 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and four unidentified glycolipids. On the basis of phenotypic, genotypic and phylogenetic data, strain CFH S0261T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis nivea sp. nov. is proposed. The type strain is CFH S0261T (=KCTC 39515T =CCTCC AA 2014028T).
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Affiliation(s)
- Ming-Ming Niu
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Hong Ming
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Li-Jiao Cheng
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Zhuo-Li Zhao
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Wei-Li Ji
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Meng Li
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Bing-Fang Yi
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Ting-Ting Xia
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
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Advances in microbial culturing conditions to activate silent biosynthetic gene clusters for novel metabolite production. ACTA ACUST UNITED AC 2019; 46:1381-1400. [DOI: 10.1007/s10295-019-02198-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
Abstract
Natural products (NPs) produced by bacteria and fungi are often used as therapeutic agents due to their complex structures and wide range of bioactivities. Enzymes that build NPs are encoded by co-localized biosynthetic gene clusters (BGCs), and genome sequencing has recently revealed that many BGCs are “silent” under standard laboratory conditions. There are numerous methods used to activate “silent” BGCs that rely either upon altering culture conditions or genetic modification. In this review, we discuss several recent microbial cultivation methods that have been used to expand the scope of NPs accessible in the laboratory. These approaches are divided into three categories: addition of a physical scaffold, addition of small molecule elicitors, and co-cultivation with another microbe.
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A genetics-free method for high-throughput discovery of cryptic microbial metabolites. Nat Chem Biol 2019; 15:161-168. [PMID: 30617293 PMCID: PMC6339573 DOI: 10.1038/s41589-018-0193-2] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/09/2018] [Indexed: 11/21/2022]
Abstract
Bacteria harbor an immense, untapped trove of novel secondary metabolites in the form of ‘silent’ biosynthetic gene clusters (BGCs). These can be identified bioinformatically but are not expressed under normal laboratory growth conditions. Methods to access their products would dramatically expand our pool of bioactive compounds. We report a universal high-throughput method for activating silent BGCs in diverse microorganisms. Our approach relies on elicitor screening to induce the secondary metabolome of a given strain and imaging mass spectrometry to visualize the resulting metabolomes in response to ~500 conditions. Because it does not require challenging genetic, cloning, or culturing procedures, it can be used with both sequenced and unsequenced bacteria. We demonstrate the power of the approach by applying it to diverse bacteria and report the discovery of nine cryptic metabolites with potentially therapeutic bioactivities, including a new glycopeptide chemotype with potent inhibitory activity against a pathogenic virus.
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Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF. Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism. Nat Commun 2018; 9:4147. [PMID: 30297823 PMCID: PMC6175910 DOI: 10.1038/s41467-018-06587-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/29/2018] [Indexed: 11/25/2022] Open
Abstract
Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (RifR). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant RifR mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of RifR RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.
