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Bacteria Collection: Photobacterium damselae

NCTC Number: NCTC 11647
Current Name: Photobacterium damselae
Original Strain Reference: VL 12480, CDC 2588-80
Other Collection No: ATCC 33539; DSM 7482
Previous Catalogue Name: Photobacterium damsela
Type Strain: Yes
Family: Vibrionaceae
Hazard Group (ACDP): 2
Release Restrictions: Terms & Conditions of Supply of Microbial Pathogens: Safety
Conditions for growth on solid media: Nutrient agar, 24-48 hours, 30°C, aerobic
Conditions for growth on liquid media: meat broth,37, facultative anaerobe
Isolated From: fish;skin lesions on damsel fish
Whole Genome Sequence:
16S rRNA Gene Sequence: >gb|X74700|ATCC 33539T|V.damsela (ATCC 33539T) gene for 16S ribosomal RNA.| attnaagagtttgat... >gb|AB255703|ATCC 33539|Photobacterium damselae subsp. damselae DNA, 16S-23S rRNAintergenic spacer, partial sequence, strain: ATCC 33539.| tagctctttaacaat... >gb|AY191126|ATCC 33539|Photobacterium damselae subsp. damselae strain ATCC 33539 16Sribosomal RNA gene, partial sequence.| ggctggcggcaggcc... >gb|D11228|ATCC33539|Listonella damsela 16S rRNA.| ggtgaaatgcgtaga... >gb|D11179|ATCC33539|Listonella damsela 16S rRNA.| ggggaatattgcrca... >gb|AB032015|ATCC33539|Photobacterium damselae subsp. damselae gene for 16S rRNA, partialsequence.| ttggagagtttgatc...
23S rRNA Gene Sequence: >gb|AB255703|ATCC 33539|Photobacterium damselae subsp. damselae DNA, 16S-23S rRNAintergenic spacer, partial sequence, strain: ATCC 33539.| tagctctttaacaat...
Miscellaneous Sequence Data: >gb|AY455889|ATCC 33539|Photobacterium damselae strain ATCC 33539 DNA gyrase subunit B(gyrB) gene, partial cds.| acgctggtggtaagt...
Bibliography: VALIDATON LIST NO 8 1982 INT J SYST BACT 32 266
Extended Bibliography: showhide Show bibliography
Ref #: 68441
Author(s): Kimura,B.;Hokimoto,S.;Takahashi,H.;Fujii,T.
Journal: Int J Syst Evol Microbiol
Title: Photobacterium histaminum Okuzumi et al. 1994 is a later subjective synonym of Photobacterium damselae subsp. damselae (Love et al. 1981) Smith et al. 1991
Volume: 50 Pt 3
Page(s): 1339-42
Year: 2000
Keyword(s): GENBANK/AB032014 GENBANK/AB032015 DNA, Bacterial/genetics DNA, Ribosomal/genetics Genes, rRNA Histamine/metabolism Molecular Sequence Data Nucleic Acid Hybridization Phenotype Photobacterium/*classification/*genetics/metabolism RNA, Ribosomal, 16S/genetics Sequence Analysis, DNA Sequence Homology, Nucleic Acid *Terminology
Remarks: The type strain of Photobacterium histaminum, JCM 8968T (= ATCC 51805T), and that of Photobacterium damselae subsp. damselae, ATCC 33539T, exhibit 100% identity in their 16S rRNA sequence, more than 80% DNA-DNA homology and only one phenotypic difference. Also, like P. histaminum, P. damselae subsp. damselae was shown to excrete a large amount of histamine when cells were grown on medium containing excessive histidine under acidic conditions. Therefore, the name P. histaminum should be considered to be a later subjective synonym of P. damselae subsp. damselae.
URL: 10843080
Ref #: 72321
Author(s): Kita-Tsukamoto,K.;Oyaizu,H.;Nanba,K.;Simidu,U.
