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The journal of microbiology 26건

  1. [국내논문]   TBC: A Clustering Algorithm Based on Prokaryotic Taxonomy   SCIE SCOPUS 피인용횟수: 6

    Lee, Jae-Hak (Interdisciplinary Graduate Program in Bioinformatics, Seoul National University ) , Yi, Ha-Na (Inst. of Molecular Biology and Genetics, Seoul National University ) , Jeon, Yoon-Seong (Interdisciplinary Graduate Program in Bioinformatics, Seoul National University ) , Won, Sung-Ho (Department of Statistics, Chung-Ang University ) , Chun, Jong-Sik (Interdisciplinary Graduate Program in Bioinformatics, Seoul National University)
    The journal of microbiology v.50 no.2 ,pp. 181 - 185 , 2012 , 1225-8873 ,

    초록

    High-throughput DNA sequencing technologies have revolutionized the study of microbial ecology. Massive sequencing of PCR amplicons of the 16S rRNA gene has been widely used to understand the microbial community structure of a variety of environmental samples. The resulting sequencing reads are clustered into operational taxonomic units that are then used to calculate various statistical indices that represent the degree of species diversity in a given sample. Several algorithms have been developed to perform this task, but they tend to produce different outcomes. Herein, we propose a novel sequence clustering algorithm, namely Taxonomy-Based Clustering (TBC). This algorithm incorporates the basic concept of prokaryotic taxonomy in which only comparisons to the type strain are made and used to form species while omitting full-scale multiple sequence alignment. The clustering quality of the proposed method was compared with those of MOTHUR, BLASTClust, ESPRIT-Tree, CD-HIT, and UCLUST. A comprehensive comparison using three different experimental datasets produced by pyrosequencing demonstrated that the clustering obtained using TBC is comparable to those obtained using MOTHUR and ESPRIT-Tree and is computationally efficient. The program was written in JAVA and is available from http://sw.ezbiocloud.net/tbc.

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  2. [국내논문]   Identification and Enumeration of Microcystis Using a Sandwich Hybridization Assay   SCIE SCOPUS

    Zhu, Jing-Ping (School of Environmental Science and Engineering, Huazhong University of Science & Technology ) , Li, Xian (School of Environmental Science and Engineering, Huazhong University of Science & Technology ) , Du, Shi (School of Environmental Science and Engineering, Huazhong University of Science & Technology)
    The journal of microbiology v.50 no.2 ,pp. 186 - 190 , 2012 , 1225-8873 ,

    초록

    Based on sequence analyses of phycocyanin intergenic spacers (PC-IGS) from Microcystis, Anabaena, Aphanizomenon, and Planktothrix (Oscillatoria) strains, a genus-specific probe pair TF/TR was designed, and a sandwich hybridization assay was established to quantitatively detect Microcystis. Through BLAST and cyanobacterial culture tests, TF/TR was demonstrated to be specific for Microcystis. A calibration curve for the sandwich hybridization assay was established, and the lowest detected concentration was 100 cell/ml. Laboratory and field samples were analyzed with both sandwich hybridization assay and microscopy. The biotic and abiotic components of the samples were of little disturbance to the sandwich hybridization assay. The results showed no distinct difference between the two methods. In this study, a sandwich hybridization assay was established to detect Microcystis, providing an alternative to traditional microscopic, morphology-based methods.

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  3. [국내논문]   Isolation and Characterization of Plant Growth-Promoting Rhizobacteria from Wheat Roots by Wheat Germ Agglutinin Labeled with Fluorescein Isothiocyanate   SCIE SCOPUS 피인용횟수: 2

    Zhang, Jian (School of Life Science, Anhui Agricultural University ) , Liu, Jingyang (School of Life Science, Anhui Agricultural University ) , Meng, Liyuan (School of Life Science, Anhui Agricultural University ) , Ma, Zhongyou (Department of Biology, Anhui Science and Technology University ) , Tang, Xinyun (School of Life Science, Anhui Agricultural University ) , Cao, Yuanyuan (School of Life Science, Anhui Agricultural University ) , Sun, Leni (School of Life Science, Anhui Agricultural University)
    The journal of microbiology v.50 no.2 ,pp. 191 - 198 , 2012 , 1225-8873 ,

