Extended Bibliography: |
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Ref #: |
93196 |
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
Photobacterium/classification/genetics
*Phylogeny
Plesiomonas/classification/genetics
RNA, Bacterial/*genetics
RNA, Ribosomal/*genetics
Sequence Homology, Nucleic Acid
Species Specificity
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: |
7520733 |
|
Ref #: |
95519 |
Author(s): |
Venkateswaran,K.;Dohmoto,N.;Harayama,S. |
Journal: |
Appl Environ Microbiol |
Title: |
Cloning and nucleotide sequence of the gyrB gene of Vibrio parahaemolyticus and its application in detection of this pathogen in shrimp |
Volume: |
64 |
Page(s): |
681-7 |
Year: |
1998 |
Keyword(s): |
GENBANK/AF007287
GENBANK/AF007288
GENBANK/AF007289
GENBANK/AF007290
GENBANK/AF007291
GENBANK/AF007292
GENBANK/AF007293
Amino Acid Sequence
Animals
Base Sequence
Cloning, Molecular
DNA Gyrase
DNA Topoisomerases, Type II/*genetics
Decapoda (Crustacea)/*microbiology
Molecular Sequence Data
Polymerase Chain Reaction
Sensitivity and Specificity
Vibrio parahaemolyticus/*genetics/*isolation & purification
|
Remarks: |
Because biochemical testing and 16S rRNA sequence analysis have proven inadequate for the differentiation of Vibrio parahaemolyticus from closely related species, we employed the gyrase B gene (gyrB) as a molecular diagnostic probe. The gyrB genes of V. parahaemolyticus and closely related Vibrio alginolyticus were cloned and sequenced. Oligonucleotide PCR primers were designed for the amplification of a 285-bp fragment from within gyrB specific for V. parahaemolyticus. These primers recognized 117 of 117 reference and wild-type V. parahaemolyticus strains, whereas amplification did not occur when 90 strains of 37 other Vibrio species or 60 strains representing 34 different nonvibrio species were tested. In 100-microliter PCR mixtures, the lower detection limits were 5 CFU for live cells and 4 pg for purified DNA. The possible application of gyrB primers for the routine identification of V. parahaemolyticus in food was examined. We developed and tested a procedure for the specific detection of the target organism in shrimp consisting of an 18-h preenrichment followed by PCR amplification of the 285-bp V. parahaemolyticus-specific fragment. This method enabled us to detect an initial inoculum of 1.5 CFU of V. parahaemolyticus cells per g of shrimp homogenate. By this approach, we were able to detect V. parahaemolyticus in all of 27 shrimp samples artificially inoculated with this bacterium. We present here a rapid, reliable, and sensitive protocol for the detection of V. parahaemolyticus in shrimp. |
URL: |
9464408 |
|
Ref #: |
27372 |
Author(s): |
Dorsch,M.;Lane,D.;Stackebrandt,E. |
Journal: |
Int J Syst Bacteriol |
Title: |
Towards a phylogeny of the genus Vibrio based on 16S rRNA sequences |
Volume: |
42 |
Page(s): |
58-63 |
Year: |
1992 |
Keyword(s): |
GENBANK/L05178
GENBANK/X54744
GENBANK/X54745
GENBANK/X56575
GENBANK/X56576
GENBANK/X56577
GENBANK/X56578
GENBANK/X56579
GENBANK/X56580
GENBANK/X56581
GENBANK/X56582
GENBANK/X56583
Base Sequence
Molecular Sequence Data
Phylogeny
RNA Probes
RNA, Bacterial/*chemistry
RNA, Ribosomal, 16S/*chemistry
Vibrio/*classification/genetics/isolation & purification
|
Remarks: |
The inter- and intrageneric relationships of the genus Vibrio were investigated by performing a comparative analysis of the 16S rRNAs of 10 species, including four pathogenic representatives. The results of immunological and 5S rRNA studies were confirmed in that the genus is a neighboring taxon of the family Enterobacteriaceae. With regard to the intrageneric structure, Vibrio alginolyticus, Vibrio campbellii, Vibrio natriegens, Vibrio harveyi, Vibrio proteolyticus, Vibrio parahaemolyticus, and Vibrio vulnificus form the core of the genus, while Vibrio (Listonella) anguillarum, Vibrio diazotrophicus, and Vibrio hollisae are placed on the outskirts of the genus. Variable regions around positions 80, 180, and 450 could be used as target sites for genus- and species-specific oligonucleotide probes and polymerase chain reaction primers to be used in molecular identification. |
URL: |
1371064 |
|
Ref #: |
95445 |
Author(s): |
Eiler,A.;Bertilsson,S. |
Journal: |
J Microbiol Methods |
Title: |