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Affiliation(s)
- James Peek
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Daniel Montiel
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Ian Woodworth
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - John B Biggins
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Paula Y Calle
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Michael Danziger
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Thulasi Warrier
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kohta Saito
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nathaniel Braffman
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Allison Fay
- Immunology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | | | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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Xu X, Han L, Zhao L, Chen X, Miao C, Hu L, Huang X, Chen Y, Li Y. Echinosporin antibiotics isolated from Amycolatopsis strain and their antifungal activity against root-rot pathogens of the Panax notoginseng. Folia Microbiol (Praha) 2018; 64:171-175. [PMID: 30117099 DOI: 10.1007/s12223-018-0642-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/09/2018] [Indexed: 01/10/2023]
Abstract
Actinomycete strain YIM PH20520, isolated from the rhizosphere soil sample of Panax notoginseng collected in Wenshang, Yunnan Province, China, exhibited antifungal activity against root-rot pathogens of the Panax notoginseng. The structures of bioactive molecules, isolated from the ethyl acetate extract of the fermentation broth of the strain, were identified as echinosporin (1) and 7-deoxyechinosporin (2) based on extensive spectroscopic analyses. 1 exhibited antifungal activity against four tested root-rot pathogens of Panax notoginseng include Fusarium oxysporum, Fusarium solani, Alternaria panax, and Phoma herbarum with the MIC value at 64, 64, 32, and 64 μg/mL, respectively. 2 exhibited antifungal activities against F. oxysporum, F. solani, A. panax, and P. herbarum with the MIC value at 128, 128, 64, and 128 μg/mL, respectively. Based on the phylogenetic analyses, the closest phylogenetic relative of strain YIM PH20520 is Amycolatopsis speibonae JS72T (97.69%), so strain YIM PH20520 was identified as Amycolatopsis strain. To the best of our knowledge, this is the first report of echinosporin antibiotics isolated from Amycolatopsis strain besides Streptomyces strain and their antifungal activity against four tested root-rot pathogens of the Panax notoginseng. The results provide a reliable evidence for the following related biosynthetic investigations on Amycolatopsis strain YIM PH20520 due to echinosporins antibiotics' unique tricyclic acetal-lactone structures.
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Affiliation(s)
- Xindong Xu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Li Han
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China.
| | - Lixing Zhao
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Xiao Chen
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Cuiping Miao
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Linfang Hu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Xueshi Huang
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China
| | - Youwei Chen
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yiqing Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, College of Life Sciences, Yunnan University, Kunming, 650091, China.
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Sánchez-Hidalgo M, González I, Díaz-Muñoz C, Martínez G, Genilloud O. Comparative Genomics and Biosynthetic Potential Analysis of Two Lichen-Isolated Amycolatopsis Strains. Front Microbiol 2018; 9:369. [PMID: 29593664 PMCID: PMC5859366 DOI: 10.3389/fmicb.2018.00369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/16/2018] [Indexed: 11/15/2022] Open
Abstract
Actinomycetes have been extensively exploited as one of the most prolific secondary metabolite-producer sources and continue to be in the focus of interest in the constant search of novel bioactive compounds. The availability of less expensive next generation genome sequencing techniques has not only confirmed the extraordinary richness and broad distribution of silent natural product biosynthetic gene clusters among these bacterial genomes, but also has allowed the incorporation of genomics in bacterial taxonomy and systematics. As part of our efforts to isolate novel strains from unique environments, we explored lichen-associated microbial communities as unique assemblages to be studied as potential sources of novel bioactive natural products with application in biotechnology and drug discovery. In this work, we have studied the whole genome sequences of two new Amycolatopsis strains (CA-126428 and CA-128772) isolated from tropical lichens, and performed a comparative genomic analysis with 41 publicly available Amycolatopsis genomes. This work has not only permitted to infer and discuss their taxonomic position on the basis of the different phylogenetic approaches used, but has also allowed to assess the richness and uniqueness of the biosynthetic pathways associated to primary and secondary metabolism, and to provide a first insight on the potential role of these bacteria in the lichen-associated microbial community.
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Affiliation(s)
- Marina Sánchez-Hidalgo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
| | - Ignacio González
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
| | - Cristian Díaz-Muñoz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
| | - Germán Martínez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores de Andalucía, Granada, Spain
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Idris H, Nouioui I, Pathom-Aree W, Castro JF, Bull AT, Andrews BA, Asenjo JA, Goodfellow M. Amycolatopsis vastitatis sp. nov., an isolate from a high altitude subsurface soil on Cerro Chajnantor, northern Chile. Antonie van Leeuwenhoek 2018; 111:1523-1533. [PMID: 29428970 DOI: 10.1007/s10482-018-1039-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/02/2018] [Indexed: 10/18/2022]
Abstract
The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5T, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H4) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina, its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5T (= NCIMB 14970T = NRRL B-65279T).