    초록

    Thirty-two isolates were obtained from wheat rhizosphere by wheat germ agglutinin (WGA) labeled with fluorescein isothiocyanate (FITC). Most isolates were able to produce indole acetic acid (65.6%) and siderophores (59.3%), as well as exhibited phosphate solubilization (96.8%). Fourteen isolates displayed three plant growth-promoting traits. Among these strains, two phosphate-dissolving ones, WS29 and WS31, were evaluated for their beneficial effects on the early growth of wheat (Triticum aestivum Wan33). Strain WS29 and WS31 significantly promoted the development of lateral roots by 34.9% and 27.6%, as well as increased the root dry weight by 25.0% and 25.6%, respectively, compared to those of the control. Based on 16S rRNA gene sequence comparisons and phylogenetic positions, both isolates were determined to belong to the genus Bacillus. The proportion of isolates showing the properties of plant growth-promoting rhizobacteria (PGPR) was higher than in previous reports. The efficiency of the isolation of PGPR strains was also greatly increased by WGA labeled with FITC. The present study indicated that WGA could be used as an effective tool for isolating PGPR strains with high affinity to host plants from wheat roots. The proposed approach could facilitate research on biofertilizers or biocontrol agents.

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  4. [국내논문]   Detecting Nonculturable Bacteria in the Active Mycorrhizal Zone of the Pine Mushroom Tricholoma matsutake   SCIE SCOPUS 피인용횟수: 2

    Kataoka, Ryota (Laboratory of Environmental Mycoscience, Graduate School of Agriculture, Kyoto University ) , Siddiqui, Zaki Anwar (Laboratory of Environmental Mycoscience, Graduate School of Agriculture, Kyoto University ) , Kikuchi, Junichi (Science Education, Nara University of Education ) , Ando, Masaki (Kyoto Forest Research Institute ) , Sriwati, Rina (Laboratory of Environmental Mycoscience, Graduate School of Agriculture, Kyoto University ) , Nozaki, Ai (Kyoto Forest Research Institute ) , Futai, Kazuyoshi (Laboratory of Environmental Mycoscience, Graduate School of Agriculture, Kyoto University)
    The journal of microbiology v.50 no.2 ,pp. 199 - 206 , 2012 , 1225-8873 ,

    초록

    The fungus Tricholoma matsutake forms an ectomycorrhizal relationship with pine trees. Its sporocarps often develop in a circle, which is commonly known as a fairy ring. The fungus produces a solid, compact, white aggregate of mycelia and mycorrhizae beneath the fairy ring, which in Japanese is called a 'shiro'. In the present study, we used soil dilution plating and molecular techniques to analyze the bacterial communities within, beneath, and outside the T. matsutake fairy ring. Soil dilution plating confirmed previous reports that bacteria and actinomycetes are seldom present in the soil of the active mycorrhizal zone of the T. matsutake shiro. In addition, the results showed that the absence of bacteria was strongly correlated with the presence of T. matsutake mycorrhizae. The results demonstrate that bacteria, especially aerobic and heterotrophic forms, and actinomycetes, are strongly inhibited by T. matsutake. Indeed, neither bacteria nor actinomycetes were detected in 11.3% of 213 soil samples from the entire shiro area by culture-dependent methods. However, molecular techniques demonstrated that some bacteria, such as individual genera of Sphingomonas and Acidobacterium, were present in the active mycorrhizal zone, even though they were not detected in soil assays using the dilution plating technique.

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  5. [국내논문]   Molecular Analysis of Spatial Variation of Iron-Reducing Bacteria in Riverine Alluvial Aquifers of the Mankyeong River   SCIE SCOPUS

    Kim, So-Jeong (Department of Microbiology, Chungbuk National University ) , Koh, Dong-Chan (Korea Institute of Geoscience and Mineral Resources ) , Park, Soo-Je (Department of Microbiology, Chungbuk National University ) , Cha, In-Tae (Department of Microbiology, Chungbuk National University ) , Park, Joong-Wook (Department of Biochemistry and Microbiology, Biotechnology Center for Agriculture and the Environment, Rutgers, The State University of New Jersey ) , Na, Jong-Hwa (Department of Information & Statistics, Chungbuk National University ) , Roh, Yul (Faculty of Earth Systems and Environmental Sciences, Chonnam National University ) , Ko, Kyung-Seok (Korea Institute of Geoscience and Mineral Resources ) , Kim, Kang-Joo (School of Civil and Environmental Engineering, Kunsan National University ) , Rhee, Sung-Keun (Department of Microbiology, Chungbuk National University)
    The journal of microbiology v.50 no.2 ,pp. 207 - 217 , 2012 , 1225-8873 ,

