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Deng A, Fu L, Mo P, Zheng Y, Tang T, Gao J. New insights into the relationship between the average nucleotide identity and the digital DNA-DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis. Front Microbiol 2024; 15:1359021. [PMID: 38686110 PMCID: PMC11056570 DOI: 10.3389/fmicb.2024.1359021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/27/2024] [Indexed: 05/02/2024] Open
Abstract
At present, it is widely believed that a 95-96% average nucleotide identity (ANI) value is equivalent to a 70% digital DNA-DNA hybridization (dDDH) value in the prokaryotic taxonomy. However, in the present study, comparative genome analysis of 29 pairs of Amycolatopsis type strains revealed that a 70% dDDH value did not correspond to a 95-96% ANI based on the MuMmer ultra-rapid aligning tool (ANIm) but approximately corresponded to a 96.6% ANIm value in the genus Amycolatopsis. Based on this corresponding relationship, phenotypic and chemotaxonomical characteristics, as well as phylogenetic analysis, an actinobacterial strain HUAS 11-8T isolated from the rhizosphere soil of Cynara scolymus, was subjected to a polyphasic taxonomic characterization. Based on EzBioCloud alignment, it was found that strain HUAS11-8T had the 16S rRNA gene similarities of 99.78% with A. rhizosphaerae JCM 32589T, 97.8% with A. dongchuanensis YIM 75904T, and < 97.8% sequence similarities to other Amycolatopsis species. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences revealed that strain HUAS 11-8T was closely related to A. rhizosphaerae JCM 32589T. ANIm and dDDH values between strains HUAS 11-8T and A. rhizosphaerae JCM 32589T were 96.3 and 68.5%, respectively, lower than the 96.6 and 70% thresholds recommended for the delineation of a novel Amycolatopsis species. Consequently, strain HUAS 11-8T should represent a novel Amycolatopsis species, for which the name Amycolatopsis cynarae sp. nov. (type strain HUAS 11-8T = MCCC 1K08337T = JCM 35980T) is proposed. Furthermore, based on comparative genomic analysis and rule 42 of the Prokaryotic Code, we propose that Amycolatopsis niigatensis is a later heterotypic synonym of Amycolatopsis echigonensis.
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Affiliation(s)
- Aihua Deng
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Li Fu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, China
| | - Ping Mo
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Yaxi Zheng
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Ting Tang
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Jian Gao
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, China
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Wannawong T, Mhuantong W, Macharoen P, Niemhom N, Sitdhipol J, Chaiyawan N, Umrung S, Tanasupawat S, Suwannarach N, Asami Y, Kuncharoen N. Comparative genomics reveals insight into the phylogeny and habitat adaptation of novel Amycolatopsis species, an endophytic actinomycete associated with scab lesions on potato tubers. FRONTIERS IN PLANT SCIENCE 2024; 15:1346574. [PMID: 38601305 PMCID: PMC11004387 DOI: 10.3389/fpls.2024.1346574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
A novel endophytic actinomycete, strain MEP2-6T, was isolated from scab tissues of potato tubers collected from Mae Fag Mai Sub-district, San Sai District, Chiang Mai Province, Thailand. Strain MEP2-6T is a gram-positive filamentous bacteria characterized by meso-diaminopimelic acid in cell wall peptidoglycan and arabinose, galactose, glucose, and ribose in whole-cell hydrolysates. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and hydroxy-phosphatidylethanolamine were the major phospholipids, of which MK-9(H6) was the predominant menaquinone, whereas iso-C16:0 and iso-C15:0 were the major cellular fatty acids. The genome of the strain was 10,277,369 bp in size with a G + C content of 71.7%. The 16S rRNA gene phylogenetic and core phylogenomic analyses revealed that strain MEP2-6T was closely related to Amycolatopsis lexingtonensis NRRL B-24131T (99.4%), A. pretoriensis DSM 44654T (99.3%), and A. eburnea GLM-1T (98.9%). Notably, strain MEP2-6T displayed 91.7%, 91.8%, and 87% ANIb and 49%, 48.8%, and 35.4% dDDH to A. lexingtonensis DSM 44653T (=NRRL B-24131T), A. eburnea GLM-1T, and A. pretoriensis DSM 44654T, respectively. Based on phenotypic, chemotaxonomic, and genomic data, strain MEP2-6T could be officially assigned to a novel species within the genus Amycolatopsis, for which the name Amycolatopsis solani sp. nov. has been proposed. The type of strain is MEP2-6T (=JCM 36309T = TBRC 17632T = NBRC 116395T). Amycolatopsis solani MEP2-6T was strongly proven to be a non-phytopathogen of potato scab disease because stunting of seedlings and necrotic lesions on potato tuber slices were not observed, and there were no core biosynthetic genes associated with the BGCs of phytotoxin-inducing scab lesions. Furthermore, comparative genomics can provide a better understanding of the genetic mechanisms that enable A. solani MEP2-6T to adapt to the plant endosphere. Importantly, the strain smBGCs accommodated 33 smBGCs encoded for several bioactive compounds, which could be beneficially applied in the fields of agriculture and medicine. Consequently, strain MEP2-6T is a promising candidate as a novel biocontrol agent and antibiotic producer.
