16S rDNA genotyping using PCR/RFLP (restriction fragment length polymorphism) analysis among the family vibrionaceae

FEMS Microbiology Letters

Volumn 152, Issue 1, 1997, Pages 125-132

  Urakawa, Hidetoshi ^a   Kita Tsukamoto, Kumiko ^a   Ohwada, Kouichi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

16S rDNA; Genotyping; Polymerase chain reaction; Restriction fragment length polymorphism; Vibrio iliopiscarius; Vibrionaceae; Vibro

Indexed keywords

ENDONUCLEASE; RIBOSOME DNA; RNA 16S;

ARTICLE; EVOLUTION; GENE SEQUENCE; GENETIC ANALYSIS; GENOTYPE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; VIBRIONACEAE;

BASE SEQUENCE; DNA, BACTERIAL; DNA, RIBOSOMAL; GENOTYPE; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; VIBRIONACEAE;

PHOTOBACTERIUM ILIOPISCARIUM; VIBRIO; VIBRIONACEAE;

EID: 0030785666     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(97)00191-2     Document Type: Article

References (20)

1. Huq, A. and Colwell, R.R. (1995) Vibrios in the marine and estuarine environments. J. Mar. Biotechnol. 3, 60-63.
2. Sochard, M.R., Wilson, D.F., Austin, B. and Colwell, R.R. (1979) Bacteria associated with the surface and gut of marine copepods. Appl. Environ. Microbiol. 37, 750-759.
3. Blake, P.A., Weaver, R.E. and Hollis, D.G. (1980) Disease of humans (other than cholera) caused by vibrios. Annu. Rev. Microbiol. 34, 341-367.
4. Wiik, R., Stackebrandt, E., Valle, O., Daae, F.L., Rodseth, O.M. and Andersen, K. (1995) Classification of fish-pathogenic vibrios based on comparative 16S rRNA analysis. Int. J. Syst. Bacteriol. 45, 421-428.
5. Ishimaru, K., Akagawa-Matsushita, M., Muroga, K. (1995) Vibrio penaeicida sp.nov., a pathogen of kuruma prawns (Penaeus japonicus). Int. J. Syst. Bacteriol. 45, 134-138.
6. Ishimaru, K., Akagawa-Matsushita, M. and Muroga, K. (1996) Vibrio ichthyoenteri sp. nov., a pathogen of Japanese flounder (Paralichthys olivaceus). Int. J. Syst. Bacteriol. 49, 155-159.
7. Woese, C.R. (1987) Bacterial evolution. Microbiol. Rev. 51, 221-271.
8. Kita-Tsukamoto, K., Oyaizu, H., Nanba, K. and Simidu, U. (1993) Phylogenetic relationships of marine bacteria, mainly members of the family Vibrionaceae, determined on the basis of 16S rRNA sequences. Int. J. Syst. Bacteriol. 43, 8-19.
9. Stackebrandt, E. and Goebel, B.M. (1994) Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44, 846-849.
10. Laguerre, G., Allard, M.-R., Revoy, F. and Amarger, N. (1994) Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbiol. 60, 56-63.
11. Hiraishi, A., Kamagata, Y. and Nakamura, K. (1995) Polymerase chain reaction amplification and restriction fragment length polymorphism analysis of 16S rRNA genes from Methanogens. J. Ferment. Bioeng. 79, 523-529.
12. Oppenheimer, C.H. and ZoBell, C.E. (1952) The growth and viability of sixty-three species of marine bacteria as influenced by hydrostatic pressure. J. Mar. Res. 11, 10-18.
13. ZoBell, C.E. (1946) Marine Microbiology. Chronica Botanica, Waltham, MA.
14. Weisburg, W.G., Barns, S.M., Pelletier, D.A. and Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697-703.
15. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
16. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
17. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. J. Mol. Evol. 4, 406-425.
18. Moyer, C.L., Tiedje, J.M., Dobbs, F.C. and Karl, D.M. (1996) A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl. Environ. Microbiol. 62, 2501-2507.
19. Ruimy, R., Breittmayer, V., Elbaze, P., Lafay, B., Boussemart, O., Gauthier, M. and Christen, R. (1994) Phylogenetic analysis and assessment of the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas deduced from small-subunit rRNA sequences. Int. J. Syst. Bacteriol. 44, 416-426.
20. Navarro, E., Simonet, P., Normand, P. and Bardin, R. (1992) Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch. Microbiol. 157, 107-115.