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Affiliation(s)
- Hamidah Idris
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,Biology Department, Sultan Idris Education University, 35900, Tanjung Malim, Perak, Malaysia
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Wasu Pathom-Aree
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jean Franco Castro
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beaucheff 851, Santiago, Chile
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Barbara A Andrews
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beaucheff 851, Santiago, Chile
| | - Juan A Asenjo
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beaucheff 851, Santiago, Chile
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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11
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Human ZR, Crous CJ, Roets F, Venter SN, Wingfield MJ, de Beer ZW. Biodiversity and ecology of flower-associated actinomycetes in different flowering stages of Protea repens. Antonie van Leeuwenhoek 2017; 111:209-226. [PMID: 28936706 DOI: 10.1007/s10482-017-0942-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/06/2017] [Indexed: 02/07/2023]
Abstract
Actinomycete bacteria have previously been reported from reproductive structures (infructescences) of Protea (sugarbush/suikerbos) species, a niche dominated by fungi in the genera Knoxdaviesia and Sporothrix. It is probable that these taxa have symbiotic interactions, but a lack of knowledge regarding their diversity and general ecology precludes their study. We determined the diversity of actinomycetes within Protea repens inflorescence buds, open inflorescences, young and mature infructescences, and leaf litter surrounding these trees. Since the P. repens habitat is fire-prone, we also considered the potential of these bacteria to recolonise infructescences after fire. Actinomycetes were largely absent from flower buds and inflorescences but were consistently present in young and mature infructescences. Two Streptomyces spp. were the most consistent taxa recovered, one of which was also routinely isolated from leaf litter. Lower colonisation rates were evident in samples from a recently burnt site. One of the most consistent taxa isolated from older trees in the unburnt site was absent from this site. Our findings show that P. repens has a distinct community of actinomycetes dominated by a few species. These communities change over time and infructescence developmental stage, season and the age of the host population. Mature infructescences appear to be important sources of inoculum for some of the actinomycetes, seemingly disrupted by fire. Increased fire frequency limiting maturation of P. repens infructescences could thus impact future actinomycete colonisation in the landscape. Streptomyces spp. are likely to share this niche with the ophiostomatoid fungi, which merits further study regarding their interactions and mode of transfer.
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Affiliation(s)
- Zander R Human
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Casparus J Crous
- Department of Plant and Soil Sciences, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa.,Faculdade de Ciências, Centre for Ecology, Evolution and Environmental Changes (cE3c), Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Francois Roets
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Z Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
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Oyuntsetseg B, Cho SH, Jeon SJ, Lee HB, Shin KS, Kim IS, Kim SB. Amycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil. Int J Syst Evol Microbiol 2017; 67:3387-3392. [DOI: 10.1099/ijsem.0.002126] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bilguun Oyuntsetseg
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Sung-Heun Cho
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Sun Jeong Jeon
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Hyang Burm Lee
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Kee-Sun Shin
- Industrial Bio-materials Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong, Daejeon 34141, Republic of Korea
| | - In-Seop Kim
- Department of Biological Sciences and Biotechnology, College of Life Science and Nano Technology, Hannam University, 70 Hannam-ro, Daedeok, Daejeon 34430, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
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Kumari R, Singh P, Lal R. Genetics and Genomics of the Genus Amycolatopsis. Indian J Microbiol 2016; 56:233-46. [PMID: 27407288 PMCID: PMC4920768 DOI: 10.1007/s12088-016-0590-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/23/2016] [Indexed: 02/06/2023] Open
Abstract
Actinobacteria are gram-positive filamentous bacteria which contains some of the most deadly human pathogens (Mycobacterium tuberculosis, M. leprae, Corynebacterium diphtheriae, Nocardia farcinica), plant pathogens (Streptomyces scabies, Leifsonia xyli) along with organisms that produces antibiotic (Streptomycetes, Amycolatopsis, Salinospora). Interestingly, these bacteria are equipped with an extraordinary capability of producing antibiotics and other metabolites which have medicinal properties. With the advent of inexpensive genome sequencing techniques and their clinical importance, many genomes of Actinobacteria have been successfully sequenced. These days, with the constant increasing number of drug-resistant bacteria, the urgent need for discovering new antibiotics has emerged as a major scientific challenge. And, unfortunately the traditional method of screening bacterial strains for the production of antibiotics has decreased leading to a paradigm shift in the planning and execution of discovery of novel biosynthetic gene clusters via genome mining process. The entire focus has shifted to the evaluation of genetic capacity of organisms for metabolite production and activation of cryptic gene clusters. This has been made possible only due to the availability of genome sequencing and has been augmented by genomic studies and new biotechnological approaches. Through this article, we present the analysis of the genomes of species belonging to the genus Amycolatopsis, sequenced till date with a focus on completely sequenced genomes and their application for further studies.
