| Extended Bibliography: |
Show bibliography
| Ref #: |
95537 |
| Author(s): |
East,A.K.;Collins,M.D. |
| Journal: |
FEMS Microbiol Lett |
| Title: |
Molecular characterization of DNA encoding 23S rRNA and 16S-23S rRNA intergenic spacer regions of Aeromonas hydrophila |
| Volume: |
106 |
| Page(s): |
129-33 |
| Year: |
1993 |
| Keyword(s): |
GENBANK/X67946
Aeromonas hydrophila/*genetics
Base Sequence
DNA, Bacterial/*chemistry
DNA, Ribosomal/*chemistry
Molecular Sequence Data
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/*genetics
RNA, Ribosomal, 23S/*genetics
|
| Remarks: |
Amplification of the gene encoding 23S rRNA of Aeromonas hydrophila by polymerase chain reaction, with primers complementary to conserved regions of 16S and the 3'-end of 23S rRNA genes, resulted in a DNA fragment of approximately 3 kb. This fragment was cloned in Escherichia coli, and its nucleotide sequence determined. The region encoding 23S rRNA shows high homology with the published sequences of 23S rRNA from other members of the gamma division of Proteobacteria. The sequence of the intergenic spacer region, between the 16S and 23S rRNA genes, was determined in five clones. Three types of spacer were identified: two clones were identical and encoded tRNA(Ile) and tRNA(Ala) while the remaining three clones contained tRNA(Glu), only two had the same spacer sequences. This variation in sequence indicates that the different clones may be derived from different ribosomal RNA operons. |
| URL: |
7681020 |
|
| Ref #: |
95513 |
| Author(s): |
Sipos,R.;Szekely,A.J.;Palatinszky,M.;Revesz,S.;Marialigeti,K.;Nikolausz,M. |
| Journal: |
FEMS Microbiol Ecol |
| Title: |
Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis |
| Volume: |
60 |
| Page(s): |
341-50 |
| Year: |
2007 |
| Remarks: |
In the attempt to explore complex bacterial communities of environmental samples, primers hybridizing to phylogenetically highly conserved regions of 16S rRNA genes are widely used, but differential amplification is a recognized problem. The biases associated with preferential amplification of multitemplate PCR were investigated using 'universal' bacteria-specific primers, focusing on the effect of primer mismatch, annealing temperature and PCR cycle number. The distortion of the template-to-product ratio was measured using predefined template mixtures and environmental samples by terminal restriction fragment length polymorphism analysis. When a 1 : 1 genomic DNA template mixture of two strains was used, primer mismatches inherent in the 63F primer presented a serious bias, showing preferential amplification of the template containing the perfectly matching sequence. The extent of the preferential amplification showed an almost exponential relation with increasing annealing temperature from 47 to 61 degrees C. No negative effect of the various annealing temperatures was observed with the 27F primer, with no mismatches with the target sequences. The number of PCR cycles had little influence on the template-to-product ratios. As a result of additional tests on environmental samples, the use of a low annealing temperature is recommended in order to significantly reduce preferential amplification while maintaining the specificity of PCR. |
| URL: |
17343679 |
|
| Ref #: |
17468 |
| Author(s): |
Pidiyar,V.J.;Jangid,K.;Dayananda,K.M.;Kaznowski,A.;Gonzalez,J.M.;Patole,M.S.;Shouche,Y.S. |
| Journal: |
Syst Appl Microbiol |