Journal: Int J Syst Bacteriol
Title: Phylogenetic relationships of marine bacteria, mainly members of the family Vibrionaceae, determined on the basis of 16S rRNA sequences
Volume: 43
Page(s): 8-19
Year: 1993
Keyword(s): GENBANK/D11169 GENBANK/D11170 GENBANK/D11171 GENBANK/D11172 GENBANK/D11173 GENBANK/D11174 GENBANK/D11175 GENBANK/D11176 GENBANK/D11177 GENBANK/D11178 GENBANK/D11179 GENBANK/D11180 GENBANK/D11181 GENBANK/D11182 GENBANK/D11183 GENBANK/D11184 GENBANK/D11185 GENBANK/D11186 GENBANK/D11187 GENBANK/D11188 GENBANK/D11189 GENBANK/D11190 GENBANK/D11191 GENBANK/D11192 GENBANK/D11193 GENBANK/D11194 GENBANK/D11195 GENBANK/D11196 GENBANK/D11197 GENBANK/D11198 etc. Base Sequence Molecular Sequence Data *Phylogeny RNA, Ribosomal, 16S/classification/*genetics/*isolation & purification Seawater Sequence Homology, Nucleic Acid Vibrionaceae/*classification/*genetics/metabolism *Water Microbiology
Remarks: The phylogenetic relationships of 50 reference strains, mostly marine bacteria which require Na+ for growth, were determined on the basis of 600 16S rRNA nucleotides by using reverse transcriptase sequencing. Strains belonging to 10 genera were included (four genera of the family Vibrionaceae, the genus Aeromonas of the family Aeromonadaceae, and the genera Alteromonas, Marinomonas, Shewanella, Pseudomonas, and Deleya). The sequences were aligned, the similarity values and evolutionary distance values were determined, and a phylogenetic tree was constructed by using the neighbor-joining method. On the basis of our results, the family Vibrionaceae was separated into at least seven groups (genera and families). Vibrio marinus clearly was on a line of descent that was remote from other vibrios. As determined by the similarity and evolutionary distance values, V. marinus is more distantly related to the family Vibrionaceae than the members of the Aeromonadaceae are. Also, Vibrio cholerae strains formed a separate group with Vibrio mimicus at the genus level. Of 30 species of the Vibrionaceae, 17 formed a large phylogenetic cluster. The genus Listonella was found to be a heterogeneous group, and the species were distributed in various subgroups of the Vibrionaceae. The separation of the family Aeromonadaceae from the family Vibrionaceae and the separation of the genera Marinomonas and Shewanella from the genus Alteromonas were confirmed in this phylogenetic study. However, a marine Pseudomonas species, Pseudomonas nautica, was clearly separated from two terrestrial Pseudomonas species. Each group that was separated by the phylogenetic analysis had characteristic 16S rRNA sequence patterns that were common only to species in that group. Therefore, the characteristic sequences described in this paper may be useful for identification purposes.
URL: 8427811
Ref #: 68414
Author(s): Osorio,C.R.;Collins,M.D.;Romalde,J.L.;Toranzo,A.E.
Journal: Dis Aquat Organ
Title: Characterization of the 23S and 5S rRNA genes and 23S-5S intergenic spacer region (ITS-2) of Photobacterium damselae
Volume: 61
Page(s): 33-9
Year: 2004
Keyword(s): GENBANK/AJ250695 GENBANK/AJ250696 GENBANK/AJ250697 GENBANK/AJ250698 GENBANK/AJ274379 GENBANK/Y17901 GENBANK/Y18520 Base Sequence Cluster Analysis DNA Primers DNA, Ribosomal Spacer/*genetics Molecular Sequence Data Photobacterium/*genetics *Phylogeny Sequence Alignment Sequence Analysis, DNA Species Specificity *Variation (Genetics)
Remarks: The 23S ribosomal RNA (rRNA) gene has been sequenced in strains of the fish pathogens Photobacterium damselae subsp. damselae (ATCC 33539) and subsp. piscicida (ATCC 29690), showing that 3 nucleotide positions are clearly different between subspecies. In addition, the 5S rRNA gene plus the intergenic spacer region between the 23S and 5S rRNA genes (ITS-2) were amplified, cloned and sequenced for the 2 reference strains as well as the field isolates RG91 (subsp. damselae) and DI21 (subsp. piscicida). A 100% similarity was found for the consensus 5S rRNA gene sequence in the 2 subspecies, although some microheterogeneity was detected as inter-cistronic variability within the same chromosome. Sequence analysis of the spacer region between the 23S and 5S rRNA genes revealed 2 conserved and 3 variable nucleotide sequence blocks, and 4 different modular organizations were found. The ITS-2 spacer region exhibited both inter-subspecies and intercistronic polymorphism, with a mosaic-like structure. The EMBL accession numbers for the 23S, 5S and ITS-2 sequences are: P. damselae subsp. piscicida 5S gene (AJ274379), P. damselae subsp. damselae 23S gene (Y18520), subsp. piscicida 23S gene (Y17901), P. damselae subsp. piscicida ITS-2 (AJ250695, AJ250696), P. damselae subsp. damselae ITS-2 (AJ250697, AJ250698).
