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Natronosporangium hydrolyticum gen. nov., sp. nov., a haloalkaliphilic polyhydrolytic actinobacterium from a soda solonchak soil in central asia. Syst Appl Microbiol 2022; 45:126307. [DOI: 10.1016/j.syapm.2022.126307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022]
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2
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Nguyen TV, Wibberg D, Vigil-Stenman T, Berckx F, Battenberg K, Demchenko KN, Blom J, Fernandez MP, Yamanaka T, Berry AM, Kalinowski J, Brachmann A, Pawlowski K. Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams. Genome Biol Evol 2019; 11:2273-2291. [PMID: 31368478 PMCID: PMC6735867 DOI: 10.1093/gbe/evz153] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 11/14/2022] Open
Abstract
Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show that cluster-2 inocula represent groups of strains, and that strains not represented in symbiotic structures, that is, unable to perform symbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that North American strains contain more transposase genes than Eurasian strains. An analysis of the evolution and distribution of the host plants indicated that bursts of transposition may have coincided with niche competition with other cluster-2 Frankia strains. The first genome of an inoculum from the Southern Hemisphere, obtained from nodules of Coriaria papuana in Papua New Guinea, represents a novel species, postulated as Candidatus Frankia meridionalis. All Frankia-enriched metagenomes obtained in this study contained homologs of the canonical nod genes nodABC; the North American genomes also contained the sulfotransferase gene nodH, while the genome from the Southern Hemisphere only contained nodC and a truncated copy of nodB.
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Affiliation(s)
- Thanh Van Nguyen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | | | - Fede Berckx
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Gießen, Germany
| | - Maria P Fernandez
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université Lyon I, Villeurbanne Cedex, France
| | | | - Alison M Berry
- Department of Plant Sciences, University of California, Davis
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | - Andreas Brachmann
- Biocenter, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
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Sun Y, Jiang ZM, Zhao LL, Su J, Yu LY, Tian YQ, Zhang YQ. Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum. Int J Syst Evol Microbiol 2019; 69:109-115. [DOI: 10.1099/ijsem.0.003114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ye Sun
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Zhu-Ming Jiang
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Li-Li Zhao
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Jing Su
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Li-Yan Yu
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Yong-Qiang Tian
- 2Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education and College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yu-Qin Zhang
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
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4
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 421] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Liu SW, Tuo L, Li XJ, Li FN, Li J, Jiang MG, Chen L, Hu L, Sun CH. Mangrovihabitans endophyticus gen. nov., sp. nov., a new member of the family Micromonosporaceae isolated from Bruguiera sexangula. Int J Syst Evol Microbiol 2017; 67:1629-1636. [DOI: 10.1099/ijsem.0.001764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shao-Wei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li Tuo
- Research Center for Medicine & Biology, Zunyi Medical University, Zunyi 563003, PR China
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Xiao-Jun Li
- College of Laboratory Medical Science, Hebei North University, Zhangjiakou 075000, PR China
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Fei-Na Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Jing Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Ming-Guo Jiang
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, Guangxi University for Nationalities, Nanning 530006, PR China
| | - Li Chen
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Li Hu
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Cheng-Hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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Gu G, Chen Y, Duan C, Zhou L, Chen C, Chen J, Cheng J, Shi N, Jin Y, Xi Q, Zhong J. Overexpression of ARF1 is associated with cell proliferation and migration through PI3K signal pathway in ovarian cancer. Oncol Rep 2017; 37:1511-1520. [DOI: 10.3892/or.2017.5388] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/15/2016] [Indexed: 11/06/2022] Open
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Bae KS, Kim MS, Lee JH, Kang JW, Kim DI, Lee JH, Seong CN. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria. J Microbiol 2016; 54:789-795. [PMID: 27888457 DOI: 10.1007/s12275-016-6446-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/02/2016] [Indexed: 11/26/2022]
Abstract
To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.