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Affiliation(s)
- Thippawan Wannawong
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Wuttichai Mhuantong
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Enzyme Technology Research Team, Biorefinery and Bioproducts Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pipat Macharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Nantawan Niemhom
- Microbiological and Molecular Biological Laboratory, Scientific Instruments Center, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Jaruwan Sitdhipol
- Biodiversity Research Centre, Research and Development Group for Bio-Industries, Thailand Institute of Scientific and Technological Research, Pathum Thani, Thailand
| | - Neungnut Chaiyawan
- Biodiversity Research Centre, Research and Development Group for Bio-Industries, Thailand Institute of Scientific and Technological Research, Pathum Thani, Thailand
| | - Sarinna Umrung
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Nakarin Suwannarach
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Yukihiro Asami
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
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Ren CY, Zhao HP. Synthetic Nuclease-Producing Microbiome Achieves Efficient Removal of Extracellular Antibiotic Resistance Genes from Wastewater Effluent. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21224-21234. [PMID: 38059467 DOI: 10.1021/acs.est.3c07974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Antibiotic resistance gene (ARG) transmission poses significant threats to human health. The effluent of wastewater treatment plants is demonstrated as a hotspot source of ARGs released into the environment. In this study, a synthetic microbiome containing nuclease-producing Deinococcus radiodurans was constructed to remove extracellular ARGs. Results of quantitative polymerase chain reaction (qPCR) showed significant reduction in plasmid RP4-associated ARGs (by more than 3 orders of magnitude) and reduction of indigenous ARG sul1 and mobile genetic element (MGE) intl1 (by more than 1 order of magnitude) in the synthetic microbiome compared to the control without D. radiodurans. Metagenomic analysis revealed a decrease in ARG and MGE diversity in extracellular DNA (eDNA) of the treated group. Notably, whereas eight antibiotic-resistant plasmids with mobility risk were detected in the control, only one was detected in the synthetic microbiome. The abundance of the nuclease encoding gene exeM, quantified by qPCR, indicated its enrichment in the synthetic microbiome, which ensures stable eDNA degradation even when D. radiodurans decreased. Moreover, intracellular ARGs and MGEs and pathogenic ARG hosts in the river receiving treated effluent were lower than those in the river receiving untreated effluent. Overall, this study presents a new approach for removing extracellular ARGs and further reducing the risk of ARG transmission in receiving rivers.
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Affiliation(s)
- Chong-Yang Ren
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
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Identification and antimicrobial susceptibility of Streptomyces and other unusual Actinobacteria clinical isolates in Spain. New Microbes New Infect 2021; 44:100946. [PMID: 34917388 PMCID: PMC8669300 DOI: 10.1016/j.nmni.2021.100946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 09/22/2021] [Accepted: 11/15/2021] [Indexed: 11/22/2022] Open
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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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Wang HF, Li XY, Gao R, Xie YG, Xiao M, Li QL, Li WJ. Amycolatopsis anabasis sp. nov., a novel endophytic actinobacterium isolated from roots of Anabasis elatior. Int J Syst Evol Microbiol 2020; 70:3391-3398. [DOI: 10.1099/ijsem.0.004184] [Citation(s) in RCA: 8] [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 actinobacterium, designated strain EGI 650086T, was isolated from the roots of Anabasis elatior (C.A.Mey.) Schischk. collected in Xinjiang, north-west China. The taxonomic position of the strain was investigated using a polyphasic taxonomic approach. Growth occurred at 15–40 °C, pH 6.0–8.0 and in the presence of 0–6 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence and concatenation of 22 protein marker genes revealed that strain EGI 650086T formed a monophyletic clade within the genus
Amycolatopsis
and shared the highest sequence similarities with
Amycolatopsis nigrescens
JCM 14717T (97.1 %) and
Amycolatopsis sacchari
DSM 44468T (97.0 %). Sequence similarities with type strains of other species of the genus
Amycolatopsis
were less than 97.0 %. The average nucleotide identity and DNA–DNA hybridization values between strain EGI 650086T and the reference strains were 78.1–79.8 % and 22.1–23.0 %, respectively. The genome of strain EGI 650086T was 10.9 Mb, with a DNA G+C content of 70.1 mol%. The diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. The major whole-cell sugars contained arabinose, galactose, glucose and ribose. The predominant menaquinones were MK-9 (H4) and MK-9 (H2). Major fatty acids were iso-C16 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The polar lipid profile of strain EGI 650086T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phospholipids, an unknown glycolipid and an unknown lipid. Polyphasic taxonomic characteristics indicated that strain EGI 650086T represents a novel species of the genus
Amycolatopsis
, for which the name Amycolatopsis anabasis sp. nov. is proposed. The type strain is EGI 650086T (=KCTC 49044T=CGMCC 4.7188T).
