| Extended Bibliography: |
Show bibliography
| Ref #: |
95492 |
| Author(s): |
Fukushima,M.;Kakinuma,K.;Kawaguchi,R. |
| Journal: |
J Clin Microbiol |
| Title: |
Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence |
| Volume: |
40 |
| Page(s): |
2779-85 |
| Year: |
2002 |
| Keyword(s): |
DNA Gyrase/*genetics
DNA, Bacterial/analysis
DNA, Ribosomal/analysis
Escherichia coli/classification/*genetics
Humans
Molecular Sequence Data
*Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal, 16S/genetics
Salmonella/classification/*genetics
Shigella/classification/*genetics
|
| Remarks: |
Phylogenetic analysis of about 200 strains of Salmonella, Shigella, and Escherichia coli was carried out using the nucleotide sequence of the gene for DNA gyrase B (gyrB), which was determined by directly sequencing PCR fragments. The results establish a new phylogenetic tree for the classification of Salmonella, Shigella, and Escherichia coli in which Salmonella forms a cluster separate from but closely related to Shigella and E. coli. In comparison with 16S rRNA analysis, the gyrB sequences indicated a greater evolutionary divergence for the bacteria. Thus, in screening for the presence of bacteria, the gyrB gene might be a useful tool for differentiating between closely related species of bacteria such as Shigella spp. and E. coli. At present, 16S rRNA sequence analysis is an accurate and rapid method for identifying most unknown bacteria to the genus level because the highly conserved 16S rRNA region is easy to amplify; however, analysis of the more variable gyrB sequence region can identify unknown bacteria to the species level. In summary, we have shown that gyrB sequence analysis is a useful alternative to 16S rRNA analysis for constructing the phylogenetic relationships of bacteria, in particular for the classification of closely related bacterial species. |
| URL: |
12149329 |
|
| Ref #: |
95485 |
| Author(s): |
Fuchs,B.M.;Syutsubo,K.;Ludwig,W.;Amann,R. |
| Journal: |
Appl Environ Microbiol |
| Title: |
In situ accessibility of Escherichia coli 23S rRNA to fluorescently labeled oligonucleotide probes |
| Volume: |
67 |
| Page(s): |
961-8 |
| Year: |
2001 |
| Keyword(s): |
Escherichia coli/*genetics/growth & development
Flow Cytometry
*Fluorescent Dyes
In Situ Hybridization, Fluorescence/methods
Oligonucleotide Probes/*genetics
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 23S/*genetics
|
| Remarks: |
One of the main causes of failure of fluorescence in situ hybridization with rRNA-targeted oligonucleotides, besides low cellular ribosome content and impermeability of cell walls, is the inaccessibility of probe target sites due to higher-order structure of the ribosome. Analogous to a study on the 16S rRNA (B. M. Fuchs, G. Wallner, W. Beisker, I. Schwippl, W. Ludwig, and R. Amann, Appl. Environ. Microbiol. 64:4973-4982, 1998), the accessibility of the 23S rRNA of Escherichia coli DSM 30083(T) was studied in detail with a set of 184 CY3-labeled oligonucleotide probes. The probe-conferred fluorescence was quantified flow cytometrically. The brightest signal resulted from probe 23S-2018, complementary to positions 2018 to 2035. The distribution of probe-conferred cell fluorescence in six arbitrarily set brightness classes (classes I to VI, 100 to 81%, 80 to 61%, 60 to 41%, 40 to 21%, 20 to 6%, and 5 to 0% of the brightness of 23S-2018, respectively) was as follows: class I, 3%; class II, 21%; class III, 35%; class IV, 18%; class V, 16%; and class VI, 7%. A fine-resolution analysis of selected areas confirmed steep changes in accessibility on the 23S RNA to oligonucleotide probes. This is similar to the situation for the 16S rRNA. Indeed, no significant differences were found between the hybridization of oligonucleotide probes to 16S and 23S rRNA. Interestingly, indications were obtained of an effect of the type of fluorescent dye coupled to a probe on in situ accessibility. The results were translated into an accessibility map for the 23S rRNA of E. coli, which may be extrapolated to other bacteria. Thereby, it may contribute to a better exploitation of the high potential of the 23S rRNA for identification of bacteria in the future. |
| URL: |
11157269 |
|
| Ref #: |
95479 |
| Author(s): |
Mitterer,G.;Huber,M.;Leidinger,E.;Kirisits,C.;Lubitz,W.;Mueller,M.W.;Schmidt,W.M. |
| Journal: |
J Clin Microbiol |
| Title: |
Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences |
| Volume: |
42 |
| Page(s): |
1048-57 |
| Year: |
2004 |
| Keyword(s): |
Abortion, Veterinary/microbiology
Animals
Bacteria/*genetics/*isolation & purification
Base Sequence
DNA Primers
DNA, Bacterial/genetics/isolation & purification
DNA, Ribosomal/*genetics/isolation & purification
Female
Horses
*Oligonucleotide Array Sequence Analysis
Polymerase Chain Reaction/*methods
Pregnancy
Pregnancy Complications, Infectious/microbiology/veterinary
RNA, Bacterial/genetics/isolation & purification
RNA, Ribosomal, 23S/*genetics/isolation & purification
|
| Remarks: |