URL: 15584408
Ref #: 68561
Author(s): Ast,J.C.;Dunlap,P.V.
Journal: Arch Microbiol
Title: Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi
Volume: 181
Page(s): 352-61
Year: 2004
Keyword(s): Animals Fishes/microbiology *Genes, Bacterial Luminescent Measurements Multigene Family *Operon Photobacterium/*classification/*genetics/isolation & purification Phylogeny
Remarks: The luminous marine bacterium Photobacterium mandapamensis was synonymized several years ago with Photobacterium leiognathi based on a high degree of phenotypic and genetic similarity. To test the possibility that P. leiognathi as now formulated, however, actually contains two distinct bacterial groups reflecting the earlier identification of P. mandapamensis and P. leiognathi as separate species, we compared P. leiognathi strains isolated from light-organ symbiosis with leiognathid fishes (i.e., ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1) with strains from seawater originally described as P. mandapamensis and later synonymized as P. leiognathi (i.e., ATCC 27561(T) and ATCC 33981) and certain strains initially identified as P. leiognathi (i.e., PL-721, PL-741, 554). Analysis of the 16S rRNA and gyrB genes did not resolve distinct clades, affirming a close relationship among these strains. However, strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 were found to bear a luxF gene in the lux operon ( luxABFE), whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 lack this gene ( luxABE). Phylogenetic analysis of the luxAB(F)E region confirmed this distinction. Furthermore, ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 all produced a higher level of luminescence on high-salt medium, as previously described for PL-721, whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 all produced a higher level of luminescence on low-salt medium, a characteristic of P. leiognathi from leiognathid fish light organs. These results demonstrate that P. leiognathi contains two evolutionarily and phenotypically distinct clades, P. leiognathi subsp. leiognathi (strains ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1), and P. leiognathi subsp. mandapamensis (strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554).
URL: 15034641
Ref #: 68411
Author(s): Osorio,C.R.;Collins,M.D.;Romalde,J.L.;Toranzo,A.E.
Journal: Appl Environ Microbiol
Title: Variation in 16S-23S rRNA intergenic spacer regions in Photobacterium damselae: a mosaic-like structure
Volume: 71
Page(s): 636-45
Year: 2005
Keyword(s): GENBANK/AJ274375 GENBANK/AJ274376 GENBANK/AJ274377 GENBANK/AJ274378 GENBANK/AJ535842 GENBANK/AJ535843 GENBANK/AJ535844 GENBANK/AJ535845 GENBANK/AJ535846 GENBANK/AJ535847 GENBANK/AJ535848 GENBANK/AJ535849 GENBANK/AJ535850 GENBANK/AJ535851 GENBANK/AJ535852 GENBANK/AJ535853 GENBANK/AJ535854 Base Sequence DNA, Bacterial/analysis DNA, Ribosomal Spacer/*analysis/genetics Molecular Sequence Data Photobacterium/*classification/genetics RNA, Ribosomal, 16S/*genetics RNA, Ribosomal, 23S/*genetics RNA, Transfer/genetics Sequence Alignment Sequence Analysis, DNA Species Specificity *Variation (Genetics) rRNA Operon
Remarks: Phenotypically, Photobacterium damselae subsp. piscicida and P. damselae subsp. damselae are easily distinguished. However, their 16S rRNA gene sequences are identical, and attempts to discriminate these two subspecies by molecular tools are hampered by their high level of DNA-DNA similarity. The 16S-23S rRNA internal transcribed spacers (ITS) were sequenced in two strains of Photobacterium damselae subsp. piscicida and two strains of P. damselae subsp. damselae to determine the level of molecular diversity in this DNA region. A total of 17 different ITS variants, ranging from 803 to 296 bp were found, some of which were subspecies or strain specific. The largest ITS contained four tRNA genes (tDNAs) coding for tRNA(Glu(UUC)), tRNA(Lys(UUU)), tRNA(Val(UAC)), and tRNA(Ala(GGC)). Five amplicons contained tRNA(Glu(UUC)) combined with two additional tRNA genes, including tRNA(Lys(UUU)), tRNA(Val(UAC)), or tRNA(Ala(UGC)). Five amplicons contained tRNA(Ile(GAU)) and tRNA(Ala(UGC)). Two amplicons contained tRNA(Glu(UUC)) and tRNA(Ala(UGC)). Two different isoacceptor tRNA(Ala) genes (GGC and UGC anticodons) were found. The five smallest amplicons contained no tRNA genes. The tRNA-gene combinations tRNA(Glu(UUC))-tRNA(Val(UAC))-tRNA(Ala(UGC)) and tRNA(Glu(UUC))-tRNA(Ala(UGC)) have not been previously reported in bacterial ITS regions. The number of copies of the ribosomal operon (rrn) in the P. damselae chromosome ranged from at least 9 to 12. For ITS variants coexisting in two strains of different subspecies or in strains of the same subspecies, nucleotide substitution percentages ranged from 0 to 2%. The main source of variation between ITS variants was due to different combinations of DNA sequence blocks, constituting a mosaic-like structure.
