| Extended Bibliography: |
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 |
|
|
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