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Affiliation(s)
- Kyung Sook Bae
- Biological Resource Center, KRIBB, Jeongeup, 56212, Republic of Korea
| | - Mi Sun Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea.
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8
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Mingma R, Tanaka K, Ōmura S, Takahashi Y, Matsumoto A. Actinorhabdospora filicis gen. nov., sp. nov., a new member of the family Micromonosporaceae. Int J Syst Evol Microbiol 2016; 66:3071-3077. [DOI: 10.1099/ijsem.0.001145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ratchanee Mingma
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kazuki Tanaka
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yōko Takahashi
- Kitasato Institute for Life 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
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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9
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Chu X, Li S, Chen W, Devi Asem M, Duan YQ, Nie GX, Hozzein WN, Zhi XY, Li WJ. Hamadaea flava sp. nov., isolated from a soil sample and emended description of the genus Hamadaea. Int J Syst Evol Microbiol 2016; 66:1818-1822. [PMID: 26842996 DOI: 10.1099/ijsem.0.000949] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic and non-motile actinobacterial strain, designated YIM C0533T, was isolated from a soil sample collected from Shiling county, Yunnan province, south-west China. The isolate grew at 15-37 °C, pH 6.0-8.0 and in the presence of 0-3% (w/v) NaCl. The whole-cell hydrolysates contained meso-diaminopimelic acid, xylose, galactose, mannose, ribose, arabinose, glucose and rhamnose. The acyl type of muramic acid was glycolyl. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified phospholipid. The major cellular fatty acids were iso-C16:0, 10-methyl C17:0 and iso-C15 : 0.MK-9(H6) was the predominant menaquinone. The genomic DNA G+C content was determined to be 69.4 mol%. These chemotaxonomic data and the morphological properties were consistent with those of the genus Hamadaea. The strain showed highest sequence similarities to Hamadaea tsunoensis CGMCC 4.1403T on phylogenetic analysis of 16S rRNA gene sequences and was found to form a coherent cluster in the neighbour-joining tree. The DNA-DNA hybridization experiment indicated that the DNA-DNA relatedness value between strain YIM C0533T and H. tsunoensis CGMCC 4.1403T was 34.4±1.3 %. In addition, the results of physiological and biochemical tests allowed the isolate to be differentiated phenotypically from H. tsunoensis CGMCC 4.1403T. On the basis of data from this polyphasic study, strain YIM C0533T is characterized as a novel species of the genus Hamadaea, for which the name Hamadaea flava sp. nov. is proposed. The type strain is YIM C0533T (=CPCC 204160T=KCTC 39591T=CGMCC 4.7289T). An emended description of the genus Hamadaea is also provided.
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Affiliation(s)
- Xiao Chu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PRChina
| | - Shuai Li
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PRChina
| | - Wei Chen
- China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, PRChina
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PRChina
| | - Yan-Qing Duan
- China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, PRChina
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PRChina
| | - Wael N Hozzein
- Bioproducts Research Chair (BRC), College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PRChina
| | - Wen-Jun Li
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PRChina.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PRChina
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Liu C, Zhao J, Guan X, Li L, Li W, Wang X, Xiang W. Catellatospora aurea sp. nov., a novel actinomycete isolated from soil. Antonie van Leeuwenhoek 2014; 106:1185-90. [DOI: 10.1007/s10482-014-0287-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/14/2014] [Indexed: 10/24/2022]
