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Zhou EM, Yu TT, Liu L, Ming H, Yin YR, Dong L, Tseng M, Nie GX, Li WJ. Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae. Int J Syst Evol Microbiol 2014; 64:2998-3004. [DOI: 10.1099/ijs.0.059766-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains YIM 77562T and YIM 77580, two novel Gram-staining-positive, filamentous bacterial isolates, were recovered from the Rehai geothermal field, Tengchong, Yunnan province, south-west China. Good growth was observed at 50–55 °C and pH 7.0. Aerial mycelium was absent on all media tested. Substrate mycelium was well-developed, long and moderately flexuous, and formed abundant, single, warty, ornamented endospores. Phylogenetic analysis of the 16S rRNA gene sequences of the two strains indicated that they belong to the family
Thermoactinomycetaceae
. Similarity levels between the 16S rRNA gene sequences of the two strains and those of type strains of members of the
Thermoactinomycetaceae
were 88.33–93.24 %; the highest sequence similarity was with
Hazenella coriacea
DSM 45707T. In both strains, the predominant menaquinone was MK-7, the diagnostic diamino acid was meso-diaminopimelic acid and the major cellular fatty acids were iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, unidentified polar lipids and unidentified phospholipids. The genomic DNA G+C contents of strains YIM 77562T and YIM 77580 were 45.5 and 44.2 mol%, respectively. DNA–DNA relatedness data suggest that the two isolates represent a single species. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that the two strains represent a single novel species in a new genus, Geothermomicrobium terrae gen. nov., sp. nov. The type strain of Geothermomicrobium terrae is YIM 77562T ( = CCTCC AA 2011022T = JCM 18057T).
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Affiliation(s)
- En-Min Zhou
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Tian-Tian Yu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Lan Liu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, 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
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Yi-Rui Yin
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Lei Dong
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Min Tseng
- Bio-resource Collection and Research Center, Food Industry Research and Development Institute, HsinChu 300, Taiwan
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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Parajuli S, Potula R, Ciccolella D, Truant AL. Isolation of Laceyella sp. from the Blood of a Patient with Interstitial Lung Disease. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.clinmicnews.2014.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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3
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Tsubouchi T, Shimane Y, Mori K, Usui K, Hiraki T, Tame A, Uematsu K, Maruyama T, Hatada Y. Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment. Int J Syst Evol Microbiol 2013; 63:1972-1981. [DOI: 10.1099/ijs.0.043596-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel filamentous bacterium, designated strain JIR-001T, was isolated from hemipelagic sediment in deep seawater. This strain was non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form and ivory coloured with wrinkles between the centre and the edge of the colony on ISP2 medium. The isolate grew aerobically at 55–73 °C with the formation of aerial mycelia; spores were produced singly along the aerial mycelium. These morphological features show some similarities to those of the type strains of some species belonging to the family
Thermoactinomycetaceae
. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain JIR-001T belongs to the family
Thermoactinomycetaceae
within the class
Bacilli
. Similarity levels between the 16S rRNA gene sequence of strain JIR-001T and those of the type strains of
Thermoactinomycetaceae
species were 85.5–93.5 %; highest sequence similarity was with
Melghirimyces algeriensis
NariEXT. In the DNA–DNA hybridization assays between strain JIR-001T and its phylogenetic neighbours the mean hybridization levels with
Melghirimyces algeriensis
NariEXT,
Planifilum fimeticola
H0165T,
Planifilum fulgidum
500275T and
Planifilum yunnanense
LA5T were 5.3–7.5, 2.3–4.7, 2.1–4.8 and 2.5–4.9 %, respectively. The DNA G+C content of strain JIR-001T was 55.1 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and C16 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, glucolipid, phosphatidylserine, an amino-group containing phospholipid, an unknown phospholipid and two unknown lipids. The predominant menaquinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, strain JIR-001T is considered to represent a novel species in a new genus of the family
Thermoactinomycetaceae
, for which the name Polycladomyces abyssicola gen. nov., sp. nov. is proposed. The type strain of Polycladomyces abyssicola is JIR-001T ( = JCM 18147T = CECT 8074T).