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Affiliation(s)
- Hong-Fei Wang
- School of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Xin-Yang Li
- School of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Rui Gao
- Dandong Forestry and Grassland Development Service Center, Dandong 118000, PR China
| | - Yuan-Guo Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qiu-Li Li
- School of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Wen-Jun Li
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, 830011, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, PR 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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Chaiya L, Matsumoto A, Wink J, Inahashi Y, Risdian C, Pathom-Aree W, Lumyong S. Amycolatopsis eburnea sp. nov., an actinomycete associated with arbuscular mycorrhizal fungal spores. Int J Syst Evol Microbiol 2019; 69:3603-3608. [PMID: 31433288 DOI: 10.1099/ijsem.0.003669] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain GLM-1T, was isolated from arbuscular mycorrhizal fungal spores from Funneliformis mosseae RYA08, collected from Aquilaria crassna Pierre ex Lec. rhizosphere soil in Klaeng, Rayong Province, Thailand. Morphological characteristics of this strain included long chains of rod-like cells and squarish elements. The cell-wall composition of this novel isolate contained meso-diaminopimelic acid. The whole-cell diagnostic sugars were arabinose and galactose. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 and iso-C15 : 0. Only phosphatidylethanolamine was detected as a polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GLM-1T was closely related to Amycolatopsis rhabdoformis SB026T (99.11 %) with a low DNA-DNA hybridization value of 22.6-34.7 %. Genome sequencing revealed a genome size of 10 Mbp. There were obvious distinctions in the average nucleotide identity values between stain GLM-1T and its closely related strains at around 86-93 % (ANIb) and 89-94 % (ANIm). The digital DNA-DNA hybridization values between strain GLM-1T and type strains of phylogenetically related species were 34-55 %. The G+C content of the genomic DNA was 71.8 mol%. Based on these data, strain GLM-1T is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsiseburnea sp. nov. is proposed. The type strain is GLM-1T (=TBRC 9315T=NBRC 113658T).
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Affiliation(s)
- Leardwiriyakool Chaiya
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Atsuko Matsumoto
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.,Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - Yuki Inahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.,Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Chandra Risdian
- Research Unit for Clean Technology, Indonesian Institute of Sciences (LIPI), Bandung 40135, Indonesia.,Microbial Strain Collection, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - Wasu Pathom-Aree
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Science and Technology Research Institute, Chiang Mai University, Chiang Mai 50200, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- The Royal Society of Thailand, Academy of Science, Bangkok 10300, Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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9
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Amycolatopsis alkalitolerans sp. nov., isolated from Gastrodia elata Blume. J Antibiot (Tokyo) 2019; 73:35-39. [PMID: 31434994 DOI: 10.1038/s41429-019-0222-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/19/2019] [Accepted: 08/06/2019] [Indexed: 11/08/2022]
Abstract
A Gram-staining positive and nonmotile strain designated SYSUP0005T was isolated from tubers of Gastrodia elata Blume. The 16S rRNA gene sequence result showed that strain SYSUP0005T shared highest sequence similarity with the type strain of Amycolatopsis cappadoca (95.7%), Amycolatopsis taiwanensis (95.4%), Amycolatopsis pigmentata (95.4%), Amycolatopsis ruanii (95.1%), and Amycolatopsis helveola (94.8%). Growth occurs at 14-37 °C (optimum temperature, 28 °C), at pH 6-9 (optimum, pH 8) and in the presence of up to 6% (w/v) NaCl. Strain SYSUP0005T had meso-diaminopimelic acid in its peptidoglycan. The whole cell sugars were galactose, ribose, and xylose. The predominant menaquinone was MK-9(H4) and minor menaquinones were MK-9(H2) and MK-9(H8). The polar lipids were diphosphatidylglycerol (DPG); phosphatidylmonomethylethanolamine (PME), phosphatidylethanolamine (PE), phosphatidylinositol (PI), unidentified glycolipid (GL), and unidentified phospholipid (PL). The genomic DNA G + C content was 69.6 mol%. The major fatty acids were iso-C16:0, anteiso-C17:0, C16:0, iso-C14:0, C17:1 ω6c, C17:0, and Summed Feature 3 (C16:1 ω7c/C16:1 ω6c). On the basis of the phenotypic, phylogenetic, chemotaxonomic characters, and genomic comparison, SYSUP0005T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis alkalitolerans sp. nov. is proposed. The type strain is SYSUP0005T (=KCTC 49024T = CGMCC4.7463T).
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10
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Adamek M, Alanjary M, Sales-Ortells H, Goodfellow M, Bull AT, Winkler A, Wibberg D, Kalinowski J, Ziemert N. Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species. BMC Genomics 2018; 19:426. [PMID: 29859036 PMCID: PMC5984834 DOI: 10.1186/s12864-018-4809-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 05/21/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary. RESULTS Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis' strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes. CONCLUSIONS Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.
