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González-Salazar LA, Quezada M, Rodríguez-Orduña L, Ramos-Aboites H, Capon RJ, Souza-Saldívar V, Barona-Gomez F, Licona-Cassani C. Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments. Microb Genom 2023; 9:mgen000921. [PMID: 36748531 PMCID: PMC9973853 DOI: 10.1099/mgen.0.000921] [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] [Indexed: 01/21/2023] Open
Abstract
Calculations predict that testing of 5 000-10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come to the market. A solution to this problem is to establish more efficient protocols that reduce the high rate of re-isolation and continuous rediscovery of natural products during early stages of the drug development process. The study of 'rare actinobacteria' has emerged as a possible approach for increasing the discovery rate of drug leads from natural sources. Here, we define a simple genomic metric, defined as biosynthetic novelty index (BiNI), that can be used to rapidly rank strains according to the novelty of the subset of encoding biosynthetic clusters. By comparing a subset of high-quality genomes from strains of different taxonomic and ecological backgrounds, we used the BiNI score to support the notion that rare actinobacteria encode more biosynthetic gene cluster (BGC) novelty. In addition, we present the isolation and genomic characterization, focused on specialized metabolites and phenotypic screening, of two isolates belonging to genera Lentzea and Actinokineospora from a highly oligotrophic environment. Our results show that both strains harbour a unique subset of BGCs compared to other members of the genera Lentzea and Actinokineospora. These BGCs are responsible for potent antimicrobial and cytotoxic bioactivity. The experimental data and analysis presented in this study contribute to the knowledge of genome mining analysis in rare actinobacteria and, most importantly, can serve to direct sampling efforts to accelerate early stages of the drug discovery pipeline.
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Affiliation(s)
- Luz A González-Salazar
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Michelle Quezada
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lorena Rodríguez-Orduña
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Hilda Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico
| | - Robert J Capon
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Valeria Souza-Saldívar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico.,Present address: Microbial Diversity and Specialized Metabolism Laboratory, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Cuauhtémoc Licona-Cassani
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico.,Division of Integrative Biology, Institute for Obesity Research, Tecnológico de Monterrey, Nuevo León, Mexico
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2
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Wang Y, Shi J, Liu T, Zhang Y, Zhang L, Zhang X. Actinokineospora xionganensis sp. nov., a filamentous actinomycete isolated from the lakeside soil of Baiyangdian. Antonie van Leeuwenhoek 2021; 114:487-496. [PMID: 33674994 DOI: 10.1007/s10482-021-01532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
A novel actinomycete, strain HBU206404T, belonging to the genus Actinokineospora, was isolated from the lakeside soil of Baiyangdian, in China. Cells grew at 9-37 °C (optimum temperature, 28 °C) and pH 6-9 (optimum, pH 7). Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan, and sugars present in whole-cell hydrolysates were arabinose, mannose, glucose and galactose. The predominant menaquinone was MK-9(H4). The predominant cellular fatty acids (> 5%) of the strain HBU206404T were iso-C16:0 (21.5%), iso-C15:0 (20.3%), C16:1ω7c/C16:1ω6c and/or C16:1ω6c/C16:1ω7c (15.0%), iso-C17:0 (8.6%), C16:0 (7.0%) and C17:1ω8c (6.9%). The major polar lipids of the strain HBU206404T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, six unknown aminolipids, two unknown aminolipids and an unidentified lipid. The 16S rRNA gene sequence analysis indicated that the strain HBU206404T was most closely related to Actinokineospora alba KCTC 19294T (99.58%), but whole-genome comparisons, using average nucleotide identity (ANI) value (91.77%) and digital DNA-DNA hybridization (dDDH) value (60%), confirmed low genome relatedness. Nitrogen metabolism pathway was found in the genome of strain HBU206404T which haboured nitrate reductase and nitrite reductase. Other phenotypic characteristics, such as ability to hydrolyze substances, enzyme activity, acid production from carbon source, etc., could also distinguish strain HBU206404T from Actinokineospora alba KCTC 19294T. On the basis of genetic and phenotypic evidence, strain HBU206404T represents a novel species of the genus Actinokineospora, for which the name Actinokineospora xionganensis sp. nov. is proposed. The type strain is HBU206404T (= MCCC 1K04412T = KCTC 49404T).