    초록

    Alluvial aquifers are one of the mainwater resources in many countries. Iron reduction in alluvial aquifers is often a major anaerobic process involved in bioremediation or causing problems, including the release of As trapped in Fe(III) oxide. We investigated the distribution of potential iron-reducing bacteria (IRB) in riverine alluvial aquifers (B1, B3, and B6 sites) at the Mankyeong River, Republic of Korea. Inactive iron reduction zones, the diversity and abundance of IRB can be examined using a clone library and quantitative PCR analysis of 16S rRNA genes. Geobacter spp. are potential IRB in the iron-reducing zone at the B6 (9 m) site, where high Fe(II) and arsenic (As) concentrations were observed. At the B3 (16 m) site, where low iron reduction activity was predicted, a dominant clone (10.6%) was 99% identical in 16S rRNA gene sequence with Rhodoferax ferrireducens. Although a major clone belonging to Clostridium spp. was found, possible IRB candidates could not be unambiguously determined at the B1 (18 m) site. Acanonical correspondence analysis demonstrated that, among potential IRB, only the Geobacteraceae were well correlated with Fe(II) and As concentrations. Our results indicate high environmental heterogeneity, and thus high spatial variability, in thedistribution of potential IRB in the riverine alluvial aquifersnear the Mankyeong River.

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  6. [국내논문]   Microbial Fingerprinting Detects Unique Bacterial Communities in the Faecal Microbiota of Rats with Experimentally-Induced Colitis   SCIE SCOPUS

    Samanta, Ashis K. (National Institute of Animal Nutrition and Physiology ) , Torok, Valeria A. (South Australian Research and Development Institute, Plant and Soil Health, Waite Campus ) , Percy, Nigel J. (South Australian Research and Development Institute, Plant and Soil Health, Waite Campus ) , Abimosleh, Suzanne M. (Discipline of Physiology, School of Health Sciences, The University of Adelaide ) , Howarth, Gordon S. (Gastroenterology Department, Women's and Children's Hospital)
    The journal of microbiology v.50 no.2 ,pp. 218 - 225 , 2012 , 1225-8873 ,

    초록

    An abnormal composition of the gut microbiota is believed to be associated with the pathogenesis of inflammatory bowel disease (IBD). We utilized terminal restriction fragment length polymorphism (T-RFLP) analysis to quantify faecal bacterial communities from rats with experimental colitis. Male Sprague Dawley rats (n=10/group) ingested 2% dextran sulfate sodium (DSS) or water for up to 7 days. Rats were killed and colonic tissues collected for histological analysis. Damage severity score in the distal colon was significantly greater (P

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  7. [국내논문]   Effect of Natural Mediators on the Stability of Trametes trogii Laccase during the Decolourization of Textile Wastewaters   SCIE SCOPUS 피인용횟수: 2

    Khlifi-Slama, Rim (Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax ) , Mechichi, Tahar (Ecole Nationale d'Ingenieurs de Sfax, Laboratory of Enzyme Engineering and Microbiology, University of Sfax ) , Sayadi, Sami (Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax ) , Dhouib, Abdelhafidh (Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax)
    The journal of microbiology v.50 no.2 ,pp. 226 - 234 , 2012 , 1225-8873 ,

    초록

    The purpose of the present study was to determine the effect of natural mediators on the stability of the Trametes trogii crude laccase in the process of decolourization of textile effluents. Acetosyringone allowed the highest waste-waters decolourization rate of 25%. At higher concentrations of acetosyringone, the relative activity of laccase decreased approximately by between 38% and 88% after 5 days of incubation. T. trogii laccase was strongly inactivated at 3 mM syringaldehyde, after 3 days of incubation. However, laccase activity is more stable in the presence of the vanillin and m-coumarate. The T. trogii growth on solid effluentbased-medium was examined and evaluated by measuring the colony diameter in cm. T. trogii was completely inhibited on 100:0 and 80:20 effluent:water solid medium, however, colony diameter reached 5 cm on 60:40 effluent:water solid medium after 13-14 days incubation. When the textile effluent was pre-treated with laccase and laccase-acetosyringone system, the colony diameter of 2 cm of T. trogii on 80:20 effluent:water solid medium was reached after 14 and 10 days of incubation respectively.