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Affiliation(s)
- Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Mohammad Alanjary
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Helena Sales-Ortells
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Michael Goodfellow
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU UK
| | - Alan T. Bull
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Anika Winkler
- Universität Bielefeld, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Daniel Wibberg
- Universität Bielefeld, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Jörn Kalinowski
- Universität Bielefeld, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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11
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Thawai C. Amycolatopsis rhizosphaerae sp. nov., isolated from rice rhizosphere soil. Int J Syst Evol Microbiol 2018. [PMID: 29537361 DOI: 10.1099/ijsem.0.002704] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chitti Thawai
- Department of Biology, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
- Actinobacterial Research Unit, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
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12
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Abstract
The group of Gram-positive bacillary organisms broadly known as "aerobic actinomycetes" consists of heterogeneous and taxonomically divergent genera. They are found in a wide variety of natural and man-made environments but are rarely considered a part of the normal human flora, with infections normally originating from exogenous sources. An extensive number of genera have been described, but only a minority of these has been associated with human or veterinary health. The association with human disease is usually of an opportunistic nature, either through accidental means of inoculation or through involvement with immunocompromising conditions in the host. They cause a wide spectrum of diseases in humans, which may differ greatly between the genera and even between species, but which also may have a great amount of overlap. The occurrence of such infections is probably greater than appreciated, since many may go unrecognized. Etiologic prevalence of specific genera and species varies geographically within the United States and worldwide. Traditional phenotypic identification methods for separation of the many genera and species of aerobic actinomycetes have found great difficulties. Recent use of chemotaxonomic analyses and emerging technologies such as molecular analysis of nucleic acids, and more recently proteomics for identification to the genus/species level, has provided a far more robust technique to understand the organisms' relatedness, distribution, epidemiology, and pathogenicity in humans.
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13
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Zhang G, Wang L, Li J, Zhou Y. Amycolatopsis albispora sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:3860-3864. [DOI: 10.1099/ijsem.0.001277] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, PR China
| | - Lina Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
- School of Biological Engineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Jinglong Li
- School of Biological Engineering, Qilu University of Technology, Jinan 250353, Shandong, PR China
| | - Yuan Zhou
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, PR China
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14
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Klykleung N, Tanasupawat S, Pittayakhajonwut P, Ohkuma M, Kudo T. Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant. Int J Syst Evol Microbiol 2015; 65:3894-3899. [PMID: 28875918 DOI: 10.1099/ijsem.0.000509] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
A novel actinomycete, strain ST1-08T, was isolated from the stem of Stemona sp. in Thailand. The taxonomic position of this isolate was determined by using a polyphasic approach. Strain ST1-08T contained meso-diaminopimelic acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars of the whole-cell hydrolysate, which are typical properties of members of the genus Amycolatopsis. Strain ST1-08T grew at 15-40 °C, pH 6-9 and on 5 % (w/v) NaCl. Gelatin liquefaction, starch hydrolysis and skimmed milk peptonization were positive. The strain utilized l-arabinose, d-glucose, glycerol, myo-inositol, d-mannitol and l-rhamnose. The predominant menaquinone was MK-9(H4) and the major cellular fatty acids were iso-C16 : 0 and iso-C15 : 0.The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. The 16S rRNA gene sequence analysis revealed that the strain was closely related to Amycolatopsis pretoriensis JCM 12673T (98.99 %) and Amycolatopsis lexingtonensis JCM 12672T (98.87 %). The DNA G+C content of strain ST1-08T was 71.2 mol%. The DNA-DNA relatedness values among strain ST1-08T, A. pretoriensis JCM 12673T and A. lexingtonensis JCM 12672T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of phenotypic and genotypic characteristics, strain ST1-08T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis stemonae is proposed. The type strain is ST1-08T( = JCM 30050T = PCU 339T = TISTR 2278T).
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Affiliation(s)
- Nattaporn Klykleung
- Department of Biochemistry and Microbiology, 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
| | - Pattama Pittayakhajonwut
- Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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15
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Wei X, Jiang Y, Chen X, Jiang Y, Lai H. Amycolatopsis flava sp. nov., a halophilic actinomycete isolated from Dead Sea. Antonie van Leeuwenhoek 2015; 108:879-85. [DOI: 10.1007/s10482-015-0542-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 07/19/2015] [Indexed: 10/23/2022]
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16
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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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17
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Hamedi J, Mohammadipanah F, Panahi HKS. Biotechnological Exploitation of Actinobacterial Members. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2015. [DOI: 10.1007/978-3-319-14595-2_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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18
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Nie GX, Ming H, Li S, Zhou EM, Cheng J, Tang X, Feng HG, Tang SK, Li WJ. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:2650-2656. [DOI: 10.1099/ijs.0.038125-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, designated YIM 75904T, was isolated from a soil sample that had been collected from a dry and hot river valley in Dongchuan county, Yunnan province, south-western China. The taxonomic position of the novel strain was investigated by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain YIM 75904T formed a distinct clade within the genus
Amycolatopsis
and appeared to be closely related to
Amycolatopsis sacchari
K24T (99.3 % sequence similarity). Strain YIM 75904T had a type-IV cell wall, with no detectable mycolic acids, and had MK-9(H4) as its predominant menaquonine. Its cell wall contained meso-diaminopimelic acid, galactose, glucose and arabinose, and its major cellular fatty acids were iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of the novel strain was 68.5 mol%. Based on the results of physiological and biochemical tests and DNA–DNA hybridizations, strain YIM 75904T represents a novel species of the genus
Amycolatopsis
for which the name Amycolatopsis dongchuanensis sp. nov. is proposed. The type strain is YIM 75904T ( = CCTCC AA 2011016T = JCM 18054T).
