Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences

Diseases of Aquatic Organisms

Volumn 58, Issue 2-3, 2004, Pages 143-150

  Le Roux, Frédérique ^a   Gay, Mélanie ^a   Lambert, Christophe ^b   Nicolas, Jean Louis ^c   Gouy, Manolo ^d   Berthe, Franck ^a  

^a Inst Francais Rech Pour l'E   (France)

^b UNIVERSITÉ DE BRETAGNE OCCIDENTALE   (France)

^c IFREMER   (France)

^d UNIVERSITÉ LYON 1   (France)

Author keywords

GyrB; Phylogenetic; Polyphyletic; Taxonomy; Vibrio splendidus

Indexed keywords

GENETIC VARIATION; IDENTIFICATION METHOD; PHYLOGENETICS; TAXONOMY;

ANIMALIA; BIVALVIA; CRASSOSTREA; CRASSOSTREA GIGAS; OSTREIDAE; PROKARYOTA; VIBRIO; VIBRIO CHAGASII; VIBRIO KANALOAE; VIBRIO LENTUS; VIBRIO POMEROYI; VIBRIO SPLENDIDUS; VIBRIO TASMANIENSIS;

DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); RIBOSOME DNA;

ANIMAL; ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OYSTER; PHYLOGENY; SPECIES DIFFERENCE; VIBRIO;

ANIMALS; BASE SEQUENCE; CLUSTER ANALYSIS; DNA; DNA GYRASE; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; OSTREIDAE; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS); VIBRIO;

EID: 3042532644     PISSN: 01775103     EISSN: None     Source Type: Journal    
DOI: 10.3354/dao058143     Document Type: Article

References (37)