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Affiliation(s)
- Yuhui Wang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Jiangli Shi
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Tongtong Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Yufan Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Liping Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Xiumin Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China.
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3
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Lei YJ, Xia ZF, Luo XX, Zhang LL. Actinokineospora pegani sp. nov., an endophytic actinomycete isolated from the surface-sterilized root of Peganum harmala L. Int J Syst Evol Microbiol 2020; 70:4358-4363. [PMID: 32618556 DOI: 10.1099/ijsem.0.004299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-positive, aerobic and motile endophytic actinomycete, designated TRM 65233T, was isolated from the root of Peganum harmala L. collected from Xinjiang Uygur Autonomous Region of China. The isolate had white aerial mycelium and brown substrate mycelium on Gause's synthetic agar. Growth occurred at 10-40 °C, pH 6-9 with NaCl concentration of 0-6 % (w/v). Strain TRM 65233T contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell hydrolysates included glucose and galactose as the major whole-cell sugars. The menaquinones were MK-9 (H4) and MK-7. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phospholipids, phosphatidylinositol and one unidentified lipid. Strain TRM 65233T showed the highest 16S rRNA gene sequence similarity to Actinokineospora cianjurensis BTCC B-558T (98.13 %), Actinokineospora auranticolor IFO 16518T (98.06 %), Actinokineospora spheciospongiae EG49T (97.99 %), Actinokineospora baliensis ID03-0561T (97.97 %), Actinokineospora mzabensis PAL84T (97.95 %) and Actinokineospora bangkokensis 44EHWT (97.06 %). The isolate was distinguished from these phylogenetically related strains by digital DNA-DNA hybridization and average nucleotide identity analyses and by a range of physiological and biochemical characteristics. The G+C content of the genomic DNA was 72.6 mol%. On the basis of polyphasic taxonomic data, strain TRM 65233T represents a novel species of the genus Actinokineospora, for which the name Actinokineospora pegani sp. nov. is proposed. The type strain is TRM 65233T (KCTC 49342=CCTCC AA 2019050).
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Affiliation(s)
- Yan-Juan Lei
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar 843300, PR China
| | - Zhan-Feng Xia
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar 843300, PR China
| | - Xiao-Xia Luo
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar 843300, PR China
| | - Li-Li Zhang
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin/College of Life Science, Tarim University, Alar 843300, PR China
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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: 414] [Impact Index Per Article: 69.0] [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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5
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Dahal RH, Shim DS, Kim J. Description of Actinokineospora acnipugnans sp. nov., an actinomycete isolated from soil, showing potential uses in cosmetics. Int J Syst Evol Microbiol 2017; 67:3043-3049. [DOI: 10.1099/ijsem.0.002078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Dong Seop Shim
- Innogene, Co., #301 Woolim E-biz Center1, 28, Digital-ro 33-gil, Guro-gu, Seoul 08337, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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6
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The Draft Genome Sequence of Actinokineospora bangkokensis 44EHW T Reveals the Biosynthetic Pathway of the Antifungal Thailandin Compounds with Unusual Butylmalonyl-CoA Extender Units. Molecules 2016; 21:molecules21111607. [PMID: 27886115 PMCID: PMC6273641 DOI: 10.3390/molecules21111607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/17/2016] [Accepted: 11/19/2016] [Indexed: 11/16/2022] Open
Abstract
We report the draft genome sequence of Actinokineospora bangkokensis 44EHWT, the producer of the antifungal polyene compounds, thailandins A and B. The sequence contains 7.45 Mb, 74.1% GC content and 35 putative gene clusters for the biosynthesis of secondary metabolites. There are three gene clusters encoding large polyketide synthases of type I. Annotation of the ORF functions and targeted gene disruption enabled us to identify the cluster for thailandin biosynthesis. We propose a plausible biosynthetic pathway for thailandin, where the unusual butylmalonyl-CoA extender unit is incorporated and results in an untypical side chain.