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Matsumoto A, Kawaguchi Y, Nakashima T, Iwatsuki M, Ōmura S, Takahashi Y. Rhizocola hellebori gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae containing 3,4-dihydroxydiaminopimelic acid in the cell-wall peptidoglycan. Int J Syst Evol Microbiol 2014; 64:2706-2711. [DOI: 10.1099/ijs.0.060293-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete strain, K12-0602T, was isolated from the root of a Helleborus orientalis plant in Japan. The 16S rRNA gene sequence of strain K12-0602T showed that it had a close relationship with members of the family
Micromonosporaceae
and the 16S rRNA gene sequence similarity values between strain K12-0602T and type strains of type species of 27 genera belonging to the family
Micromonosporaceae
were below 96.2 %. MK-9 (H4) and MK-9 (H6) were detected as major menaquinones, and galactose, xylose, mannose and ribose were present in the whole-cell hydrolysate. The acyl type of the peptidoglycan was glycolyl. Major fatty acids were iso-C15 : 0, iso-C16 : 0, C17 : 1ω9c and anteiso-C17 : 0. Phosphatidylethanolamine was detected as the phospholipid corresponding to phospholipid type II. The G+C content of the genomic DNA was 67 mol%. Analyses of the cell-wall peptidoglycan by TLC and LC/MS showed that it was composed of alanine, glycine, hydroxylglutamic acid and an unknown amino acid, which was subsequently determined to be 3,4-dihydroxydiaminopimelic acid using instrumental analyses, including NMR and mass spectrometry. On the basis of the phylogenetic analysis and chemotaxonomic characteristics, strain K12-0602T represents a novel species of a new genus in the family
Micromonosporaceae
, for which the name Rhizocola hellebori gen. nov., sp. nov. is proposed. The type strain of the type species is K12-0602T ( = NBRC 109834T = DSM 45988T). This is the first report, to our knowledge, of 3,4-dihydroxydiaminopimelic acid being found as a diamino acid in bacterial cell-wall peptidoglycan.
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Affiliation(s)
- Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yoko Kawaguchi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takuji Nakashima
- Research Organization for Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Masato Iwatsuki
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yōko Takahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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12
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Jia F, Liu C, Wang X, Zhao J, Liu Q, Zhang J, Gao R, Xiang W. Wangella harbinensis gen. nov., sp. nov., a new member of the family Micromonosporaceae. Antonie Van Leeuwenhoek 2013; 103:399-408. [PMID: 23011010 DOI: 10.1007/s10482-012-9820-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
Abstract
A novel endophytic actinomycete, designated strain NEAU-J3(T), was isolated from soybean root (Glycine max (L.) Merr) and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain NEAU-J3(T) fell within the family Micromonosporaceae. The strain was observed to form an extensively branched substrate mycelium, which carried non-motile oval spores with a smooth surface. The cell walls of strain NEAU-J3(T) were determined to contain meso-diaminopimelic acid and galactose, ribose and glucose were detected as whole-cell sugars. The major menaquinones were determined to be MK-9(H(4)) and MK-9(H(6)). The phospholipids detected were phosphatidylcholine and phosphatidylethanolamine. The major cellular fatty acids were determined to be C(16:0), C(18:1) ω9c, C(18:0), C(17:0), C(17:1) ω7c, anteiso-C(17:0), C(16:1) ω7c and C(15:0). The DNA G + C content was 62.5 mol%. On the basis of the morphological and chemotaxonomic characteristics, phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides, strain NEAU-J3(T) is considered to represent a novel species of a new genus within the family Micromonosporaceae, for which the name Wangella harbinensis gen. nov., sp. nov. is proposed. The type strain of Wangella harbinensis is strain NEAU-J3(T) (=CGMCC 4.7039(T) = DSM 45747(T)).