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Affiliation(s)
- Rashmi Kumari
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Priya Singh
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
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Souza WR, Silva RE, Goodfellow M, Busarakam K, Figueiro FS, Ferreira D, Rodrigues-Filho E, Moraes LAB, Zucchi TD. Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil. Int J Syst Evol Microbiol 2015; 65:1786-1793. [DOI: 10.1099/ijs.0.000176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus
Amycolatopsis
and formed a branch in the
Amycolatopsis
16S rRNA gene tree together with
Amycolatopsis bullii
NRRL B-24847T,
Amycolatopsis plumensis
NRRL B-24324T,
Amycolatopsis tolypomycina
DSM 44544T and
Amycolatopsis vancoresmycina
NRRL B-24208T. It was related most closely to
A. bullii
NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus
Amycolatopsis
as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).
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Affiliation(s)
- Wallace Rafael Souza
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, Brazil
| | - Rafael Eduardo Silva
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, Brazil
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | | | - Fernanda Sales Figueiro
- Laboratório de Espectrometria de Massa Aplicado à Química de Produtos Naturais, Faculdade de Filosofia, Ciencias e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida dos Bandeirantes, 3900, 14040-901, Ribeirão Preto, Brazil
| | - Douglas Ferreira
- Laboratório de Bioquímica Micromolecular de Microorganismos, Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luiz, Km 235, Caixa Postal 676, 13565-905, São Carlos, Brazil
| | - Edson Rodrigues-Filho
- Laboratório de Bioquímica Micromolecular de Microorganismos, Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luiz, Km 235, Caixa Postal 676, 13565-905, São Carlos, Brazil
| | - Luiz Alberto Beraldo Moraes
- Laboratório de Espectrometria de Massa Aplicado à Química de Produtos Naturais, Faculdade de Filosofia, Ciencias e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida dos Bandeirantes, 3900, 14040-901, Ribeirão Preto, Brazil
| | - Tiago Domingues Zucchi
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, Brazil
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Overproduction of Ristomycin A by activation of a silent gene cluster in Amycolatopsis japonicum MG417-CF17. Antimicrob Agents Chemother 2014; 58:6185-96. [PMID: 25114137 DOI: 10.1128/aac.03512-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The emergence of antibiotic-resistant pathogenic bacteria within the last decades is one reason for the urgent need for new antibacterial agents. A strategy to discover new anti-infective compounds is the evaluation of the genetic capacity of secondary metabolite producers and the activation of cryptic gene clusters (genome mining). One genus known for its potential to synthesize medically important products is Amycolatopsis. However, Amycolatopsis japonicum does not produce an antibiotic under standard laboratory conditions. In contrast to most Amycolatopsis strains, A. japonicum is genetically tractable with different methods. In order to activate a possible silent glycopeptide cluster, we introduced a gene encoding the transcriptional activator of balhimycin biosynthesis, the bbr gene from Amycolatopsis balhimycina (bbrAba), into A. japonicum. This resulted in the production of an antibiotically active compound. Following whole-genome sequencing of A. japonicum, 29 cryptic gene clusters were identified by genome mining. One of these gene clusters is a putative glycopeptide biosynthesis gene cluster. Using bioinformatic tools, ristomycin (syn. ristocetin), a type III glycopeptide, which has antibacterial activity and which is used for the diagnosis of von Willebrand disease and Bernard-Soulier syndrome, was deduced as a possible product of the gene cluster. Chemical analyses by high-performance liquid chromatography and mass spectrometry (HPLC-MS), tandem mass spectrometry (MS/MS), and nuclear magnetic resonance (NMR) spectroscopy confirmed the in silico prediction that the recombinant A. japonicum/pRM4-bbrAba synthesizes ristomycin A.