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7
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Hatano M, Kinoshita N, Igarashi M, Nomoto A. Actinocrispum wychmicini gen. nov., sp. nov., a novel member of the family Pseudonocardiaceae, isolated from soil. Int J Syst Evol Microbiol 2016; 66:4779-4784. [PMID: 27535579 DOI: 10.1099/ijsem.0.001429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated MI503-A4T, was isolated from soil. Comparative analysis of 16S rRNA gene sequences indicated that MI503-A4T was phylogenetically related to members of the family Pseudonocardiaceae. The most closely related genus was Kibdelosporangium (95.7-96.2 % sequence similarity). Substrate mycelia were branched and pale yellow to pale yellowish-brown. Straight- to zigzag-shaped aerial mycelia were observed, but Sporangium-like structures were absent. The whole-cell hydrolysate contained meso-diaminopimelic acid. The muramic acid residues in the peptidoglycan were N-acetylated. Whole-cell sugars were rhamnose, ribose, arabinose and galactose (cell wall chemotype IV). The predominant menaquinone was MK-9(H4). A small amount of MK-8(H4) was also detected. The DNA G+C content was 70.3-71.1 mol%. Polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine and hydroxyl-phosphatidylethanolamine. Cellular fatty acid analysis of MI503-A4T detected predominantly iso-C14 : 0 (11.5 %), iso-C15 : 0 (13.3 %) and iso-C16 : 0 (35.7 %). Phenotypic and phylogenetic characteristics differentiated MI503-A4T from members of all genera within the family Pseudonocardiaceae with validly published names. Therefore, MI503-A4T is proposed to be a representative of a novel species in a novel genus, Actinocrispum wychmicini gen. nov., sp. nov. The type strain of the type species is MI503-A4T (=NBRC 109632T=DSM 45934T).
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Affiliation(s)
- Masaki Hatano
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Naoko Kinoshita
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Masayuki Igarashi
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Akio Nomoto
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
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8
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Wu H, Liu B. Actinokineospora guangxiensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:4650-4654. [PMID: 26410559 DOI: 10.1099/ijsem.0.000627] [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
A novel actinomycete, designated strain GK-6T, was isolated from a soil sample from Nanning, Guangxi province, PR China. The strain grew at 20-40 °C, pH 6.0-11.0 and with 0-7.0 % NaCl. It formed well-developed aerial and vegetative mycelia. The aerial mycelium was white and the vegetative mycelium was yellow. The long branching aerial mycelia yielded rod-shaped arthrospores, the spores had smooth surfaces and were non-motile. Strain Gk-6T contained meso-diaminopimelic acid as the diagnostic diamino acid, the whole-cell sugars were galactose, glucose and arabinose. Major fatty acids were iso-C16 : 0, iso-C15 : 0 and C17 : 0. MK-9(H4) was the predominant menaquinone. The polar phospholipids were phosphatidylethanolamine, phosphatidylethanolamine-containing hydroxylated fatty acids, diphosphatidylglycerol, ninhydrin-positive glycophospholipid and an unknown phospholipid. The G+C content of the genomic DNA was 73.4 mol%. The 16S rRNA gene sequence analysis indicated that the organism was a member of the genus Actinokineospora and its closest relative among recognized species was Actinokineospora soli JCM 17695T (97.7 % sequence similarity). But the phenotypic characteristics of strain Gk-6T were significantly different from those of A. soli JCM 17695T, and DNA-DNA hybridization showed low relatedness (22.6-28.3 %) between strain Gk-6T and JCM 17695T. On the basis of the phenotypic and phylogenetic data, strain Gk-6T represents a novel species of the genus Actinokineospora, and the name Actinokineospora guangxiensis sp. nov. is proposed. The type strain is Gk-6T ( = DSM 46779 T = CGMCC 4.7154T).