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Affiliation(s)
- Feiyu Jia
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
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Wang X, Jia F, Liu C, Zhao J, Wang L, Shen Y, Wang J, Zhang J, Li C, Xiang W. Xiangella phaseoli gen. nov., sp. nov., a member of the family Micromonosporaceae. Int J Syst Evol Microbiol 2012; 63:2138-2145. [PMID: 23104362 DOI: 10.1099/ijs.0.045732-0] [Citation(s) in RCA: 16] [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 endophytic actinomycete, designated strain NEAU-J5(T) was isolated from roots of snap bean (Phaseolus vulgaris L.). Comparative analysis of the 16S rRNA gene sequence indicated that NEAU-J5(T) is phylogenetically related to members of the family Micromonosporaceae. The whole-cell sugars were galactose, mannose and glucose. The predominant menaquinones were MK-9(H4) and MK-9(H6). The major fatty acids were C16:0, C18:0, C17:1ω7c, iso-C15:0 and C17:0. The phospholipids were phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C content was 72.2 mol%. On the basis of the morphological and chemotaxonomic characteristics, phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides, strain NEAU-J5(T) represents a novel species of a new genus within the family Micromonosporaceae, for which the name Xiangella phaseoli gen. nov., sp. nov. is proposed. The type strain of Xiangella phaseoli is strain NEAU-J5(T) (=CGMCC 4.7038(T)=DSM 45730(T)).
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Affiliation(s)
- Xiangjing Wang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Feiyu Jia
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Chongxi Liu
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Liang Wang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yue Shen
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Jidong Wang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Ji Zhang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Chuang Li
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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Li J, Zhao GZ, Zhu WY, Huang HY, Xu LH, Zhang S, Li WJ. Phytomonospora endophytica gen. nov., sp. nov., isolated from the roots of Artemisia annua L. Int J Syst Evol Microbiol 2011; 61:2967-2973. [PMID: 21278413 DOI: 10.1099/ijs.0.030205-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel endophytic actinomycete, strain YIM 65646T, was isolated from the roots of Artemisia annua L. collected from Yunnan Province, south-west China. Growth was observed in the temperature range 10–40 °C (optimum 20–28 °C) and at pH 6.0–9.0 (optimum pH 7.0). The organism formed well-developed, branched substrate mycelia, but aerial mycelium was not produced. Phenotypic characterization and 16S rRNA gene sequence analysis indicated that strain YIM 65646T belonged to the family Micromonosporaceae (sharing ≤93.6 % sequence similarity with members of this family) and formed a distinct clade in the Micromonosporaceae phylogenetic tree. The strain contained meso-diaminopimelic acid in the cell wall and mannose, ribose, galactose and glucose in whole-cell hydrolysates. The major menaquinones were MK-10(H4), MK-10(H2), MK-8(H2), MK-9(H2) and MK-10(H6). The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 0 and iso-C16 : 0. The DNA G+C content of strain YIM 65646T was 70.0 mol%. On the basis of morphological and chemotaxonomic properties and phylogenetic analysis based on 16S rRNA gene sequence data, it is proposed that this strain should be classified in a novel genus and species, Phytomonospora endophytica gen. nov., sp. nov., in the family Micromonosporaceae. The type strain is YIM 65646T ( = CCTCC AA 209041T = DSM 45386T).
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Affiliation(s)
- Jie Li
- Key Laboratory of Marine Bio-Resources Sustainable Utilization, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, 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, Yunnan 650091, PR China
| | - Guo-Zhen Zhao
- 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, Yunnan 650091, PR China
| | - Wen-Yong Zhu
- 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, Yunnan 650091, PR China
| | - Hai-Yu Huang
- 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, Yunnan 650091, PR China
| | - Li-Hua Xu
- 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, Yunnan 650091, PR China