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Everest GJ, le Roes-Hill M, Rohland J, Enslin S, Meyers PR. Amycolatopsis roodepoortensis sp. nov. and Amycolatopsis speibonae sp. nov.: antibiotic-producing actinobacteria isolated from South African soils. J Antibiot (Tokyo) 2014; 67:813-8. [DOI: 10.1038/ja.2014.79] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 04/14/2014] [Accepted: 05/25/2014] [Indexed: 11/09/2022]
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Everest GJ, le Roes-Hill M, Omorogie C, Cheung SK, Cook AE, Goodwin CM, Meyers PR. Amycolatopsis umgeniensis sp. nov., isolated from soil from the banks of the Umgeni River in South Africa. Antonie van Leeuwenhoek 2012. [PMID: 23180373 DOI: 10.1007/s10482-012-9851-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A novel member of the genus Amycolatopsis was isolated from soil collected from the banks of the Umgeni River, KwaZulu Natal province, South Africa. The strain, designated UM16(T), grouped with the type strains of Amycolatopsis alba, Amycolatopsis coloradensis and Amycolatopsis thailandensis by 16S rRNA gene based phylogeny. Genetic distance values, based on the gyrB and recN genes, between strain UM16(T) and its closest relatives were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis type strains. DNA-DNA hybridisation experiments confirmed that strain UM16(T) represents a unique genomic species, sharing 18.4 ± 5.1, 16.2 ± 1.8 and 45.8 ± 8.9 % DNA relatedness to the type strains of A. alba, A. coloradensis and A. thailandensis, respectively. The physiological, phylogenetic and DNA-relatedness data support the description of strain UM16(T) as the type strain of a novel species, for which the name Amycolatopsis umgeniensis sp. nov. is proposed (= DSM 45272(T) = NRRL B-24724(T)).
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Affiliation(s)
- Gareth J Everest
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
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Zucchi TD, Bonda ANV, Frank S, Kim BY, Kshetrimayum JD, Goodfellow M. Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils. Antonie van Leeuwenhoek 2012; 102:91-8. [PMID: 22434348 DOI: 10.1007/s10482-012-9716-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 02/27/2012] [Indexed: 10/28/2022]
Abstract
The status of two mesophilic filamentous actinomycetes isolated from an arid Australian soil sample was determined using a polyphasic taxonomic approach. The isolates had chemical and morphological properties consistent with their classification in the genus Amycolatopsis, assignments that were supported by analysis of 16S rRNA gene sequence data. Isolate SF26(T) formed a distinct phyletic line and hence was sharply separated from its nearest phylogenetic neighbour, Amycolatopsis sacchari DSM 44468(T). In contrast, isolate SF27(T) formed a subclade in the Amycolatopsis tree with Amycolatopsis vancoresmycina DSM 44592(T) but was separated readily from the latter by DNA:DNA pairing data. The two isolates were distinguished from one another and from their respective nearest phylogenetic neighbours using a range of phenotypic properties. These data indicate that the two isolates should be recognized as new species in the genus Amycolatopsis. The names proposed for these new taxa are Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov. with isolates SF26(T) (=NCIMB 14706(T) = NRRL B-2846(T)) and SF27(T) (=NCIMB 14707(T) = NRRL B-24847(T)) as the respective type strains.
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2012. [DOI: 10.1099/ijs.0.041269-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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