Detection and quantification of Vibrio populations using denaturant gradient gel electrophoresis |
Volume: |
67 |
Page(s): |
339-48 |
Year: |
2006 |
Keyword(s): |
DNA, Bacterial/chemistry/genetics
Electrophoresis, Polyacrylamide Gel/*methods
Formamides/chemistry
Oceans and Seas
Organic Chemicals/chemistry
Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal, 16S/chemistry/genetics
Sequence Analysis, DNA
Sweden
Urea/chemistry
Vibrio/genetics/*isolation & purification
*Water Microbiology
|
Remarks: |
Bacteria affiliated with the genus Vibrio are endemic in marine and estuarine ecosystems and are also found in many freshwater environments. Vibrios can enter viable but non-culturable states and since many species are pathogenic, there is a great need for culture-independent methods that identify and quantify multiple Vibrio populations. We adopted Vibrio-specific 16S rRNA-directed primers and a competitive PCR protocol (QC-PCR; [Thompson, J.R., Randa, M.A., Marcelino, L.A., Tomita-Mitchell, A., Lim, E., Polz, M.F., 2004b. Diversity and dynamics of a North Atlantic coastal Vibrio community. Appl. Environ. Microbiol. 70, 4103-4110]) for separation and quantification of Vibrio populations using denaturant gradient gel electrophoresis (DGGE). Sixteen Vibrio isolates and eight environmental samples were used to assess the precision and resolution of the method. A 45-70% gradient of Urea and formamide enabled separation of Vibrio populations with single nucleotide differences in the amplified fragment. A titration curve for the QC-PCR-DGGE, verified by amending surface water bacterioplankton samples with up to 3 x 10(5)Vibrio cholerae cells, could be approximated by a linear regression of log-transformed values (R(2)=0.96). The limit of detection for single populations was 180 cells per extracted sample or about 4 cells per PCR reaction. Environmental samples from the southern Stockholm archipelago in the Baltic Sea and the more saline coastal waters of Skagerrak each carried between 2 and 6 Vibrio populations, and there were major differences between the locations. Notably, multiple Vibrio populations could be detected and quantified against a background of native bacterioplankton exceeding Vibrio population abundance by more than 6 orders of magnitude. Putative identification based on migration in the DGGE gel was verified by parallel cloning and sequencing of PCR products, and representative clones were also characterized by DGGE. This general approach could also be useful for targeting other phylogenetically constrained bacterial groups and assess their abundance and distribution in complex environmental settings. |
URL: |
16730823 |
|
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 |
|
Ref #: |
13615 |
Author(s): |
Dorsch,M.;Lane,D.;Stackebrandt,E. |
Journal: |
Int J Syst Bacteriol |
Title: |
Towards a phylogeny of the genus Vibrio based on 16S rRNA sequences |
Volume: |
42 |
Page(s): |
58-63 |
Year: |
1992 |
Keyword(s): |
GENBANK/L05178
GENBANK/X54744
GENBANK/X54745
GENBANK/X56575
GENBANK/X56576
GENBANK/X56577
GENBANK/X56578
GENBANK/X56579
GENBANK/X56580
GENBANK/X56581
GENBANK/X56582
GENBANK/X56583
Base Sequence
Molecular Sequence Data
Phylogeny
RNA Probes
RNA, Bacterial/*chemistry
RNA, Ribosomal, 16S/*chemistry
Support, Non-U.S. Gov't
Vibrio/*classification/genetics/isolation & purification
|
Remarks: |
The inter- and intrageneric relationships of the genus Vibrio were investigated by performing a comparative analysis of the 16S rRNAs of 10 species, including four pathogenic representatives. The results of immunological and 5S rRNA studies were confirmed in that the genus is a neighboring taxon of the family Enterobacteriaceae. With regard to the intrageneric structure, Vibrio alginolyticus, Vibrio campbellii, Vibrio natriegens, Vibrio harveyi, Vibrio proteolyticus, Vibrio parahaemolyticus, and Vibrio vulnificus form the core of the genus, while Vibrio (Listonella) anguillarum, Vibrio diazotrophicus, and Vibrio hollisae are placed on the outskirts of the genus. Variable regions around positions 80, 180, and 450 could be used as target sites for genus- and species-specific oligonucleotide probes and polymerase chain reaction primers to be used in molecular identification. |
URL: |
92144377 |
|
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