| Title: |
Phylogenetic affiliation of Aeromonas culicicola MTCC 3249(T) based on gyrB gene sequence and PCR-amplicon sequence analysis of cytolytic enterotoxin gene |
| Volume: |
26 |
| Page(s): |
197-202 |
| Year: |
2003 |
| Keyword(s): |
Aeromonas/*classification/genetics
Bacterial Proteins/*genetics
Bacterial Typing Techniques
DNA Gyrase/*genetics
DNA, Bacterial/genetics
Enterotoxins/*genetics
*Genes, Bacterial
Nucleic Acid Amplification Techniques
Nucleic Acid Hybridization
Phylogeny
Polymerase Chain Reaction
Ribotyping
Sequence Homology, Nucleic Acid
Species Specificity
|
| Remarks: |
We determined the gyrB gene sequences of all 17 hybridizations groups of Aeromonas. Phylogenetic trees showing the evolutionary relatedness of gyrB and 16S rRNA genes in the type strains of Aeromonas were compared. Using this approach, we determined the phylogenetic position of Aeromonas culicicola MTCC 3249(T), isolated from midgut of Culex quinquefasciatus. In the gyrB based-analysis A. culicicola MTCC 3249(T) grouped with A. veronii whereas, it grouped with A. jandaei in the 16S rRNA based tree. The number of nucleotide differences in 16S rRNA sequences was less than found with the gyrB sequence data. Most of the observed nucleotide differences in the gyrB gene were synonymous. The Cophenetic Correlation Coefficient (CCC) for gyrB sequences was 0.87 indicating this gene to be a better molecular chronometer compared to 16S rRNA for delineation of Aeromonas species. This strain was found to be positive for the cytolytic enterotoxin gene. PCR-Amplicon Sequence Analysis (PCR-ASA) of this gene showed that the isolate is affiliated to type I and is potentially pathogenic. These PCR-ASA results agreed in part with the gyrB sequence results. |
| URL: |
12866846 |
|
| Ref #: |
95484 |
| Author(s): |
Martinez-Murcia,A.J.;Benlloch,S.;Collins,M.D. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridizations |
| Volume: |
42 |
| Page(s): |
412-21 |
| Year: |
1992 |
| Keyword(s): |
GENBANK/M34114
GENBANK/X07652
GENBANK/X07714
GENBANK/X13695
GENBANK/X16895
GENBANK/X60404
GENBANK/X60405
GENBANK/X60406
GENBANK/X60407
GENBANK/X60408
GENBANK/X60409
GENBANK/X60410
GENBANK/X60411
GENBANK/X60412
GENBANK/X60413
GENBANK/X60414
GENBANK/X60415
GENBANK/X60416
GENBANK/X60417
GENBANK/X60418
Aeromonas/*classification/genetics
Base Sequence
DNA, Bacterial/*chemistry/isolation & purification
DNA, Ribosomal/*chemistry/isolation & purification
Molecular Sequence Data
Nucleic Acid Hybridization
*Phylogeny
Plesiomonas/*classification/genetics
Polymerase Chain Reaction
RNA, Bacterial/chemistry/genetics
RNA, Ribosomal, 16S/chemistry/*genetics
Sequence Homology, Nucleic Acid
|
| Remarks: |
The phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas were investigated by using small-subunit ribosomal DNA (rDNA) sequencing. Members of the genus Aeromonas formed a distinct line within the gamma subclass of the Proteobacteria. Plesiomonas shigelloides also clustered within the confines of the gamma subclass of the Proteobacteria but exhibited a closer association with members of the family Enterobacteriaceae than with members of the family Aeromonadaceae. Species of the genus Aeromonas exhibited very high levels of overall sequence similarity (ca. 98 to 100%) with each other. Several of the relationships derived from an analysis of the rDNA sequence data were in marked disagreement with the results of chromosomal DNA-DNA pairing experiments. Diagnostic rDNA signatures that have possible value for differentiating most Aeromonas species were discerned. |