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Affiliation(s)
- Taishi Tsubouchi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kozue Mori
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Keiko Usui
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Toshiki Hiraki
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Akihiro Tame
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Katsuyuki Uematsu
- Section 1 Geochemical Oceanography, Office of Marine Research Department of Marine Science, Marine Works Japan Ltd, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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Extracellular serine proteases produced by Thermoactinomyces strains from hot springs and soils of West Anatolia. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0280-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Chen JJ, Lin LB, Zhang LL, Zhang J, Tang SK, Wei YL, Li WJ. Laceyella sediminis sp. nov., a thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2011; 62:38-42. [PMID: 21317276 DOI: 10.1099/ijs.0.028282-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic bacterium, designated strain RHA1(T), was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China, and was characterized by using a polyphasic approach. Based on its phenotypic and phylogenetic characteristics, strain RHA1(T) was affiliated to the genus Laceyella. The strain formed white aerial and yellow-white substrate mycelia, bearing single endospores on short sporophores. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Whole-cell hydrolysates contained ribose and glucose. The major fatty acids were iso-C(15:0) (62.39%) and anteiso-C(15:0) (17.55%)(.) The predominant menaquinone was MK-9. The G+C content of the genomic DNA of strain RHA1(T) was 47.9 mol%. Based on DNA-DNA hybridization data, chemotaxonomic characteristics and differential physiological properties, strain RHA1(T) is considered to represent a novel species of the genus Laceyella, for which the name Laceyella sediminis sp. nov. is proposed; the type strain is RHA1(T) (=DSM 45263(T)=CCTCC AA 208058(T)).
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Affiliation(s)
- Jiu-Jiu Chen
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China.,Biotechnology Research Center, Faculty of Life Science and Technology, Kunming University of Science and Technology (KUST), Kunming 650093, PR China
| | - Lian-Bing Lin
- Biotechnology Research Center, Faculty of Life Science and Technology, Kunming University of Science and Technology (KUST), Kunming 650093, PR China
| | - Lan-Lan Zhang
- Biotechnology Research Center, Faculty of Life Science and Technology, Kunming University of Science and Technology (KUST), Kunming 650093, PR China
| | - Jin Zhang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Shu-Kun Tang
- Biotechnology Research Center, Faculty of Life Science and Technology, Kunming University of Science and Technology (KUST), Kunming 650093, PR China
| | - Yun-Lin Wei
- Biotechnology Research Center, Faculty of Life Science and Technology, Kunming University of Science and Technology (KUST), Kunming 650093, PR China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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Zhang J, Tang SK, Zhang YQ, Yu LY, Klenk HP, Li WJ. Laceyella tengchongensis sp. nov., a thermophile isolated from soil of a volcano. Int J Syst Evol Microbiol 2009; 60:2226-2230. [PMID: 19915116 DOI: 10.1099/ijs.0.011767-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic strain, designated YIM 10002(T), was isolated from a soil sample of Big Empty Volcano in Tengchong county, Yunnan province, south-west China, and a polyphasic approach was used to investigate its taxonomic position. Strain YIM 10002(T) formed endospores on both aerial and substrate mycelia. Whole-cell hydrolysates contained meso-diaminopimelic acid, ribose, xylose and glucose. The major fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). The predominant menaquinone was MK-9. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides, together with some unknown phospholipids. The G+C content of its genomic DNA was 48.6 mol%. All of these chemotaxonomic data together with morphological characters consistently assigned strain YIM 10002(T) to the genus Laceyella. 16S rRNA gene sequence analysis showed that strain YIM 10002(T) was most closely related to Laceyella sacchari KCTC 9790(T) and Laceyella putida KCTC 3666(T) (99.9 and 98.0 % 16S rRNA gene sequence similarity, respectively). However, strain YIM 10002(T) showed relatively low DNA-DNA relatedness (34.0 and 39.0 %, respectively) with the above strains. Therefore, strain YIM 10002(T) represents a novel species of the genus Laceyella, for which the name Laceyella tengchongensis sp. nov. is proposed. The type strain is YIM 10002(T) (=DSM 45262(T) =CCTCC AA 208050(T)).