1. AL. In: Krieg NR, Holt JG (eds) Bergey's manual systematic of bacteriology. Williams & Wilkins, Baltimore, p 516-517
2. Baumann P, Baumann L, Bang SS, Woolkalis MJ (1980) Reevaluation of the taxonomy of Vibrio, Beneckea, and Photobacterium: abolition of the genus Beneckea. Curr Microbiol 4:127-132
3. Crosa JH, Brenner DJ, Falkow S (1973) Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J Bacteriol 115:904-911
4. Farto R, Montes M, Perez MJ, Nieto TP, Larsen JL, Pedersen K (1999) Characterization by numerical taxonomy and ribotyping of Vibrio splendidus biovar I and Vibrio scophthalmi strains associated with turbot cultures. J Appl Microbiol 86:796-804
5. Fox GE, Wisotzkey JD, Jurtshuk PJ (1992) How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166-170
6. Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_WIN: 2 graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543-548
7. Garrity GM, Holt JG (2001) The road map to the manual. In: Boone DR, Castenholtz RW, Garrity GM (eds) Bergey's manual of systematic bacteriology, 2nd edn. Springer-Verlag, New York, p 119-166
8. Gascuel O (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14:685-695
9. Gatesoupe FJ, Lambert C, Nicolas JL (1999) Pathogenicity of Vibrio splendidus strains associated with turbot larvae, Scophthalmus maximus. J Appl Microbiol 87:757-763
10. Grimont PAD (1984) Use of DNA reassociation in bacterial classification. Can J Microbiol 34:541-546
11. Grimont PAD, Popoff MY, Grimont F, Coynault C, Lemelin M (1980) Reproducibility and correlation study of three deoxyribonucleic acid hybridisation procedure. Curr Microbiol 4:325-330
12. Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microbiol Mol Biol Rev 62:1425-1491
13. Kwok AY, Wilson JT, Coulthart M, Ng LK, Mutharia L, Chow AW (2002) Phylogenetic study and identification of human pathogenic Vibrio species based on partial hsp60 gene sequences. Can J Microbiol 48:903-910
14. Lacoste A, Jalabert F, Malham S, Cueff A, Gélébart F, Cordevant C, Lange M, Poulet SA (2001) A Vibrio splendidus strain is associated with summer mortality of juvenile oysters Crassostrea gigas in the Bay of Morlaix (North Brittany, France). Dis Aquat Org 46:139-145
15. Lambert C, Nicolas JL, Cilia V, Corre S (1998) Vibrio pectenicida sp. nov. a pathogen of scallop (Pecten maximus) larvae. Int J Syst Bacteriol 48:481-487
16. Le Roux F, Gay M, Lambert C, Waechter M, Poubalanne S, Chollet B, Nicolas JL, Berthe F (2002) Comparative analysis of Vibrio splendidus-related strains isolated during Crassostrea gigas mortality events. Aquat Living Resour 15:251-258
17. Ludwig W, Klenk HP (2001) Overview: a phylogenetic backbone and taxonomic frame work for prokaryotic systematics. In: Boone DR, Castenholtz RW, Garrity GM (eds) Bergey's manual of systematic bacteriology, 2nd edn. Springer-Verlag, New York, p 49-65
18. Macian MC, Ludwig W, Aznar R, Grimont PA, Schleifer KH, Garay E, Pujalte MJ (2001) Vibrio lentus sp. nov., isolated from Mediterranean oysters. Int J Syst Evol Microbiol 51:1449-1456
19. Nealson KH, Wimpee B, Wimpee C (1993) Identification of Vibrio splendidus as a member of the planktonic luminous bacteria from Persian Gulf and Kuwait region with LuxA probes. Appl Environ Microbiol 59:2684-2689
20. Nicolas JL, Corre S, Gauthier G, Robert R, Ansquer D (1996) Bacterial problems associated with scallop Pecten maximus larval culture. Dis Aquat Org 27:67-76
21. Ochman H, Wilson AC (1987) Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol 26:74-86
22. Ohnishi M, Kurokawa K, Hayashi T (2001) Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol 9:481-485
23. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor, NY
24. Sneath PHA (1972) Computer taxonomy. Methods Microbiol 7A:29-98
25. Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. WH Freeman, San Francisco, p 188-1308
26. Stackebrandt E, Goebel BM (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
27. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD and 9 others (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043-1047
28. Sugumar G, Nakai T, Hirata Y, Matsubara D, Muroga K (1998) Vibrio splendidus biovar II as the causative agent of bacillary necrosis of Japanese oyster Crassostrea gigas larvae. Dis Aquat Org 33:111-118
29. Suzuki M, Nakagawa Y, Harayama S, Yamamoto S (1999) Phylogenetic analysis of genus Marinilabilia and related bacteria based on the amino acid sequences of gyrB and amended description of Marinilabilia salmonicolor with Marinilabilia agarovorans as its subjective synonym. Int J Syst Bacteriol 49:1551-1557
30. Thompson FL, Hoste B, Vandemeulebroecke K, Swings J (2001) Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism. Syst Appl Microbiol 24:520-38
31. Thompson FL, Thompson CC, Li Y, Gomez-Gil B, Vandenberghe J, Hoste B, Swings J (2003a) Vibrio kanaloae sp. nov., Vibrio pomeroyi sp. nov. and Vibrio chagasii sp. nov., from sea water and marine animals. Int J Syst Evol Microbiol 53:753-759
32. Thompson FL, Thompson CC, Swings J (2003b) Vibrio tasmaniensis sp. nov., isolated from Atlantic salmon (Salmo salar L.). Syst Appl Microbiol 26:65-69
33. Waechter M, Le Roux F, Nicolas JL, Marissal E, Berthe F (2002) Characterisation of Crassostrea gigas spat pathogenic bacteria. C R Acad Sci 325:231-238
34. Watanabe K, Nelson J, Harayama S, Kasai H (2001) ICB database: the gyrB database for identification and classification of bacteria. Nucleic Acids Res 29:344-145
35. Yamamoto S, Harayama S (1995) PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61:1104-1109
36. Yamamoto S, Harayama S (1998) Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16SrRNA genes. Int J Syst Bacteriol 48:813-819
37. Yamamoto S, Bouvet PJ, Harayama S (1999) Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-hybridisation. Int J Syst Bacteriol 49:87-95