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2006 Fiscal Year Final Research Report Summary

Construction of DnaJ Database for Medically important Bacteria to determine Species Definition

Research Project

Project/Area Number 16390129
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bacteriology (including Mycology)
Research InstitutionGifu University

Principal Investigator

EZAKI Takayuki  Gifu University, Graduate School of Medicine, Professor, 大学院医学系研究科, 教授 (90151977)

Co-Investigator(Kenkyū-buntansha) OHKUSU Kiyofumi  Gifu University, Graduate School of Medicine, Associate professor, 大学院医学系研究科, 助教授 (40362173)
Project Period (FY) 2004 – 2006
KeywordsTaxonomy / Definition of Species / DnaJ gene / Phylum / Identification / Detection / Gene variation / Diagnosis of Infectious disease
Research Abstract

Bacteria is phylogenetically classified with 16S rDNA gene sequence variation
The information is especially useful to find phylogenetic position of unidentified bacteria, however, the sequence variation among closely related species are almost identical in many cases. Bacterial species is genetically defined as, "Species is a population of strains, which shares more than 70% chromosome similarity ". However, methods to measure this chromosome DNA similarity are different from one laboratory to another and as a result, the similarity values of same species group are different among different laboratories. So Judicial commission announced to accumulate at least 5 different house keeping gene sequences, which are more variable than 16SD rDNA and useful to determine bacterial species.
We focused on DnaJ sequences and collected the sequences of medically important bacterial groups. Staphylococcus, Streptococccus, Legionella, Mycobacterium, Vibrio, Aeromonas and members of Family Enterobacteriaceae.
The sequence variation of dnaJ is bigger than 16S rDNA. M. gastri and M. kansasiishares identical 16S rDNA sequence, however, type strains and clinical strains of these species were different more than 4%. Vibrio alginolyticus and Vibrio parahaemolyticus group, Vibrio cholerae and Vibrio mimicus group also shares identical 16S rDNA sequences, however, their dnaJ sequence are 4 to 7 percent different. Generally, DnaJ variation in a genus ranged from 75% to 100%,. On the Other hand, Variation of 16S rDNA within a genus ranged from 90 to 100%.
These data supported that the dnaj sequence information is extremely useful to define species and also to design specific sequence to detect bacteria at species level.

  • Research Products

    (25 results)

All 2007 2006 2005 2004

All Journal Article (22 results) Book (1 results) Patent(Industrial Property Rights) (2 results)

  • [Journal Article] dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus.2007

    • Author(s)
      Shah MM, Iihara H, Noda M, Sun X, Nhung PH, Ohkusu K, Kawamura Y, Ezaki T
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology 57

      Pages: 25-30

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] dnaJ gene as a novel phylogenetic marker for identification of Vibrio species.2007

    • Author(s)
      Nhung PH, Shah MM, Ohkusu K, Noda M, Hata H, Sun X, Iihara H, Goto K, Masaki T, Ezaki T
    • Journal Title

      Systematic and Applied Microbiology 30 (in press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Phylogeny and species identification of the family Enterobacteriaceae based on dnaJ sequences.2007

    • Author(s)
      Nhung PH, Ohkusu K, Mishima N, Noda M, Shah MM, Sun X, Hayashi M, Ezaki T
    • Journal Title

      Diagnostic Microbiology and Infectious Disease xx (in press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Novel phylogenetic marker dnaJ and DNA-DNA hybridization for clarifying interrelationships among the genus Aeromonas ; A. culicicola and A. allosaccharophila as later synonyms of A. veronii..2007

    • Author(s)
      Pham Hong Nhung^1, Hiroyuki Hata^1, Kiyofumi Ohkusu^1, Makiko Noda^1, Mohammad Monir Shah^1, Keiichi Goto^2, Takayuki Ezaki
    • Journal Title