| | - Si Zhang
- Key Laboratory of Marine Bio-Resources Sustainable Utilization, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Wen-Jun Li
- Key Laboratory of Marine Bio-Resources Sustainable Utilization, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, 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, Yunnan 650091, PR China
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15
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Core gene set as the basis of multilocus sequence analysis of the subclass Actinobacteridae. PLoS One 2011; 6:e14792. [PMID: 21483493 PMCID: PMC3069002 DOI: 10.1371/journal.pone.0014792] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 12/13/2010] [Indexed: 11/20/2022] Open
Abstract
Comparative genomic sequencing is shedding new light on bacterial identification, taxonomy and phylogeny. An in silico assessment of a core gene set necessary for cellular functioning was made to determine a consensus set of genes that would be useful for the identification, taxonomy and phylogeny of the species belonging to the subclass Actinobacteridae which contained two orders Actinomycetales and Bifidobacteriales. The subclass Actinobacteridae comprised about 85% of the actinobacteria families. The following recommended criteria were used to establish a comprehensive gene set; the gene should (i) be long enough to contain phylogenetically useful information, (ii) not be subject to horizontal gene transfer, (iii) be a single copy (iv) have at least two regions sufficiently conserved that allow the design of amplification and sequencing primers and (v) predict whole-genome relationships. We applied these constraints to 50 different Actinobacteridae genomes and made 1,224 pairwise comparisons of the genome conserved regions and gene fragments obtained by using Sequence VARiability Analysis Program (SVARAP), which allow designing the primers. Following a comparative statistical modeling phase, 3 gene fragments were selected, ychF, rpoB, and secY with R2>0.85. Selected sets of broad range primers were tested from the 3 gene fragments and were demonstrated to be useful for amplification and sequencing of 25 species belonging to 9 genera of Actinobacteridae. The intraspecies similarities were 96.3–100% for ychF, 97.8–100% for rpoB and 96.9–100% for secY among 73 strains belonging to 15 species of the subclass Actinobacteridae compare to 99.4–100% for 16S rRNA. The phylogenetic topology obtained from the combined datasets ychF+rpoB+secY was globally similar to that inferred from the 16S rRNA but with higher confidence. It was concluded that multi-locus sequence analysis using core gene set might represent the first consensus and valid approach for investigating the bacterial identification, phylogeny and taxonomy.
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Inahashi Y, Matsumoto A, Danbara H, Ōmura S, Takahashi Y. Phytohabitans suffuscus gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae isolated from plant roots. Int J Syst Evol Microbiol 2010; 60:2652-2658. [DOI: 10.1099/ijs.0.016477-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete strain, K07-0523T, was isolated from the roots of an orchid collected in Okinawa prefecture, Japan. 16S rRNA gene sequence analysis indicated that the new strain belonged to the family Micromonosporaceae and the similarity values between strain K07-0523T and the type species of 24 genera in the family Micromonosporaceae were 93.3–97.7 %. Strain K07-0523T contained d-glutamic acid, glycine, d-alanine, meso-diaminopimelic acid, hydroxydiaminopimelic acid and l-lysine in the cell wall. The major menaquinones were MK-9(H6), MK-10(H4) and MK-10(H6). Galactose, glucose, mannose, ribose and xylose were present in the whole-cell sugars. The acyl type of the peptidoglycan was glycolyl. Major fatty acids were anteiso-C17 : 0, iso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. Phosphatidylethanolamine was detected as the major phospholipid and corresponded to phospholipid type II. The G+C content of the genomic DNA was 73 mol%. On the basis of phylogenetic and chemotaxonomic data, the new strain represents a member of a new genus and novel species, namely Phytohabitans suffuscus gen. nov., sp. nov., in the family Micromonosporaceae. The type strain of the type species is K07-0523T (=DSM 45306T=NBRC 105367T).