| URL: |
1380289 |
|
| Ref #: |
95480 |
| Author(s): |
Oakey,H.J.;Levy,N.;Bourne,D.G.;Cullen,B.;Thomas,A. |
| Journal: |
J Appl Microbiol |
| Title: |
The use of PCR to aid in the rapid identification of Vibrio harveyi isolates |
| Volume: |
95 |
| Page(s): |
1293-303 |
| Year: |
2003 |
| Keyword(s): |
Animals
Bacterial Typing Techniques/*methods
Base Sequence
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
Molecular Sequence Data
Polymerase Chain Reaction/methods
RNA, Ribosomal, 16S/genetics
Reproducibility of Results
Sensitivity and Specificity
Vibrio/*classification/genetics/isolation & purification
Vibrio Infections/*diagnosis/veterinary
*Water Microbiology
|
| Remarks: |
AIMS: Vibrio harveyi is an important pathogen, causing potential devastation to marine aquaculture. This organism, however, is extremely difficult to identify because it is phenotypically diverse. Biochemical identification can involve many tests and take weeks to perform. The aim of this work is to develop a PCR that can reduce the number of biochemical tests, and the time taken, to get a definitive identification of this organism. METHODS AND RESULTS: The PCR was developed using 16S rDNA sequences from a number of V. harveyi strains, and other vibrios. The described test gave positive results for all strains of V. harveyi tested. However, some strains of V. alginolyticus also gave positive results and a small number of biochemical tests were required to differentiate between these two species. This indicated that preisolation of the bacteria was needed and therefore the test was not applicable to the testing of mixed populations directly. CONCLUSION, SIGNIFICANCE AND IMPACT OF THE STUDY: The duration of identification of this species was significantly reduced from a number of weeks to a few days. Hence, diagnosis of affected animals will be faster and earlier treatment can be administered which may increase the survival rate from vibriosis. |
| URL: |
14633004 |
|
| Ref #: |
95437 |
| Author(s): |
Kupfer,M.;Kuhnert,P.;Korczak,B.M.;Peduzzi,R.;Demarta,A. |
| Journal: |
Int J Syst Evol Microbiol |
| Title: |
Genetic relationships of Aeromonas strains inferred from 16S rRNA, gyrB and rpoB gene sequences |
| Volume: |
56 |
| Page(s): |
2743-51 |
| Year: |
2006 |
| Keyword(s): |
GENBANK/AF417626
GENBANK/AF417627
GENBANK/AF417631
GENBANK/AF417632
GENBANK/AJ868362
GENBANK/AJ868363
GENBANK/AJ868364
GENBANK/AJ868365
GENBANK/AJ868366
GENBANK/AJ868367
GENBANK/AJ868368
GENBANK/AJ868369
GENBANK/AJ868370
GENBANK/AJ868371
GENBANK/AJ868372
GENBANK/AJ868373
GENBANK/AJ868374
GENBANK/AJ868375
GENBANK/AJ868376
GENBANK/AJ868377
GENBANK/AJ868378
GENBANK/AJ868379
GENBANK/AJ868380
GENBANK/AJ868381
GENBANK/AJ868382
GENBANK/AJ868383
GENBANK/AJ868384
GENBANK/AJ868385
GENBANK/AJ868386
GENBANK/AJ868387
GENBANK/AJ868388
GENBANK/AJ868389
GENBANK/AJ868390
GENBANK/AJ868391
GENBANK/AJ868392
GENBANK/AJ868393
GENBANK/AJ868394
GENBANK/AJ868395
GENBANK/AJ868396
GENBANK/AJ868397
GENBANK/AJ868398
GENBANK/AJ868399
GENBANK/AJ868400
GENBANK/AJ868401
GENBANK/AJ868402
GENBANK/AJ964951
GENBANK/AM179827
GENBANK/AM262158
GENBANK/AM262159
GENBANK/AM262160
GENBANK/AM262161
GENBANK/AM262162
GENBANK/AM262163
GENBANK/AM262164
GENBANK/AY294485
GENBANK/AY851091
GENBANK/AY851092
GENBANK/AY851093
GENBANK/AY851094
GENBANK/AY851095