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Affiliation(s)
- Jing Zhang
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Shu-Kun Tang
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Yu-Qin Zhang
- 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
| | - Hans-Peter Klenk
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7b, D-38124 Braunschweig, Germany
| | - Wen-Jun Li
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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Matsuo Y, Katsuta A, Matsuda S, Shizuri Y, Yokota A, Kasai H. Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov. Int J Syst Evol Microbiol 2006; 56:2837-2842. [PMID: 17158985 DOI: 10.1099/ijs.0.64223-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A study was carried out to clarify the taxonomy of four Gram-positive, heterotrophic mesophiles isolated from marine lakes in the Republic of Palau. The strains, designated YM3-251T, YM3-653, YM3-671 and YM11-542T, formed aerial and substrate mycelia. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. The G+C content of their genomic DNA was approximately 45 mol%. The major fatty acid was iso-C15 : 0 and the major isoprenoid quinone was MK-9. The strains formed a distinct group in the 16S rRNA gene tree and shared a range of phenotypic properties that distinguished them from members of related genera in Thermoactinomycetaceae fam. nov. The name proposed to accommodate the new isolates is Mechercharimyces gen. nov., comprising two species based on genotypic and phenotypic criteria, including comparative gyrB and DNA–DNA relatedness data. The names proposed for these taxa are Mechercharimyces mesophilus sp. nov., the type species, and Mechercharimyces asporophorigenens sp. nov., with the type strains YM3-251T (=MBIC06230T=DSM 44894T) and YM11-542T (=MBIC06487T=DSM 44955T), respectively.
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Affiliation(s)
- Yoshihide Matsuo
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
| | - Atsuko Katsuta
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
| | - Satoru Matsuda
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
| | - Yoshikazu Shizuri
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113, Japan
| | - Hiroaki Kasai
- Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
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Suihko ML, Kroppenstedt RM, Stackebrandt E. Occurrence and characterization of actinobacteria and thermoactinomycetes isolated from pulp and board samples containing recycled fibres. J Ind Microbiol Biotechnol 2005; 33:183-91. [PMID: 16292555 DOI: 10.1007/s10295-005-0055-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Accepted: 10/18/2005] [Indexed: 10/25/2022]
Abstract
The aim of this study was to characterize the actinobacterial population present in pulps and boards containing recycled fibres. A total of 107 isolates was identified on the basis of their pigmentation, morphological properties, fatty acid profiles and growth temperature. Of the wet pulp and water sample isolates (n=87), 74.7% belonged to the genus Streptomyces, 17.2% to Nocardiopsis and 8.0% to thermoactinomycetes, whereas all the board sample isolates (n=20) were thermoactinomycetes. The identification of 53 isolates was continued by molecular methods. Partial 16S rDNA sequencing and automated ribotyping divided the Streptomyces isolates (n=31) into 14 different taxa. The most common streptomycetes were the mesophilic S. albidoflavus and moderately thermophilic S. thermocarboxydus. The Nocardiopsis isolates (n=11) belonged to six different taxa, whereas the thermoactinomycetes were mainly members of the species Laceyella sacchari (formerly Thermoactinomyces sacchari). The results indicated the probable presence of one or more new species within each of these genera. Obviously, the drying stage used in the board making processes had eliminated all members of the species Streptomyces and Nocardiopsis present in the wet recycled fibre pulp samples. Only the thermotolerant endospores of L. sacchari were still present in the final products. The potential of automated ribotyping for identifying actinobacteria was indicated, as soon as comprehensive identification libraries became available.
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Affiliation(s)
- M-L Suihko
- VTT Biotechnology, PO Box 1500, 02044 VTT, Finland.
