Nobutada Kimura

Summary

Affiliation: National Institute of Advanced Industrial Science and Technology
Country: Japan

Publications

  1. ncbi request reprint The microbial community in a 2,4-dinitrophenol-digesting reactor as revealed by 16S rDNA gene analysis
    Nobutada Kimura
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, AIST Tsukuba Central 6, 1 1 1 Higashi, Tsukuba, Ibaraki 305 8566, Japan
    J Biosci Bioeng 96:70-5. 2003
  2. pmc Draft Genome Sequence of Pseudomonas abietaniphila KF717 (NBRC 110669), Isolated from Biphenyl-Contaminated Soil in Japan
    Nobutada Kimura
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Genome Announc 3:. 2015
  3. pmc A novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, Rhodococcus opacus SAO101
    Wataru Kitagawa
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305 8566, Japan
    J Bacteriol 186:4894-902. 2004
  4. ncbi request reprint Isolation and characterization of a 4-nitrotoluene-oxidizing enzyme from activated sludge by a metagenomic approach
    Nobutada Kimura
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1, Higashi, Tsukuba, Ibaraki 305 8566, Japan
    Microbes Environ 25:133-9. 2010
  5. doi request reprint Impact of dibenzofuran/dibenzo-p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations
    Nobutada Kimura
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki, 305 8566, Japan
    Appl Microbiol Biotechnol 84:365-73. 2009
  6. ncbi request reprint Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101
    Nobutada Kimura
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki 305 8566, Japan
    Appl Microbiol Biotechnol 73:474-84. 2006
  7. pmc Primary gut symbiont and secondary, Sodalis-allied symbiont of the Scutellerid stinkbug Cantao ocellatus
    Nahomi Kaiwa
    National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
    Appl Environ Microbiol 76:3486-94. 2010
  8. pmc Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Cupriavidus basilensis KF708 (NBRC 110671) Isolated from Biphenyl-Contaminated Soil
    Hikaru Suenaga
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Genome Announc 3:. 2015
  9. pmc Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas putida KF703 (NBRC 110666) Isolated from Biphenyl-Contaminated Soil
    Hikaru Suenaga
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Genome Announc 3:. 2015
  10. pmc Draft Genome Sequence of Burkholderia stabilis LA20W, a Trehalose Producer That Uses Levulinic Acid as a Substrate
    Yuya Sato
    Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki, Japan
    Genome Announc 4:. 2016