      Int. J. syst. Bacteriol. (in press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] dnaJ and gyrB gene sequence relationship among species and strains of the genus Streptococcus2006

    • Author(s)
      Itoh Y, Kawamura Y, Kasai H, Shah MM, Nhung PH, Yamada M, Sun X, Koyama T, Ohkusu K, Ezaki T
    • Journal Title

      Systematic and Applied Microbiology 29

      Pages: 368-374

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] dnaJ gene as a novel phylogenetic marker for identification of Vibrio species2006

    • Author(s)
      Nhung PH, Shah MM, Ohkusu K, Noda M, Hata H, Sun X, Iihara H, Goto K, Masaki T, Ezaki T
    • Journal Title

      Systematic and Applied Microbiology 30(In press)

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Streptococcus2006

    • Author(s)
      Shah MM, Iihara H, Noda M, Sun X, Nhung PH, Ohkusu K, Kawamura Y, Ezaki T
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology 57

      Pages: 25-30

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Phylogeny and species identification of the family Enterobacteriaceae based on dnaJ sequences2006

    • Author(s)
      Nhung PH, Ohkusu K, Mishima N, Noda M, Shah MM, Sun X, Hayashi M, Ezaki T
    • Journal Title

      Diagnostic Microbiology and Infectious Disease 55(In press)

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] dnaJ and gyrB gene sequence relationship among species and strains of the genus Streptococcus.2006

    • Author(s)
      Itoh Y, Kawamura Y, Kasai H, Shah MM, Nhung PH, Yamada M, Sun X, Koyama T, Ohkusu K, Ezaki T
    • Journal Title

      Systematic and Applied Microbiology 29

      Pages: 368-374

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Phylogenetic study and multiplex PCR-based detection of Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli using gryB and rpoD sequences.2006

    • Author(s)
      Maeda Y., Shinohara H., Kiba, A., Ohnishi K., Furuya N., Kawamura Y., Ezaki t., Vandamme P., Tsushima S., Hikichi, Y
    • Journal Title

      Int. J. Syst. Evol Microbiol. 56

      Pages: 1031-1038

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Mycobacterium kumamotoense sep. nov. recovered from clinical specimen and the first isolation report of Mycobacterium arupense in Japan. Novel slowly growing, nonchromogenic clinical isolates related to Mycobacterium terrae complex.2006

    • Author(s)
      Masaki, T., Ohkusu, K., Hata, H., Fujiwara, N., Iihara H., Noda, M., Nhung P.H., Hayashi, M., Asano, Y., Kawamura, Y., Ezaki.T.
    • Journal Title

      Int. J. Syst. Evol Microbiol. 50

      Pages: 889-897

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Quantitative microarray-based DNA-DNA hybridization assay for measuring genetic distances among bacterial species and its application to the identification of family Enterobacteriaceae2005

    • Author(s)
      Makoto Amano, Kiyofumi Ohkusu, Koji Kusaba, Hironori Ikedo, Zonzo Nagasawa, Yosuke Aoki, Yoshiaki Kawamura, Shinzo Kobatake, Takumi Tanaka, Shuuji Matuura, Takayuki Ezaki
    • Journal Title

      Microbiol. Immunol. 49

      Pages: 255-263

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] High genetic similarity of Streptococcus agalactiae and Streptococcus difficilis : S. difficilis Eldar et al. 1995 as a junior synonym of S. agalactiae Lehmann and Neumann 1896 (Approved Lists 1980)2005

    • Author(s)
      Kawamura, Y., I.Itoh, N.Mishiam, K.Ohkusu, H.Kasai, T.Ezaki
    • Journal Title

      Int. J. Syst. Evol. Microbiol. 55

      Pages: 961-965

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Corynebacterium resisters sp. nov., a new multidrug-resistant coryneform bacteria isolated from human infection2005

    • Author(s)
      Yoshihito Otsuka, Yoshiaki Kawamura, Takashi Koyama, Hirotoshi Iihara, Kiyofumi Ohkusu, Takayuki. Ezaki
    • Journal Title