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Affiliation(s)
- Hao Wu
- School of Life Science and Technology, Guangxi University, Nanning, PR China.,Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, PR China
| | - Bin Liu
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, PR China
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Kämpfer P, Glaeser SP, Busse HJ, Abdelmohsen UR, Ahmed S, Hentschel U. Actinokineospora spheciospongiae sp. nov., isolated from the marine sponge Spheciospongia vagabunda. Int J Syst Evol Microbiol 2014; 65:879-884. [PMID: 25519300 DOI: 10.1099/ijs.0.000031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A Gram-staining-positive, aerobic organism, isolated from the Red Sea sponge Spheciospongia vagabunda was investigated to determine its taxonomic position. On the basis of results of 16S rRNA gene sequence analysis strain EG49(T) was most closely related to Actinokineospora cibodasensis and Actinokineospora baliensis (both 97.3 % similarity) and Actinokineospora diospyrosa and Actinokineospora auranticolor (both 97.0 % similarity). The 16S rRNA gene sequence similarity to all other species of the genus Actinokineospora was <97.0 %. The quinone system of strain EG49(T) contained the menaquinones MK-9(H4) (47 %), MK-9(H6) (27 %) and MK-9(H2) (15 %) in major amounts. Minor amounts of MK-7(H4) (2 %), MK-9(H0) (1 %), MK-9(H8) (3 %) and MK-10(H4) (3 %) were detected as well in addition to MK-8(H4), MK-8(H6), MK-10(H2) and MK-10(H6) (all <1 %). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. In the polar lipid profile, diphosphatidylglycerol, phosphatidylethanolamine and hydroxyphosphatidylethanolamine were predominant. Phosphatidylinositol-mannoside, two unidentified phospholipids and two glycoglipids as well as one aminoglycolipid, one aminolipid and one unidentified lipid were found in addition. The fatty acid profile was composed of mainly iso-branched fatty acids: iso-C16 : 0, iso-C14 : 0, iso-C15 : 0 and iso-C16 : 1H. All these findings clearly supported the classification of the strain as representing a member of the genus Actinokineospora. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain EG49(T) from the most closely related species of the genus Actinokineospora. Strain EG49(T) represents a novel species of the genus Actinokineospora, for which we propose the name Actinokineospora spheciospongiae sp. nov., with strain EG49(T) ( = DSM 45935(T) = CCM 8480(T) = LMG 27700(T)) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Wuerzburg, D-97082 Wuerzburg, Germany
| | - Safwat Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Wuerzburg, D-97082 Wuerzburg, Germany
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10
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Actinokineospora mzabensis sp. nov., a novel actinomycete isolated from Saharan soil. Antonie van Leeuwenhoek 2014; 107:291-6. [DOI: 10.1007/s10482-014-0328-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 11/01/2014] [Indexed: 10/24/2022]
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11
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Intra B, Matsumoto A, Inahashi Y, Ōmura S, Takahashi Y, Panbangred W. Actinokineospora
bangkokensis sp. nov., isolated from rhizospheric soil. Int J Syst Evol Microbiol 2013; 63:2655-2660. [DOI: 10.1099/ijs.0.047928-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, strain 44EHWT, was isolated from rhizospheric soil under an Elephant ear plant (Colocasia esculenta) in Bangkok, Thailand. Strain 44EHWT produced long branching hyphae and abundant aerial mycelia with chains of rod-shaped spores. Whole-cell hydrolysates contained galactose, glucose, arabinose, ribose, mannose and rhamnose as diagnostic sugars. meso-Diaminopimelic acid was the diamino acid and glycine, alanine and glutamic acid were present in the cell-wall peptidoglycan with the acyl type of the peptidoglycan being acetyl. Phospholipids consisted of phosphatidylethanolamine, phosphatidylethanolamine with hydroxy fatty acids and diphosphatidylglycerol, as well as other unknown phospholipids; however, no mycolic acids were detected. The predominant menaquinone observed was MK-9(H4) and major fatty acids were iso-C16 : 0 and 2-OH iso-C16 : 0. The G+C content of genomic DNA was 74 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate was most similar to
Actinokineospora enzanensis
NBRC 16517T. However, DNA–DNA hybridization revealed a low relatedness between this isolate and
A. enzanensis
NBRC 16517T, indicating that this isolate represented a novel species in the genus
Actinokineospora
. On the basis of 16S rRNA gene sequence analysis, phenotypic characteristics and DNA–DNA hybridization data, we propose that strain 44EHWT represents a novel species in the genus
Actinokineospora
,
Actinokineospora
bangkokensis. The type strain is 44EHWT ( = BCC 53155T = NBRC 108932T).