Collaborators

Detail Information

Publications22

  1. ncbi request reprint The microbial community in a 2,4-dinitrophenol-digesting reactor as revealed by 16S rDNA gene analysis
    Nobutada Kimura
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, AIST Tsukuba Central 6, 1 1 1 Higashi, Tsukuba, Ibaraki 305 8566, Japan
    J Biosci Bioeng 96:70-5. 2003
    ..One of these strain types was identified as a relative of Rhodococcus koreensis, and the other was identified as a relative of Nocardioides simplex FJ21-A...
  2. pmc Draft Genome Sequence of Pseudomonas abietaniphila KF717 (NBRC 110669), Isolated from Biphenyl-Contaminated Soil in Japan
    Nobutada Kimura
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Genome Announc 3:. 2015
    ..We report here the 6,930,016-bp genome sequence of this strain, which contains 6,323 predicted coding sequences (CDSs), including the biphenyl-utilizing bph gene cluster. ..
  3. pmc A novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, Rhodococcus opacus SAO101
    Wataru Kitagawa
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305 8566, Japan
    J Bacteriol 186:4894-902. 2004
    ..These results clearly indicated that the cloned npc genes play an essential role in 4-NP mineralization in R. opacus SAO101...
  4. ncbi request reprint Isolation and characterization of a 4-nitrotoluene-oxidizing enzyme from activated sludge by a metagenomic approach
    Nobutada Kimura
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1, Higashi, Tsukuba, Ibaraki 305 8566, Japan
    Microbes Environ 25:133-9. 2010
    ..These results suggested that the icp product is an enzyme involved in catalyzing 4-nitrotoluene's oxygenation...
  5. doi request reprint Impact of dibenzofuran/dibenzo-p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations
    Nobutada Kimura
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki, 305 8566, Japan
    Appl Microbiol Biotechnol 84:365-73. 2009
    ....
  6. ncbi request reprint Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101
    Nobutada Kimura
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki 305 8566, Japan
    Appl Microbiol Biotechnol 73:474-84. 2006
    ..Strain SAO101 harbors three huge linear plasmids, pWK301 (1,100 kbp), pWK302 (1,000 kbp), and pWK303 (700 kbp), and the nar genes were found to be located on the pWK301 plasmid...
  7. pmc Primary gut symbiont and secondary, Sodalis-allied symbiont of the Scutellerid stinkbug Cantao ocellatus
    Nahomi Kaiwa
    National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
    Appl Environ Microbiol 76:3486-94. 2010
    ..Biological aspects of the primary gut symbiont and the secondary Sodalis-allied symbiont are discussed...
  8. pmc Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Cupriavidus basilensis KF708 (NBRC 110671) Isolated from Biphenyl-Contaminated Soil
    Hikaru Suenaga
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Genome Announc 3:. 2015
    ..The KF708 strain possesses genes for biphenyl catabolism and other genes involved in various aromatic compounds. ..
  9. pmc Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas putida KF703 (NBRC 110666) Isolated from Biphenyl-Contaminated Soil
    Hikaru Suenaga
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Genome Announc 3:. 2015
    ..Here, we report the draft genome sequence of the KF703 strain, which provides insight into the molecular mechanisms of adaptation to an environment polluted by aromatic compounds. ..
  10. pmc Draft Genome Sequence of Burkholderia stabilis LA20W, a Trehalose Producer That Uses Levulinic Acid as a Substrate
    Yuya Sato
    Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki, Japan
    Genome Announc 4:. 2016
    ..Here, we report the 7.97-Mb draft genome sequence of B. stabilis LA20W, which will be useful in investigations of the enzymes involved in LA metabolism and the mechanism of LA-induced trehalose production. ..
  11. pmc Phylogenetically novel LuxI/LuxR-type quorum sensing systems isolated using a metagenomic approach
    Eri Nasuno
    National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki, Japan
    Appl Environ Microbiol 78:8067-74. 2012
    ..We demonstrated that metagenomic screening is useful to provide further insight into the phylogenetic diversity of bacterial QS systems by describing two new LuxI/LuxR-type QS systems from uncultured bacteria...
  12. pmc "Mark the gene": a method for nondestructive introduction of marker sequences inside the gene frame of transgenes
    Yuki Morono
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
    Appl Environ Microbiol 73:4915-21. 2007
    ..This direct method of marking the functional transgene provides a simple, low-risk, and robust marking method without causing the gene functions to deteriorate...
  13. pmc The combination of functional metagenomics and an oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by the cultivation-based method
    Takashi Narihiro
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST
    Microbes Environ 29:154-61. 2014
    ....
  14. pmc Isolation of butanol- and isobutanol-tolerant bacteria and physiological characterization of their butanol tolerance
    Manabu Kanno
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki, Japan
    Appl Environ Microbiol 79:6998-7005. 2013
    ..0% butanol exist in the environment and have various strategies to maintain structural integrity against detrimental solvents. ..
  15. pmc Discovery of glycoside hydrolase enzymes in an avicel-adapted forest soil fungal community by a metatranscriptomic approach
    Kazuto Takasaki
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki, Japan
    PLoS ONE 8:e55485. 2013
    ..This study demonstrated that fungal communities adapt to Avicel and wheat decomposition and that metatranscriptomic sequence data can be reference data for identifying a novel gene...
  16. pmc "Candidatus Curculioniphilus buchneri," a novel clade of bacterial endocellular symbionts from weevils of the genus Curculio
    Hirokazu Toju
    National Institute of Advanced Industrial Science and Technology AIST, Tsukuba 305 8566, Japan
    Appl Environ Microbiol 76:275-82. 2010
    ..We suggest that such Sodalis-allied secondary symbionts in weevils might provide a potential source for symbiont replacements, as has occurred in an ancestor of Sitophilus grain weevils...
  17. doi request reprint Electrodialytic Separation of Levulinic Acid Catalytically Synthesized from Woody Biomass for the Use of Microbial Conversion
    Hiroshi Habe
    Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology AIST, 16 1 Onogawa, Tsukuba, Ibaraki, 305 8569, Japan
    Biotechnol Prog . 2016
    ..This is the first report on ED application for LA recovery using more than 20 g L-1 LA solutions (40-160 g L-1 ). This article is protected by copyright. All rights reserved...
  18. doi request reprint The effects of N-acylhomoserine lactones, β-lactam antibiotics and adenosine on biofilm formation in the multi-β-lactam antibiotic-resistant bacterium Acidovorax sp. strain MR-S7
    Hiroyuki Kusada
    Graduate School of Life and Environmental Sciences, University of Tsukuba, 1 1 1 Ten nodai, Tsukuba, Ibaraki 305 8572, Japan Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba, Ibaraki 305 8566, Japan Electronic address
    J Biosci Bioeng 118:14-9. 2014
    ....
  19. doi request reprint Screening, identification, and characterization of α-xylosidase from a soil metagenome
    Tomohiko Matsuzawa
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba Central 6, 1 1 1 Higashi, Tsukuba, Ibaraki 305 8566, Japan
    J Biosci Bioeng 122:393-9. 2016
    ..MeXyl31 is the first α-xylosidase isolated from the metagenome and, relative to other xyloglucan oligosaccharides, shows higher activity toward pNP α-d-xylopyranoside. ..
  20. pmc A Thermostable Bilirubin-Oxidizing Enzyme from Activated Sludge Isolated by a Metagenomic Approach
    Nobutada Kimura
    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology AIST
    Microbes Environ . 2016
    ..This enzyme is a thermostable-bilirubin oxidase that exhibits markedly higher thermostability than that previously reported for laccases...
  21. pmc Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments
    Hiroyuki Imachi
    Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603 1 Kamitomioka, Nagaoka, Niigata 940 2188, Japan
    Appl Environ Microbiol 72:2080-91. 2006
    ....