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Affiliation(s)
- Guo-Xing Nie
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China
| | - Hong Ming
- Department of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Shuai Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China
| | - En-Min Zhou
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Juan Cheng
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Xia Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Hui-Gen Feng
- Department of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Shu-Kun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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19
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Zucchi TD, Tan GYA, Bonda ANV, Frank S, Kshetrimayum JD, Goodfellow M. Amycolatopsis granulosa sp. nov., Amycolatopsis ruanii sp. nov. and Amycolatopsis thermalba sp. nov., thermophilic actinomycetes isolated from arid soils. Int J Syst Evol Microbiol 2011; 62:1245-1251. [PMID: 21764982 DOI: 10.1099/ijs.0.031039-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Amycolatopsis. 16S rRNA gene sequence data supported the classification of the isolates in the genus Amycolatopsis and showed that they formed distinct branches in the Amycolatopsis methanolica subclade. DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The three isolates were readily distinguished from one another and from the type strains of species classified in the A. methanolica subclade based on a combination of phenotypic properties and by genomic fingerprinting. Consequently, it is proposed that the three isolates be classified in the genus Amycolatopsis as representatives of Amycolatopsis granulosa sp. nov. (type strain GY307(T) = NCIMB 14709(T) = NRRL B-24844(T)), Amycolatopsis ruanii sp. nov. (type strain NMG112(T) = NCIMB 14711(T) = NRRL B-24848(T)) and Amycolatopsis thermalba sp. nov. (type strain SF45(T) = NCIMB 14705(T) = NRRL B-24845(T)).
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Affiliation(s)
- Tiago Domingues Zucchi
- Departamento de Entomologia and Acarologia, ESALQ, Universidade de São Paulo, Piracicaba, Brazil
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Sarah Frank
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | | | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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20
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Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L. Antonie van Leeuwenhoek 2011; 100:333-9. [PMID: 21594685 DOI: 10.1007/s10482-011-9588-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 05/10/2011] [Indexed: 10/18/2022]
Abstract
A novel actinomycete, designated KLBMP 1221(T), was isolated from the surface-sterilized seeds of an oil-seed plant Jatropha curcas L. collected from Sichuan Province, south-west China and was characterized taxonomically by using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequence showed that this strain formed a distinct phyletic line within the radiation of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain KLBMP 1221(T) was most closely related to Amycolatopsis eurytherma NT202(T) (98.9%), Amycolatopsis tucumanensis ABO(T) (98.8%), Amycolatopsis thermoflava N1165(T) (98.6%) and Amycolatopsis methanolica IMSNU 20055(T) (98.5%). Strain KLBMP 1221(T) had morphological and chemotaxonomic properties that were consistent with its classification in the genus Amycolatopsis. However, DNA-DNA relatedness data and phenotypic differences clearly distinguished the isolate from its closest relatives. Based on the combined genotypic and phenotypic evidence, it is proposed that strain KLBMP 1221(T) be classified as representative of a novel species for which the name Amycolatopsis endophytica sp. nov. is proposed. The type strain is KLBMP 1221(T) (= KCTC 19776(T) = CCTCC AA 2010003(T)).
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21
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Duangmal K, Mingma R, Pathom-aree W, Thamchaipenet A, Inahashi Y, Matsumoto A, Takahashi Y. Amycolatopsis samaneae sp. nov., isolated from roots of Samanea saman (Jacq.) Merr. Int J Syst Evol Microbiol 2011; 61:951-955. [DOI: 10.1099/ijs.0.022699-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain RM287T, was isolated from surface-sterilized roots of Samanea saman (Jacq.) Merr., collected from Bangkok, Thailand. The status of the novel strain was determined using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism formed a distinct phyletic line within the radiation of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain RM287T was most closely related to Amycolatopsis mediterranei IMSNU 20056T (97.4 %), A. rifamycinica DSM 46095T (97.2 %), A. kentuckyensis NRRL B-24129T (97.2 %), A. pretoriensis DSM 44654T (97 %) and A. australiensis DSM 44671T (97 %). The novel organism was found to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the dignostic diamino acid in the cell-wall peptidoglycan and arabinose and galactose as the diagnostic sugars. The major menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 iso-C15 : 0, iso 2-OH-C16 : 0 and iso-C17 : 0. The DNA G+C content was 71.7 mol%. Phenotypic data clearly distinguished the novel isolate from its closest relatives. The combined genotypic and phenotypic data indicated that strain RM287T represented a novel species of the genus Amycolatopsis. The proposed name for this organism is Amycolatopsis samaneae sp. nov., with the type strain RM287T ( = TISTR 1919T = BCC 35842T = NBRC 106095T).
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Affiliation(s)
- Kannika Duangmal
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Chatuchak, Bangkok 10900, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Ratchanee Mingma
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Chatuchak, Bangkok 10900, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Wasu Pathom-aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Chatuchak, Bangkok 10900, Thailand
| | - Yuki Inahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yoko Takahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
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22
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Zucchi TD, Tan GYA, Goodfellow M. Amycolatopsis thermophila sp. nov. and Amycolatopsis viridis sp. nov., thermophilic actinomycetes isolated from arid soil. Int J Syst Evol Microbiol 2011; 62:168-172. [PMID: 21378137 DOI: 10.1099/ijs.0.029256-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of two thermophilic actinomycetes isolated from an arid Australian soil sample were established based on an investigation using a polyphasic taxonomic approach. The organisms had chemical and morphological properties typical of members of the genus Amycolatopsis and formed distinct phyletic lines in the Amycolatopsis methanolica 16S rRNA subclade. The two organisms were distinguished from one another and from the type strains of related species of the genus Amycolatopsis using a range of phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycolatopsis thermophila sp. nov. (type strain GY088(T)=NCIMB 14699(T)=NRRL B-24836(T)) and Amycolatopsis viridis sp. nov. (type strain GY115(T)=NCIMB 14700(T)=NRRL B-24837(T)).