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  8. [국내논문]   Purification and Structure Analysis of Mycolic Acids in Corynebacterium glutamicum   SCIE SCOPUS

    Yang, Yang (State Key Laboratory of Food Science and Technology, Jiangnan University ) , Shi, Feng (State Key Laboratory of Food Science and Technology, Jiangnan University ) , Tao, Guanjun (State Key Laboratory of Food Science and Technology, Jiangnan University ) , Wang, Xiaoyuan (State Key Laboratory of Food Science and Technology, Jiangnan University)
    The journal of microbiology v.50 no.2 ,pp. 235 - 240 , 2012 , 1225-8873 ,

    초록

    Corynebacterium glutamicum is widely used for producing amino acids. Mycolic acids, the major components in the cell wall of C. glutamicum might be closely related to the secretion of amino acids. In this study, mycolic acids were extracted from 5 strains of C. glutamicum, including ATCC 13032, ATCC 13869, ATCC 14067, L-isoleucine producing strain IWJ-1, and L-valine producing strain VWJ-1. Structures of these mycolic acids were analyzed using thin layer chromatography and electrospray ionization mass spectrometry. More than twenty molecular species of mycolic acid were observed in all 5 strains. They differ in the length (20-40 carbons) and saturation (0-3 double bonds) of their constituent fatty acids. The dominant species of mycolic acid in every strain was different, but their two hydrocarbon chains were similar in length (14-18 carbons), and the meromycolate chain usually contained double bonds. As the growth temperature of cells increased from $30^{\circ}C$ to $34^{\circ}C$ , the proportion of mycolic acid species containing unsaturated and shorter hydrocarbon chains increased. These results provide new information on mycolic acids in C. glutamicum, and could be useful for modifying the cell wall to increase the production of amino acids.

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  9. [국내논문]   Effects of Exopolysaccharide Production on Liquid Vegetative Growth, Stress Survival, and Stationary Phase Recovery in Myxococcus xanthus   SCIE SCOPUS

    Hu, Wei (School of Dentistry, University of California ) , Wang, Jing (School of Dentistry, University of California ) , Mchardy, Ian (Department of Microbiology, Immunology and Molecular Genetics, University of California ) , Lux, Renate (School of Dentistry, University of California ) , Yang, Zhe (Department of Microbiology, Immunology and Molecular Genetics, University of California ) , Li, Yuezhong (State Key Laboratory of Microbial Technology, School of Life Science, Shandong University ) , Shi, Wenyuan (School of Dentistry, University of California)
    The journal of microbiology v.50 no.2 ,pp. 241 - 248 , 2012 , 1225-8873 ,

    초록

    Exopolysaccharide (EPS) of Myxococcus xanthus is a well-regulated cell surface component. In addition to its known functions for social motility and fruiting body formation on solid surfaces, EPS has also been proposed to play a role in multi-cellular clumping in liquid medium, though this phenomenon has not been well studied. In this report, we confirmed that M. xanthus clumps formed in liquid were correlated with EPS levels and demonstrated that the EPS encased cell clumps exhibited biofilm-like structures. The clumps protected the cells at physiologically relevant EPS concentrations, while cells lacking EPS exhibited significant reduction in long-term viability and resistance to stressful conditions. However, excess EPS production was counter-productive to vegetative growth and viable cell recovery declined in extended late stationary phase as cells became trapped in the matrix of clumps. Therefore, optimal EPS production by M. xanthus is important for normal physiological functions in liquid.

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  10. [국내논문]   Development of a Suicidal Vector-Cloning System Based on Butanal Susceptibility Due to an Expression of YqhD Aldehyde Reductase   SCIE SCOPUS

    Lee, Chang-Han (Department of Life Sciences, Korea Advanced Institute of Science and Technology ) , Park, Chan-Kyu (Department of Life Sciences, Korea Advanced Institute of Science and Technology)
    The journal of microbiology v.50 no.2 ,pp. 249 - 255 , 2012 , 1225-8873 ,

    초록

    Previously, we observed butanal/propanal sensitivity of Escherichia coli K-12 when cells overexpress YqhD protein, a NADPH dependent aldehyde reductase, possibly due to an accumulation of butanol/propanol in vivo as the reaction products. Based on this finding, we developed a suicidal vector-cloning system derived from pUC19, in which lacZ was substituted with the yqhD gene. As a result, when foreign DNA was inserted into its multiple cloning sites by disrupting an expression of YqhD, the recombinants survived on butanal/propanal containing plate, whereas cells containing the YqhD vector died because of the alcohol production by YqhD. The cloning efficiency, estimated based on colony PCR and enzyme digestion, was achieved more than 90% when the suicidal vector system was used. Moreover, the plasmid vector itself was stably maintained in the cell, presumably due to its ability to remove toxic aldehydes being accumulated in E. coli cell by metabolic stress.

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    Fig. 1 이미지

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