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Affiliation(s)
- 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
| | - Hirofumi Danbara
- School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yōko Takahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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Kim BY, Stach JEM, Weon HY, Kwon SW, Goodfellow M. Dactylosporangium luridum sp. nov., Dactylosporangium luteum sp. nov. and Dactylosporangium salmoneum sp. nov., nom. rev., isolated from soil. Int J Syst Evol Microbiol 2010; 60:1813-1823. [DOI: 10.1099/ijs.0.016451-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Forty strains isolated from soil taken from a hay meadow were assigned to the genus Dactylosporangium on the basis of colonial properties. 16S rRNA gene sequence analysis showed that the isolates formed a group that was most closely related to the type strain of Dactylosporangium aurantiacum, but well separated from other Dactylosporangium type strains and from ‘Dactylosporangium salmoneum’ NRRL B-16294. Twelve of 13 representative isolates had identical 16S rRNA gene sequences and formed a subclade that was distinct from corresponding phyletic lines composed of the remaining isolate, strain BK63T, the ‘D. salmoneum’ strain and the type strains of recognized Dactylosporangium species. DNA–DNA relatedness data indicated that representatives of the multi-membered 16S rRNA gene subclade, isolate BK63T and the ‘D. salmoneum’ subclade formed distinct genomic species; all of these organisms had chemotaxonomic and morphological properties consistent with their classification in the genus Dactylosporangium. They were also distinguished from one another and from the type strains of recognized Dactylosporangium species based on a range of phenotypic properties. Combined genotypic and phenotypic data showed that isolate BK63T, isolates BK51T, BK53 and BK69, and strain NRRL B-16294T should be classified in the genus Dactylosporangium as representing novel species. The names proposed for these species are Dactylosporangium luridum sp. nov. (type strain BK63T = DSM 45324T = KACC 20933T = NRRL B-24775T), Dactylosporangium luteum sp. nov. (type strain BK51T = DSM 45323T = KACC 20899T = NRRL B-24774T) and Dactylosporangium salmoneum sp. nov., nom. rev. (type strain NRRL B-16294T = ATCC 31222T = DSM 43910T = JCM 3272T = NBRC 14103T).
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Affiliation(s)
- Byung-Yong Kim
- Korean Agricultural Culture Collection, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
- Microbial Resources Laboratory, School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - James E. M. Stach
- Microbial Resources Laboratory, School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Michael Goodfellow
- Microbial Resources Laboratory, School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
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Xie QY, Wang C, Wang R, Qu Z, Lin HP, Goodfellow M, Hong K. Jishengella endophytica gen. nov., sp. nov., a new member of the family Micromonosporaceae. Int J Syst Evol Microbiol 2010; 61:1153-1159. [PMID: 20543149 DOI: 10.1099/ijs.0.025288-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel endophytic actinomycete, designated strain 202201(T), was isolated from an Acanthus illicifolius root collected from the mangrove reserve zone in Hainan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain 202201(T) fell within the family Micromonosporaceae. The strain formed an extensively branched substrate mycelium, which carried uneven warty-surfaced spores. Cell walls of strain 202201(T) contained meso-diaminopimelic acid and xylose, mannose, arabinose, ribose and glucose were detected as whole-cell sugars. The acyl type of the cell-wall polysaccharides was glycolyl. The major menaquinones were MK-9(H(4)), MK-9(H(6)), MK-9(H(8)) and MK-10(H(4)). The polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylserine. The major cellular fatty acids were 10-methyl-C(17 : 0), iso-C(15 : 0), iso-C(16 : 0) and C(17 : 1)ω8c. The DNA G+C content was 72.3 mol%. On the basis of the morphological and chemotaxonomic characteristics, phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides, strain 202201(T) ( = CGMCC 4.5597(T ) = DSM 45430(T)) represents a novel species of a new genus within the family Micromonosporaceae, for which the name Jishengella endophytica gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Qing-Yi Xie
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Cheng Wang
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Rong Wang
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Zhi Qu
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Hai-Peng Lin
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK
| | - Kui Hong
- Key Laboratory of Tropical Microbial Resources, Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, PR China
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Monciardini P, Cavaletti L, Ranghetti A, Schumann P, Rohde M, Bamonte R, Sosio M, Mezzelani A, Donadio S. Novel members of the family Micromonosporaceae, Rugosimonospora acidiphila gen. nov., sp. nov. and Rugosimonospora africana sp. nov. Int J Syst Evol Microbiol 2009; 59:2752-8. [DOI: 10.1099/ijs.0.010231-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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20
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First Record of the Isolation, Identification and Biological Activity of a New Strain of Spirillospora albida from Thai Cave Soil. ACTA ACUST UNITED AC 2009. [DOI: 10.3209/saj.saj230102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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