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Affiliation(s)
- Tiago Domingues Zucchi
- Departamento de Entomologia & Acarologia, ESALQ, Universidade de São Paulo, Piracicaba, Brazil
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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23
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Guan TW, Xia ZF, Tang SK, Wu N, Chen ZJ, Huang Y, Ruan JS, Li WJ, Zhang LL. Amycolatopsis salitolerans sp. nov., a filamentous actinomycete isolated from a hypersaline habitat. Int J Syst Evol Microbiol 2011; 62:23-27. [PMID: 21317279 DOI: 10.1099/ijs.0.030031-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, designated TRM F103(T), was isolated from a hypersaline habitat of the Tarim basin in Xinjiang province, north-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Amycolatopsis and was most closely related to Amycolatopsis halophila YIM 93223(T) (99.3% 16S rRNA gene sequence similarity). However, DNA-DNA relatedness between these two strains, based on triplicate experiments, was only 31.6%. The isolate contained meso-diaminopimelic acid and ribose, glucose and galactose as the major whole-cell sugars. The predominant menaquinone was MK-8(H(4)). The major fatty acids were iso-C(16:0) and C(16:0). The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and glucosamine-containing phospholipids. The G+C content of the genomic DNA was 66.4 mol%. The phenotypic data clearly distinguished the isolate from its closest relatives. The combined phylogenetic, chemotaxonomic and phenotypic data indicate that the isolate represents a novel species of the genus Amycolatopsis. The proposed name is Amycolatopsis salitolerans sp. nov., with TRM F103(T) (=JCM 15899(T)=CCTCC AB 208326(T)) as the type strain.
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Affiliation(s)
- Tong-Wei Guan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,Key Laboratory for Microbial Resources of the Ministry of Education, Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, Xinjiang 843300, PR China
| | - Zhan-Feng Xia
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, Xinjiang 843300, PR China
| | - Shu-Kun Tang
- Key Laboratory for Microbial Resources of the Ministry of Education, Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Nan Wu
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Zheng-Jun Chen
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, Xinjiang 843300, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ji-Sheng Ruan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen-Jun Li
- Key Laboratory for Microbial Resources of the Ministry of Education, Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Li-Li Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, Xinjiang 843300, PR China
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Mao J, Wang J, Dai HQ, Zhang ZD, Tang QY, Ren B, Yang N, Goodfellow M, Zhang LX, Liu ZH. Yuhushiella deserti gen. nov., sp. nov., a new member of the suborder Pseudonocardineae. Int J Syst Evol Microbiol 2010; 61:621-630. [PMID: 20400669 DOI: 10.1099/ijs.0.019588-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermotolerant, Gram-stain-positive, aerobic, sporangium-forming actinomycete, strain RA45(T), was isolated from a desert region in Xinjiang Uigur Autonomous Region, north-western China. Comparative analysis of the 16S rRNA gene sequence and phenotypic characterization revealed that strain RA45(T) belonged phylogenetically to the family Pseudonocardiaceae of the suborder Pseudonocardineae. Strain RA45(T) showed more than 5 % 16S rRNA gene sequence divergence from recognized species of genera in the family Pseudonocardiaceae, forming a distinct lineage within the evolutionary radiation occupied by the genera Amycolatopsis, Prauserella, Thermocrispum, Saccharomonospora, Saccharopolyspora and Sciscionella, but distinct from each of them. The affiliation to the family was supported by the presence of suborder- and family-specific 16S rRNA signature nucleotides, a DNA G+C content of 69.9 mol%, the presence of meso-diaminopimelic acid, ribose, arabinose, glucose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes, the presence of menaquinone MK-9(H₄) as the major respiratory lipoquinone, a lack of mycolic acids and the presence of an N-acetylated type of muramic acid. However, strain RA45(T) differed from known genera of the family in its polar lipid composition: the major phospholipids were phosphatidylethanolamine, phosphatidylinositol mannosides, phosphatidylmethylethanolamine, diphosphatidylglycerol, phospholipids of unknown structure and phospholipids of unknown structure containing glucosamine (phospholipid type IV). Based on its morphological, chemotaxonomic and phylogenetic characteristics, strain RA45(T) is considered to represent a novel species of a new genus in the family Pseudonocardiaceae, for which the name Yuhushiella deserti gen. nov., sp. nov. is proposed. The type strain of Yuhushiella deserti is RA45(T) (=CGMCC 4.5579(T) =JCM 16584(T)).