      J. Clin. Microbiol. 43

      Pages: 3713-3717

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Paenibacillus motobuensis sp. nov., isolated from the garbage disposal machine utilizing soil of Motobu-town, Okinawa, Japan2005

    • Author(s)
      K.Iida, Y.Ueda, Y.Kawamura, T.Ezaki, A.Takade, S.Yoshida, K.Amako
    • Journal Title

      Int. J. Syst. Evol. Microbiol. 55

      Pages: 1811-1816

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Neisseria elongata subsp. nitroreducens Endocarditis in a 7-Year-Old Boy2005

    • Author(s)
      Hoshino T, Ohkusu K, Sudo F, Nakajima H, Ishiwada N, Ezaki T, Kohno Y
    • Journal Title

      Pediatric Infectious Disease Journal 24

      Pages: 391-392

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Corynebacterium resistens sp. nov., a new multidrug-resistant coryneform bacteria isolated from human infection2005

    • Author(s)
      Yoshihito Otsuka, Yoshiaki Kawamura, Takashi Koyama, Hirotoshi Iihara, Kiyofumi Ohkusu, Takayuki. Ezaki
    • Journal Title

      J. Clin. Microbiol. 43

      Pages: 3713-3717

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Neisseria elongata subsp. nitroreducens Endocarditis in a 7-Year-Old Boy2005

    • Author(s)
      Hoshino T, Ohkusu K, Sudo F, Nakajima H, Ishiwada N, Ezaki T, Kohno Y
    • Journal Title

      Pediatric Infectious Disease Journal. 24

      Pages: 391-392

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Molecular characterization of Haemophilus influenzae type a and untypable strains isolated simultaneously from cerebrospinal fluid and blood : novel use of quantitative real-time PCR based on the cap copy number to determine virulence2005

    • Author(s)
      Ohkusu K, Nash KA, Inderlied CB
    • Journal Title

      Clin. Microbiol. Infect. 11

      Pages: 637-643

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russica sp. nov., isolated from the air in the Russian space laboratory Mir2004

    • Author(s)
      Li, Y., Y.Kawamura, et al.
    • Journal Title

      Int. J. Syst. Evol. Microbiol. 54

      Pages: 827-835

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir.2004

    • Author(s)
      Li, Y., Y.Kawamura et al.
    • Journal Title

      Int. J. Syst. Evol. Microbiol 54

      Pages: 819-825

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Borrelia turcica sp. nov., isolated from the hard tick Hyalomna aegyptium in Turkey2004

    • Author(s)
      Guner, E.S., M.Watanabe.et al.
    • Journal Title

      Int. J. Syst. Evol. Microbiol 54

      Pages: 1649-1652

    • Description
      「研究成果報告書概要(和文)」より
  • [Book] 腸内細菌の分子生物学的実験法2006

    • Author(s)
      江崎 孝行, 大楠 清文
    • Total Pages
      175
    • Publisher
      日本ビフィズス菌センター
    • Description
      「研究成果報告書概要(和文)」より
  • [Patent(Industrial Property Rights)] 病原微生物のターゲット核酸増幅方法及び増幅用プライマー混合物2007

    • Inventor(s)
      江崎孝行
    • Industrial Property Rights Holder
      岐阜大学
    • Industrial Property Number
      特出願番号:2007-079059
    • Filing Date
      20070300
    • Description
      「研究成果報告書概要(和文)」より
  • [Patent(Industrial Property Rights)] DnaJ配列を利用した細菌の検出・同定方法2006

    • Inventor(s)
      江崎孝行
    • Industrial Property Rights Holder
      岐阜大学
    • Industrial Property Number
      特出願番号:2006-272329
    • Filing Date
      20060300
    • Description
      「研究成果報告書概要(和文)」より

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Published: 2008-05-27  

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