GENBANK/AY851096
GENBANK/AY851097
GENBANK/AY851098
GENBANK/AY851099
GENBANK/AY851100
GENBANK/AY851101
GENBANK/AY851102
GENBANK/AY851103
GENBANK/AY851104
GENBANK/AY851105
GENBANK/AY851106
GENBANK/AY851107
GENBANK/AY851108
GENBANK/AY851109
GENBANK/AY851110
GENBANK/AY851111
GENBANK/AY851112
GENBANK/AY851113
GENBANK/AY851114
GENBANK/AY851115
GENBANK/AY851116
GENBANK/AY851117
GENBANK/AY851118
GENBANK/AY851119
GENBANK/AY851120
GENBANK/AY851121
GENBANK/AY851122
GENBANK/AY851123
GENBANK/AY851124
GENBANK/AY851125
GENBANK/AY851126
GENBANK/AY851127
GENBANK/AY851128
GENBANK/AY851129
GENBANK/AY851130
GENBANK/AY851131
GENBANK/AY851132
GENBANK/AY851133
GENBANK/AY851134
GENBANK/AY851135
GENBANK/AY851136
GENBANK/AY851137
GENBANK/AY851138
GENBANK/AY851139
GENBANK/AY851140
GENBANK/AY851141
GENBANK/AY851142
GENBANK/AY851143
GENBANK/DQ448280
GENBANK/DQ448285
GENBANK/DQ448286
GENBANK/DQ448287
GENBANK/DQ448288
GENBANK/DQ448289
GENBANK/DQ448290
GENBANK/DQ448291
Aeromonas/*classification/enzymology/*genetics
Animals
*Bacterial Typing Techniques
Cattle
Child
DNA Gyrase/*genetics
DNA, Bacterial/analysis/isolation & purification
DNA, Ribosomal/analysis
DNA-Directed RNA Polymerases/*genetics
Genes, Bacterial
Humans
Molecular Sequence Data
Phylogeny
RNA, Ribosomal, 16S/*genetics
Sequence Analysis, DNA
Species Specificity
|
| Remarks: |
Genetic relationships among bacterial strains belonging to the genus Aeromonas were inferred from 16S rRNA, gyrB and rpoB gene sequences. Twenty-eight type or collection strains of the recognized species or subspecies and 33 Aeromonas strains isolated from human and animal specimens as well as from environmental samples were included in the study. As reported previously, the 16S rRNA gene sequence is highly conserved within the genus Aeromonas, having only limited resolution for this very tight group of species. Analysis of a 1.1 kb gyrB sequence confirmed that this gene has high resolving power, with maximal interspecies divergence of 15.2 %. Similar results were obtained by sequencing only 517 bp of the rpoB gene, which showed maximal interspecies divergence of 13 %. The topologies of the gyrB- and rpoB-derived trees were similar. The results confirm the close relationship of species within the genus Aeromonas and show that a phylogenetic approach including several genes is suitable for improving the complicated taxonomy of the genus. |
| URL: |
17158971 |
|
| Ref #: |
13731 |
| Author(s): |
East,A.K.;Collins,M.D. |
| Journal: |
FEMS Microbiol Lett |
| Title: |
Molecular characterization of DNA encoding 23S rRNA and 16S-23S rRNA intergenic spacer regions of Aeromonas hydrophila |
| Volume: |
106 |
| Page(s): |
129-33 |
| Year: |
1993 |
| Keyword(s): |
GENBANK/X67946
Aeromonas hydrophila/*genetics
Base Sequence
DNA, Bacterial/*chemistry
DNA, Ribosomal/*chemistry
Molecular Sequence Data
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/*genetics
RNA, Ribosomal, 23S/*genetics
Support, Non-U.S. Gov't
|
| Remarks: |
Amplification of the gene encoding 23S rRNA of Aeromonas hydrophila by polymerase chain reaction, with primers complementary to conserved regions of 16S and the 3'-end of 23S rRNA genes, resulted in a DNA fragment of approximately 3 kb. This fragment was cloned in Escherichia coli, and its nucleotide sequence determined. The region encoding 23S rRNA shows high homology with the published sequences of 23S rRNA from other members of the gamma division of Proteobacteria. The sequence of the intergenic spacer region, between the 16S and 23S rRNA genes, was determined in five clones. Three types of spacer were identified: two clones were identical and encoded tRNA(Ile) and tRNA(Ala) while the remaining three clones contained tRNA(Glu), only two had the same spacer sequences. This variation in sequence indicates that the different clones may be derived from different ribosomal RNA operons. |