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Yoon JH, Kim IG, Shin YK, Park YH. Proposal of the genus Thermoactinomyces sensu stricto and three new genera, Laceyella, Thermoflavimicrobium and Seinonella, on the basis of phenotypic, phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2005; 55:395-400. [PMID: 15653907 DOI: 10.1099/ijs.0.63203-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis based on 16S rRNA gene sequences revealed that Thermoactinomyces species with validly published names can be assigned to four clusters or lineages. The type strains of Thermoactinomyces sacchari and Thermoactinomyces putidus were differentiated from the type strains of Thermoactinomyces vulgaris and Thermoactinomyces intermedius by the predominant menaquinone and fatty acid profiles. The type strains of Thermoactinomyces dichotomicus and Thermoactinomyces peptonophilus formed lines of descent distinct from other Thermoactinomyces species. Thermoactinomyces dichotomicus KCTC 3667T was distinguishable from the type strains of Thermoactinomyces vulgaris and Thermoactinomyces intermedius by the contents of two fatty acids, iso-C16 : 0 and iso-C17 : 0. Thermoactinomyces dichotomicus could be distinguished from other Thermoactinomyces species by DNA G+C content and some phenotypic properties, particularly its property of forming a yellow colour. The type strain of Thermoactinomyces peptonophilus was distinguishable from other Thermoactinomyces species by differences in menaquinone profile, major fatty acids, DNA G+C content and some physiological properties including optimal growth temperature. On the basis of these data, the creation of three new genera, Laceyella, Thermoflavimicrobium and Seinonella, is proposed in addition to the genus Thermoactinomyces sensu stricto. The genus Laceyella gen. nov. is proposed to accommodate Thermoactinomyces sacchari and Thermoactinomyces putidus as Laceyella sacchari comb. nov. and Laceyella putida comb. nov., the genus Thermoflavimicrobium gen. nov. is proposed for Thermoactinomyces dichotomicus as Thermoflavimicrobium dichotomicum comb. nov. and the genus Seinonella gen. nov. is proposed for Thermoactinomyces peptonophilus as Seinonella peptonophila comb. nov.
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - In-Gi Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Yong-Kook Shin
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Yong-Ha Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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Xu J, Rao JR, Millar BC, Elborn JS, Evans J, Barr JG, Moore JE. Improved molecular identification of Thermoactinomyces spp. associated with mushroom worker's lung by 16S rDNA sequence typing. J Med Microbiol 2002; 51:1117-1127. [PMID: 12466412 DOI: 10.1099/0022-1317-51-12-1117] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mushroom worker's lung (MWL) is a hypersensitivity pneumonitis or allergic alveolitis caused by a type III IgG-mediated immunopathogenic inflammatory reaction in the host due to the inhalation of several thermophilic organisms, including Thermoactinomyces spp. It is difficult to distinguish phenotypically the eight species of this genus; therefore, this study sought to develop an improved molecular means of identifying Thermoactinomyces spp. associated with MWL by partial 16S rDNA PCR amplification and direct sequencing. Hypervariable regions within the 16S rRNA gene, which could be employed as signature sequences of the eight individual species, were identified and employed with highly conserved flanking primers to allow initial PCR amplification, before direct DNA sequencing of the 16S rDNA amplicons. A novel 24-mer 16S rDNA oligonucleotide upstream primer was designed from in silico alignments of all Thermoactinomyces spp. and was employed in combination with downstream (reverse) 16S rDNA primers. This permitted the successful identification of all four isolates associated with mushroom workers' lung. The method may be useful in the identification of Thermoactinomyces spp. associated with allergic alveolitis or pneumonitis associated with occupational exposure in agricultural and horticultural environments.