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Affiliation(s)
- Bungonsiri Intra
- Mahidol University and Osaka Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yuki Inahashi
- 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
- 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
| | - Watanalai Panbangred
- Mahidol University and Osaka Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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12
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Tang X, Zhou Y, Zhang J, Ming H, Nie GX, Yang LL, Tang SK, Li WJ. Actinokineospora soli sp. nov., a thermotolerant actinomycete isolated from soil, and emended description of the genus
Actinokineospora. Int J Syst Evol Microbiol 2012; 62:1845-1849. [DOI: 10.1099/ijs.0.035832-0] [Citation(s) in RCA: 24] [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 strain of thermotolerant actinomycete, designated YIM 75948T, was isolated from a soil sample in Yunnan province, China. The strain grew at 25–55 °C (optimum 37 °C). The substrate mycelium and aerial mycelium produced on Czapek’s agar were both pale yellow to white. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid, and the whole-cell sugars were mannose, ribose, glucose, galactose and arabinose. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and C16 : 0 and the predominant respiratory quinone was MK-9(H4). The polar lipids consisted of phosphatidylethanolamine, phosphatidylethanolamine with hydroxy fatty acids, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The genomic DNA G+C content was 73.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 75948T belonged in the genus
Actinokineospora
and that its closest relative among recognized species was
Actinokineospora fastidiosa
DSM 43855T (97.6 % sequence similarity). The mean level of DNA–DNA relatedness between the novel strain and
A. fastidiosa
DSM 43855T was, however, only 47.8 %. Based on the phenotypic, chemotaxonomic and phylogenetic data and the results of the DNA–DNA hybridizations, strain YIM 75948T represents a novel species of the genus
Actinokineospora
for which the name Actinokineospora soli sp. nov. is proposed. The type strain is YIM 75948T ( = JCM 17695T = DSM 45613T). The description of the genus
Actinokineospora
is emended to reflect the fact that the genomic DNA G+C contents of
A. fastidiosa
DSM 43855T and the type strain of Actinokineospora soli sp. nov. recorded in the present study fell above the range given in previous descriptions of this genus.
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Affiliation(s)
- 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
| | - Yu Zhou
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, 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
| | - Jing Zhang
- Guangdong Provincial Microbial Culture Collection and Application Key Laboratory, Guangdong Institute of Microbiology, Guangzhou 510070, 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
| | - Hong Ming
- Department of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Guo-Xing Nie
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China
| | - Ling-Ling Yang
- 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
| | - 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 Biogeography and Bioresource in Arid Land, Chinese Academy of Science, Xingjiang Institue of Ecology and Geogrpahy, Chinese Academy of Sciences, Ürűmqi 830011, 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
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13
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Chen J, Su JJ, Wei YZ, Li QP, Yu LY, Liu HY, Zhang YQ, Zhang YQ. Amycolatopsis xylanica sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010; 60:2124-2128. [DOI: 10.1099/ijs.0.016865-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete, designated CPCC 202699T, was isolated from soil in Qinghai province, China, and its taxonomic status was established. Strain CPCC 202699Tcontainedmeso-diaminopimelic acid in its peptidoglycan, arabinose and galactose as the diagnostic sugars in whole-cell hydrolysates, a phospholipid pattern consisting mainly of phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylcholine, MK-9(H4) as the predominant menaquinone and iso-C16 : 0(18.8 %), iso-C15 : 0(18.1 %), iso-C14 : 0(14.2 %), C16 : 1cis9 (10.9 %) and C17 : 1cis9 (10.3 %) as the major fatty acids. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 202699Tformed a separate branch within the genusAmycolatopsis. However, strain CPCC 202699Tshowed low 16S rRNA gene sequence similarities (<97.0 %) with type strains of species with validly published names in the genusAmycolatopsis. On the basis of genotypic and phenotypic differences from the closest phylogenetic neighbours of strain CPCC 202699T, a novel species,Amycolatopsis xylanicasp. nov., is proposed. The type strain is CPCC 202699T(=DSM 45285T=KCTC 19581T=CCM 7627T).