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Affiliation(s)
- Jun Mao
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang Uigur Autonomous Region, PR China
| | - Jian Wang
- Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China.,Institute of Microbiology, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Huan-Qin Dai
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Zhi-Dong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang Uigur Autonomous Region, PR China
| | - Qi-Yong Tang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang Uigur Autonomous Region, PR China
| | - Biao Ren
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Na Yang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Li-Xin Zhang
- SynerZ Pharmaceuticals Inc., Lexington, MA 02421, USA.,Institute of Microbiology, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Zhi-Heng Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100190, PR China
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Tamura T, Ishida Y, Otoguro M, Suzuki KI. Amycolatopsis helveola sp. nov. and Amycolatopsis pigmentata sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 60:2629-2633. [PMID: 20023060 DOI: 10.1099/ijs.0.017871-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three short spore chain-forming actinomycete strains were isolated from soil samples collected from subtropical islands in Japan. The cell-wall peptidoglycan of these strains contained meso-diaminopimelic acid (meso-A(2)pm), glutamic acid and alanine. The major isoprenoid quinone was MK-9(H(4)), iso-C(16 : 0) and 2-OH iso-C(16 : 0) were the major cellular fatty acids and phosphatidylethanolamine was a component of the polar lipids. The G+C content of the genomic DNA was 67-69 mol%. Phylogenetic analyses based on the 16S rRNA gene sequences showed that the novel strains consistently formed a monophyletic cluster with Amycolatopsis taiwanensis. On the basis this polyphasic taxonomical study, it is proposed that the two new isolates represent two novel species: Amycolatopsis helveola (type strain TT00-43(T)=NBRC 103394(T)=KCTC 19329(T)) and Amycolatopsis pigmentata (type strain TT99-32(T)=NBRC 103392(T)=KCTC 19330(T)).
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Affiliation(s)
- Tomohiko Tamura
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yuumi Ishida
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Misa Otoguro
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ken-Ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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26
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Tang SK, Wang Y, Guan TW, Lee JC, Kim CJ, Li WJ. Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake. Int J Syst Evol Microbiol 2009; 60:1073-1078. [PMID: 19666809 DOI: 10.1099/ijs.0.012427-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic actinomycete, designated strain YIM 93223(T), was isolated from a salt lake in Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The isolate grew at 25-45 degrees C, at pH 6-8 and in the presence of 1-15 % (w/v) NaCl; no growth was observed in the absence of NaCl. Strain YIM 93223(T) contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids, and glucose and galactose as major whole-cell-wall sugars. Major fatty acids were iso-C(16 : 0), C(16 : 0) and C(16 : 1)omega7c/iso-C(15 : 0) 2-OH. MK-8(H(4)) was the predominant menaquinone. The genomic DNA G+C content was 66.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93223(T) belongs to the genus Amycolatopsis. It shared highest 16S rRNA gene sequence similarity with Amycolatopsis palatopharyngis 1BDZ(T) (96.6 %) and Amycolatopsis marina Ms392A(T) (96.4 %), but lower values (94.5-96.2 %) with the type strains of other recognized species of the genus Amycolatopsis. On the basis of the data from this polyphasic study, strain YIM 93223(T) is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsis halophila sp. nov. is proposed. The type strain is YIM 93223(T) (=DSM 45216(T) =KCTC 19403(T)).
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Affiliation(s)
- Shu-Kun Tang
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Yun Wang
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, Xinjiang 830091, PR China
| | - Tong-Wei Guan
- Key Laboratary of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Tarim University, Alar, Xinjiang 843300, PR China
| | - Jae-Chan Lee
- Functional Metabolite Research Center KRIBB, 52 Eoeun-dong, Yuseong gu, Daejeon 305-806, Republic of Korea
| | - Chang-Jin Kim
- Functional Metabolite Research Center KRIBB, 52 Eoeun-dong, Yuseong gu, Daejeon 305-806, Republic of Korea
| | - Wen-Jun Li
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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Bian J, Li Y, Wang J, Song FH, Liu M, Dai HQ, Ren B, Gao H, Hu X, Liu ZH, Li WJ, Zhang LX. Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment. Int J Syst Evol Microbiol 2009; 59:477-81. [DOI: 10.1099/ijs.0.000026-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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28
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Tan GYA, Robinson S, Lacey E, Brown R, Kim W, Goodfellow M. Amycolatopsis regifaucium sp. nov., a novel actinomycete that produces kigamicins. Int J Syst Evol Microbiol 2007; 57:2562-2567. [DOI: 10.1099/ijs.0.64974-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of seven soil actinomycetes provisionally assigned to the genus Amycolatopsis was established in a polyphasic study. The isolates, which had identical 16S rRNA gene sequences, had closest similarity to the type strain of Amycolatopsis orientalis. A representative isolate, strain GY080T, had chemotaxonomic properties that were typical of the genus Amycolatopsis and could be distinguished from the type strain of A. orientalis using DNA–DNA relatedness data. All of the isolates shared a phenotypic profile that distinguished them from representatives of phylogenetically closely related species. Amplified rDNA restriction analysis showed that the isolates formed a homogeneous group that was distinctly separate from single-membered groups consisting of representative Amycolatopsis type strains, including that of A. orientalis. Based on the combined genotypic and phenotypic evidence, it is proposed that the seven isolates be classified as representatives of a novel species for which the name Amycolatopsis regifaucium sp. nov. is proposed. The type strain is GY080T (=DSM 45072T =NCIMB 14277T).