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MESH Headings
- Agricultural Workers' Diseases/microbiology
- Alveolitis, Extrinsic Allergic/microbiology
- Base Sequence
- DNA, Bacterial/analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/analysis
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Gene Amplification
- Micromonosporaceae/classification
- Micromonosporaceae/genetics
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Alignment
- Sequence Analysis, DNA
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Affiliation(s)
| | - J R Rao
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, *Applied Plant Science Division, Department of Agriculture and Rural Development, Newforge Lane, Belfast BT9 5PX, †Department of Respiratory Medicine, Belfast City Hospital, Belfast BT9 7AD, ‡Department of Respiratory Medicine, Queen's University of Belfast, School of Medicine, Royal Victoria Hospital, Grosvenor Road, Belfast BT12 6BA and §Regional Mycology Reference Laboratory, Department of Microbiology, The Royal Group of Hospitals, Kelvin Building, Royal Victoria Hospital, Grosvenor Road, Belfast BT12 6BA
| | | | - J Stuart Elborn
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, *Applied Plant Science Division, Department of Agriculture and Rural Development, Newforge Lane, Belfast BT9 5PX, †Department of Respiratory Medicine, Belfast City Hospital, Belfast BT9 7AD, ‡Department of Respiratory Medicine, Queen's University of Belfast, School of Medicine, Royal Victoria Hospital, Grosvenor Road, Belfast BT12 6BA and §Regional Mycology Reference Laboratory, Department of Microbiology, The Royal Group of Hospitals, Kelvin Building, Royal Victoria Hospital, Grosvenor Road, Belfast BT12 6BA
| | - James Evans
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, *Applied Plant Science Division, Department of Agriculture and Rural Development, Newforge Lane, Belfast BT9 5PX, †Department of Respiratory Medicine, Belfast City Hospital, Belfast BT9 7AD, ‡Department of Respiratory Medicine, Queen's University of Belfast, School of Medicine, Royal Victoria Hospital, Grosvenor Road, Belfast BT12 6BA and §Regional Mycology Reference Laboratory, Department of Microbiology, The Royal Group of Hospitals, Kelvin Building, Royal Victoria Hospital, Grosvenor Road, Belfast BT12 6BA
| | - John G Barr
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, *Applied Plant Science Division, Department of Agriculture and Rural Development, Newforge Lane, Belfast BT9 5PX, †Department of Respiratory Medicine, Belfast City Hospital, Belfast BT9 7AD, ‡Department of Respiratory Medicine, Queen's University of Belfast, School of Medicine, Royal Victoria Hospital, Grosvenor Road, Belfast BT12 6BA and §Regional Mycology Reference Laboratory, Department of Microbiology, The Royal Group of Hospitals, Kelvin Building, Royal Victoria Hospital, Grosvenor Road, Belfast BT12 6BA
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11
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Harvey I, Cormier Y, Beaulieu C, Akimov VN, Mériaux A, Duchaine C. Random amplified ribosomal DNA restriction analysis for rapid identification of thermophilic Actinomycete-like bacteria involved in hypersensitivity pneumonitis. Syst Appl Microbiol 2001; 24:277-84. [PMID: 11518332 DOI: 10.1078/0723-2020-00034] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Hypersensitivity pneumonitis (HP) is a pulmonary disease characterised by inflammation that can be caused by, amongst other substances, a subset of 4 thermophilic mycelial bacteria: Saccharopolyspora rectivirgula, Saccharomonospora viridis, Thermoactinomyces sacchari, and Thermoactinomyces vulgaris. Air sampling analyses in highly contaminated environments are often performed to evaluate exposure to these species which are difficult and fastidious to identify by conventional techniques. The aim of this study was to use amplified ribosomal DNA restriction analysis (ARDRA) to develop a method of identification for those thermophilic organisms that would be more rapid and simple. Strains of these 4 species were obtained from the American type culture collection (ATCC) and were characterized using biochemical tests and ARDRA patterns obtained on their partial-lenght amplified 16S rDNAs. To validate this approach, ARDRA with two restriction enzymes, TaqI and HhaI, was applied to 49 thermophilic actinomycete-like strains from environmental samples (sawmills). The results obtained show that combining some cultural characteristics and biochemical tests, such as xanthine or hypoxanthine decomposition, growth in the presence of NaCl, lysozyme or novobiocin, and spore resistance over 100 degrees C provide a rough identification and selection of the genera of interest. Consequently, target species could be confirmed by digestion of partial-lenght 16S rDNA with the use of Taql and HhaI restriction enzymes that gave specific restriction patterns. ARDRA analyses on the 49 environmental actinomycete-like organisms revealed the presence of 8 Saccharopolyspora rectivirgula, 2 Saccharomonospora viridis, and 15 Thermoactinomyces vulgaris strains, the other strains had restriction patterns different than those of the species of interest. Results of the present study will be applicable to other potential HP environments such as dairy barns, peat bogs and compost plants.
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Affiliation(s)
- I Harvey
- Unité de recherche, Centre de recherche, Hĵpital Laval, Institut universitaire de cardiologie et de pneumologie de l'Université Laval, Ste-Foy, Québec, Canada
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