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Affiliation(s)
- Jie Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Jin-Jin Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Zhen Wei
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Qiu-Ping Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Hong-Yu Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yue-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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14
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Labeda DP, Goodfellow M, Chun J, Zhi XY, Li WJ. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009. Int J Syst Evol Microbiol 2010; 61:1259-1264. [PMID: 20601483 DOI: 10.1099/ijs.0.024984-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic status of the families Actinosynnemataceae and Pseudonocardiaceae was assessed based on 16S rRNA gene sequence data available for the 151 taxa with validly published names, as well as chemotaxonomic and morphological properties available from the literature. 16S rRNA gene sequences for the type strains of all taxa within the suborder Pseudonocardineae were subjected to phylogenetic analyses using different algorithms in arb and phylip. The description of many new genera and species within the suborder Pseudonocardineae since the family Actinosynnemataceae was proposed in 2000 has resulted in a markedly different distribution of chemotaxonomic markers within the suborder from that observed at that time. For instance, it is noted that species of the genera Actinokineospora and Allokutzneria contain arabinose in whole-cell hydrolysates, which is not observed in the other genera within the Actinosynnemataceae, and that there are many genera within the family Pseudonocardiaceae as currently described that do not contain arabinose. Phylogenetic analyses of 16S rRNA gene sequences for all taxa within the suborder do not provide any statistical support for the family Actinosynnemataceae, nor are signature nucleotides found that support its continued differentiation from the family Pseudonocardiaceae. The description of the family Pseudonocardiaceae is therefore emended to include the genera previously classified within the family Actinosynnemataceae and the description of the suborder Pseudonocardineae is also emended to reflect this reclassification.
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Affiliation(s)
- D P Labeda
- National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604, USA
| | - M Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - J Chun
- School of Biological Sciences, Seoul National University, Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
| | - X-Y Zhi
- 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
| | - W-J 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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15
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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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16
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Lisdiyanti P, Otoguro M, Ratnakomala S, Lestari Y, Hastuti RD, Triana E, Katsuhiko A, Widyastuti Y. Actinokineospora baliensis sp. nov., Actinokineospora cibodasensis sp. nov. and Actinokineospora cianjurensis sp. nov., isolated from soil and plant litter. Int J Syst Evol Microbiol 2009; 60:2331-2335. [PMID: 19933586 DOI: 10.1099/ijs.0.013276-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six actinomycete strains isolated from soil and plant-litter samples in Indonesia were studied for their taxonomic position by using a polyphasic approach. Phylogenetically, all the strains were located in the broad cluster of the genus Actinokineospora. Chemotaxonomic data [cell-wall diamino acid, meso-diaminopimelic acid; cell-wall peptidoglycan, type III (A1γ); major sugars, galactose and arabinose; major menaquinone, MK-9(H₄); major fatty acid, iso-C₁₆:₀; major phospholipid, phosphatidylethanolamine] supported the affiliation of all six strains to the genus Actinokineospora. The results of DNA-DNA hybridization with DNA from type strains of Actinokineospora species with validly published names revealed three DNA-DNA relatedness groups. Group I (ID03-0561(T)) showed low relatedness to the other strains studied. The three strains in group II (ID03-0784(T), ID03-0808 and ID03-0809) formed a group with high relatedness (98-100 %) and showed low relatedness to the other strains studied. The two strains in group III (ID03-0810(T) and ID03-0813) showed 58-68 % relatedness to Actinokineospora terrae NBRC 15668(T) and showed low relatedness (2-24 %) to the other strains studied. The description of three novel species is proposed: Actinokineospora baliensis sp. nov., for the single strain in group I (type strain ID03-0561(T) =BTCC B-554(T) =NBRC 104211(T)), Actinokineospora cibodasensis sp. nov., for the strains in group II (type strain ID03-0784(T) =BTCC B-555(T) =NBRC 104212(T)), and Actinokineospora cianjurensis sp. nov., for the strains in group III (type strain ID03-0810(T) =BTCC B-558(T) =NBRC 105526(T)).
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Affiliation(s)
- Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor Km. 46, Cibinong 16911, Indonesia
| | - Misa Otoguro
- Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusa kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shanti Ratnakomala
- Research Center for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor Km. 46, Cibinong 16911, Indonesia
| | - Yulin Lestari
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Jalan Raya Pajajaran, Bogor 16144, Indonesia
| | - Ratih D Hastuti
- Soil Research Institute, Jl. Ir. H. Juanda 98, Bogor 16002, Indonesia
| | - Evi Triana
- Research Center for Biology, Indonesian Institute of Sciences. Jl. Raya Bogor Km. 46, Cibinong 16911, Indonesia
| | - Ando Katsuhiko
- Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusa kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yantyati Widyastuti
- Research Center for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor Km. 46, Cibinong 16911, Indonesia
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