URL: 15691912
Ref #: 12044
Author(s): Ruimy,R.;Breittmayer,V.;Elbaze,P.;Lafay,B.;Boussemart,O.;Gauthier,M.;Christen,R.
Journal: Int J Syst Bacteriol
Title: Phylogenetic analysis and assessment of the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas deduced from small-subunit rRNA sequences
Volume: 44
Page(s): 416-26
Year: 1994
Keyword(s): GENBANK/X74674 GENBANK/X74675 GENBANK/X74676 GENBANK/X74677 GENBANK/X74678 GENBANK/X74679 GENBANK/X74680 GENBANK/X74681 GENBANK/X74682 GENBANK/X74683 GENBANK/X74684 GENBANK/X74685 GENBANK/X74686 GENBANK/X74687 GENBANK/X74688 GENBANK/X74689 GENBANK/X74690 GENBANK/X74691 GENBANK/X74692 GENBANK/X74693 GENBANK/X74694 GENBANK/X74695 GENBANK/X74696 GENBANK/X74697 GENBANK/X74698 GENBANK/X74699 GENBANK/X74700 GENBANK/X74701 GENBANK/X74702 GENBANK/X74703 Aeromonas/classification/genetics Comparative Study Photobacterium/classification/genetics *Phylogeny Plesiomonas/classification/genetics RNA, Bacterial/*genetics RNA, Ribosomal/*genetics Sequence Homology, Nucleic Acid Species Specificity Support, Non-U.S. Gov't Vibrio/classification/genetics Vibrionaceae/*classification/*genetics
Remarks: We sequenced nearly complete small-subunit rRNAs of 54 reference strains belonging to the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas. We then performed a phylogenetic analysis by comparing the sequences which we obtained with all other known sequences for bacteria belonging to the gamma subgroup of the Proteobacteria (thus providing a data base consisting of 70 sequences for the genera investigated), using methods such as neighbor joining, maximum likelihood, and maximum parsimony, as well as bootstrap, to assess the robustness of each topology. Our results confirmed that the family Vibrionaceae should include only Photobacterium and Vibrio species (but not Vibrio marinus); that Aeromonas species deserve family rank; and that Plesiomonas shigelloides is linked to the family Enterobacteriaceae. The genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas, together with the family Enterobacteriaceae, the family Pasteurellaceae, and probably the genus Alteromonas, form a robust monophyletic unit within the gamma 3 subgroup of the Proteobacteria.
URL: 94347604
Data: (ATCC 33539) Type strain / J. V. Lee, CAMR, Porton Down / Skin lesion on damsel fish / Love, M. D. et al. (1981) Science, 214, 1139 / Validation List No. 8 (1982) Int. J. syst. Bact. 32, 266 / Smith, S. K. et al. (1991) Int. J. syst. Bact. 41, 529
Accession Date: 01/01/1984
Authority: (Love et al. 1982) Smith et al. 1991
Depositor: LEE J V
Taxonomy: TaxLink: S4969 (Photobacterium damselae (love et al. 1982) smith et al. 1991) - Date of change: 16/06/2007 by NCTCUp to 16/06/2007: ? (NCTC 11647) - Date of change: 04/02/2003
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