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Affiliation(s)
| | - Stuart Robinson
- Microbial Screening Technologies, Building A, 28–54 Percival Road, Smithfield, New South Wales 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Building A, 28–54 Percival Road, Smithfield, New South Wales 2164, Australia
| | - Roselyn Brown
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Wonyong Kim
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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Carlsohn MR, Groth I, Tan GYA, Schütze B, Saluz HP, Munder T, Yang J, Wink J, Goodfellow M. Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 2007; 57:1640-1646. [PMID: 17625209 DOI: 10.1099/ijs.0.64903-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three actinomycetes isolated from the surfaces of rocks in a medieval slate mine were examined in a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics of the isolates were typical of strains of the genus Amycolatopsis. The isolates had identical 16S rRNA gene sequences and formed a distinct phyletic line towards the periphery of the Amycolatopsis mediterranei clade, being most closely related to Amycolatopsis rifamycinica. The organisms shared a wide range of genotypic and phenotypic markers that distinguished them from their closest phylogenetic neighbours. On the basis of these results, a novel species, Amycolatopsis saalfeldensis sp. nov., is proposed. The type strain is HKI 0457T (=DSM 44993T=NRRL B-24474T).
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MESH Headings
- Actinobacteria/chemistry
- Actinobacteria/classification
- Actinobacteria/genetics
- Actinobacteria/isolation & purification
- Bacterial Typing Techniques
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Genotype
- Germany
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction/methods
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
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Affiliation(s)
- Marc René Carlsohn
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV, Hans-Knöll-Institut, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Ingrid Groth
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV, Hans-Knöll-Institut, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Geok Yuan Annie Tan
- Division of Microbiology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Barbara Schütze
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV, Hans-Knöll-Institut, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Hans-Peter Saluz
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV, Hans-Knöll-Institut, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Thomas Munder
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV, Hans-Knöll-Institut, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Jun Yang
- Universität Tübingen, Biologisches Institut, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Joachim Wink
- Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt (Main), Germany
| | - Michael Goodfellow
- Division of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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30
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Tan GYA, Robinson S, Lacey E, Goodfellow M. Amycolatopsis australiensis sp. nov., an actinomycete isolated from arid soils. Int J Syst Evol Microbiol 2006; 56:2297-2301. [PMID: 17012550 DOI: 10.1099/ijs.0.64260-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a group of mesophilic actinomycetes isolated from arid Australian soils was determined using a polyphasic approach. The organisms shared chemical and morphological markers typical of members of the genus Amycolatopsis. They had identical 16S rRNA gene sequences and formed a distinct phyletic line in the Amycolatopsis mediterranei clade, being most closely related to A. mediterranei. In addition, they shared a range of phenotypic properties that distinguished them from representatives of all of the species classified in this clade. The combined genotypic and phenotypic data indicate that the strains merit species status within the genus Amycolatopsis. The name proposed for the novel species is Amycolatopsis australiensis sp. nov.; the type strain is GY048T (=DSM 44671T=NCIMB 14142T).
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Affiliation(s)
- Geok Yuan Annie Tan
- Microbial Resources Laboratory, Division of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Stuart Robinson
- Microbial Screening Technologies, Building A, 28-54 Percival Road, Smithfield, New South Wales 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Building A, 28-54 Percival Road, Smithfield, New South Wales 2164, Australia
| | - Michael Goodfellow
- Microbial Resources Laboratory, Division of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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Saintpierre-Bonaccio D, Amir H, Pineau R, Tan GYA, Goodfellow M. Amycolatopsis plumensis sp. nov., a novel bioactive actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil. Int J Syst Evol Microbiol 2005; 55:2057-2061. [PMID: 16166709 DOI: 10.1099/ijs.0.63630-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of an actinomycete isolated from a brown hypermagnesian ultramafic soil was examined using a polyphasic approach. The organism, which was designated SBHS Strp1T, was found to have chemical and morphological properties typical of Amycolatopsis strains. It was most closely associated with Amycolatopsis kentuckyensis, Amycolatopsis lexingtonensis, Amycolatopsis rifamycinica, Amycolatopsis pretoriensis and Amycolatopsis tolypomycina on the basis of 16S rRNA gene sequence data, and showed a unique pattern of phenotypic properties that distinguished it from the type strains of these taxa. The combined genotypic and phenotypic data show that the organism merits description as a novel species of Amycolatopsis. The name proposed for the novel species is Amycolatopsis plumensis sp. nov.; the type strain is SBHS Strp1T (=DSM 44776T=NRRL B-24324T).
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Affiliation(s)
- Danielle Saintpierre-Bonaccio
- Laboratoire de Biologie et Physiologie Végétales Appliquées, Université de la Nouvelle-Calédonie, BP4477 98847, Nouméa, New Caledonia
| | - Hamid Amir
- Laboratoire de Biologie et Physiologie Végétales Appliquées, Université de la Nouvelle-Calédonie, BP4477 98847, Nouméa, New Caledonia
| | - René Pineau
- Laboratoire de Biologie et Physiologie Végétales Appliquées, Université de la Nouvelle-Calédonie, BP4477 98847, Nouméa, New Caledonia
| | - G Y Annie Tan
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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