| URL: |
93202430 |
|
| 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 #: |
12041 |
| Author(s): |
Martinez-Murcia,A.J.;Benlloch,S.;Collins,M.D. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridizations |
| Volume: |
42 |
| Page(s): |
412-21 |
| Year: |
1992 |
| Keyword(s): |
GENBANK/M34114
GENBANK/X07652
GENBANK/X07714
GENBANK/X13695
GENBANK/X16895
GENBANK/X60404
GENBANK/X60405
GENBANK/X60406
GENBANK/X60407
GENBANK/X60408
GENBANK/X60409
GENBANK/X60410
GENBANK/X60411
GENBANK/X60412
GENBANK/X60413
GENBANK/X60414
GENBANK/X60415
GENBANK/X60416
GENBANK/X60417
GENBANK/X60418
Aeromonas/*classification/genetics
Base Sequence
DNA, Bacterial/*chemistry/isolation & purification
DNA, Ribosomal/*chemistry/isolation & purification
Molecular Sequence Data
Nucleic Acid Hybridization
*Phylogeny
Plesiomonas/*classification/genetics
Polymerase Chain Reaction
RNA, Bacterial/chemistry/genetics
RNA, Ribosomal, 16S/chemistry/*genetics
Sequence Homology, Nucleic Acid
Support, Non-U.S. Gov't
|
| Remarks: |
The phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas were investigated by using small-subunit ribosomal DNA (rDNA) sequencing. Members of the genus Aeromonas formed a distinct line within the gamma subclass of the Proteobacteria. Plesiomonas shigelloides also clustered within the confines of the gamma subclass of the Proteobacteria but exhibited a closer association with members of the family Enterobacteriaceae than with members of the family Aeromonadaceae. Species of the genus Aeromonas exhibited very high levels of overall sequence similarity (ca. 98 to 100%) with each other. Several of the relationships derived from an analysis of the rDNA sequence data were in marked disagreement with the results of chromosomal DNA-DNA pairing experiments. Diagnostic rDNA signatures that have possible value for differentiating most Aeromonas species were discerned. |
| URL: |
92368941 |
|
| Ref #: |
1300 |
| Author(s): |
Skerman,V.B.D.;McGowan,V.;Sneath,P.H.A.(ed) |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Approved Lists of Bacterial Names. |
| Volume: |
30 |
| Page(s): |
225-420 |
| Year: |
1980 |
|
| Ref #: |
4601 |
| Author(s): |
Kämpfer,P.;Altwegg,M. |
| Journal: |
J. Appl. Bacteriol. |
| Title: |
Numerical classification and identification of Aeromonas genospecies. |
| Volume: |
72 |
| Page(s): |
341-351 |
| Year: |
1992 |
|
| Ref #: |
825 |
| Author(s): |
Schubert,R.H.W. |
| Journal: |
Zentralbl. Bakteriol. Parasitenkd. Orig. Abt. I |
| Title: |
Zur Taxonomie der Voges-Proskauer negativen "hydrophila-ähnlichen" Aeromonaden. |
| Volume: |
193 |
| Page(s): |
482-490 |
| Year: |
1964 |
|
| Ref #: |
826 |
| Author(s): |
Schubert,R.H.W. |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
The taxomomy and nomenclature of the genus Aeromonas Kluyver and van Niel 1936. Part I. Suggestions on the taxonomy and nomenclature of the aerogenic Aeromonas species. |
| Volume: |
17 |
| Page(s): |
23-37 |
| Year: |
1967 |
|
|
Product Documents
Print datasheet