The rapid identification of the bacteria in clinical samples is important for patient management and antimicrobial therapy. We describe a DNA microarray-based PCR approach for the quick detection and identification of bacteria from cervical swab specimens from mares. This on-chip PCR method combines the amplification of a variable region of bacterial 23S ribosomal DNA and the simultaneous sequence-specific detection on a solid phase. The solid phase contains bacterial species-specific primers covalently bound to a glass support. During the solid-phase amplification reaction the polymerase elongates perfectly matched primers and incorporates biotin-labeled nucleotides. The reaction products are visualized by streptavidin-cyanine 5 staining, followed by fluorescence scanning. This procedure successfully identified from pure cultures 22 bacteria that are common causes of abortion and sterility in mares. Using the on-chip PCR method, we also tested 21 cervical swab specimens from mares for the presence of pathogenic bacteria and compared the results with those of conventional bacteriological culture methods. Our method correctly identified the bacteria in 12 cervical swab samples, 8 of which contained more than one bacterial species. Due to the higher sensitivity of the on-chip PCR, this method identified bacteria in five cervical swab samples which were not detected by the conventional identification procedure. Our results show that this method will have great potential to be incorporated into the routine microbiology laboratory. |
| URL: |
15004052 |
|
| Ref #: |
12690 |
| Author(s): |
Cilia,V.;Lafay,B.;Christen,R. |
| Journal: |
Mol Biol Evol |
| Title: |
Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level |
| Volume: |
13 |
| Page(s): |
451-61 |
| Year: |
1996 |
| Keyword(s): |
GENBANK/X80675
GENBANK/X80676
GENBANK/X80677
GENBANK/X80678
GENBANK/X80679
GENBANK/X80680
GENBANK/X80681
GENBANK/X80682
GENBANK/X80683
GENBANK/X80684
GENBANK/X80721
GENBANK/X80722
GENBANK/X80723
GENBANK/X80724
GENBANK/X80725
GENBANK/X80726
GENBANK/X80727
GENBANK/X80728
GENBANK/X80729
GENBANK/X80730
GENBANK/X80731
GENBANK/X80732
GENBANK/X80733
GENBANK/X80734
Bacteria/classification/*genetics
Base Sequence
Comparative Study
DNA, Bacterial/chemistry
Escherichia coli/classification/genetics
Molecular Sequence Data
Operon
*Phylogeny
Polymerase Chain Reaction
RNA, Bacterial/chemistry/genetics
RNA, Ribosomal, 16S/chemistry/*genetics
Salmonella/classification/genetics
Sequence Homology, Nucleic Acid
Shigella/classification/genetics
Support, Non-U.S. Gov't
|
| Remarks: |
We have analyzed what phylogenetic signal can be derived by small subunit rRNA comparison for bacteria of different but closely related genera (enterobacteria) and for different species or strains within a single genus (Escherichia or Salmonella), and finally how similar are the ribosomal operons within a single organism (Escherichia coli). These sequences have been analyzed by neighbor-joining, maximum likelihood, and parsimony. The robustness of each topology was assessed by bootstrap. Sequences were obtained for the seven rrn operons of E. coli strain PK3. These data demonstrated differences located in three highly variable domains. Their nature and localization suggest that since the divergence of E. coli and Salmonella typhimurium, most point mutations that occurred within each gene have been propagated among the gene family by conversions involving short domains, and that homogenization by conversions may not have affected the entire sequence of each gene. We show that the differences that exist between the different operons are ignored when sequences are obtained either after cloning of a single operon or directly from polymerase chain reaction (PCR) products. Direct sequencing of PCR products produces a mean sequence in which mutations present in the most variable domains become hidden. Cloning a single operon results in a sequence that differs from that of the other operons and of the mean sequence by several point mutations. For identification of unknown bacteria at the species level or below, a mean sequence or the sequence of a single nonidentified operon should therefore be avoided. Taking into account the seven operons and therefore mutations that accumulate in the most variable domains would perhaps increase tree resolution. However, if gene conversions that homogenize the rRNA multigene family are rare events, some nodes in phylogenetic trees will reflect these recombination events and these trees may therefore be gene trees rather than organismal trees. |
| URL: |
96351315 |
|
| Ref #: |
12687 |
| Author(s): |
Fuchs,B.M.;Syutsubo,K.;Ludwig,W.;Amann,R. |
| Journal: |
Appl Environ Microbiol |
| Title: |
In situ accessibility of Escherichia coli 23S rRNA to fluorescently labeled oligonucleotide probes |
| Volume: |
67 |
| Page(s): |
961-8 |
| Year: |
2001 |
| Keyword(s): |
Escherichia coli/*genetics/growth & development
Flow Cytometry
*Fluorescent Dyes
In Situ Hybridization, Fluorescence/methods
Oligonucleotide Probes/*genetics
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 23S/*genetics
Support, Non-U.S. Gov't
|
| Remarks: |
One of the main causes of failure of fluorescence in situ hybridization with rRNA-targeted oligonucleotides, besides low cellular ribosome content and impermeability of cell walls, is the inaccessibility of probe target sites due to higher-order structure of the ribosome. Analogous to a study on the 16S rRNA (B. M. Fuchs, G. Wallner, W. Beisker, I. Schwippl, W. Ludwig, and R. Amann, Appl. Environ. Microbiol. 64:4973-4982, 1998), the accessibility of the 23S rRNA of Escherichia coli DSM 30083(T) was studied in detail with a set of 184 CY3-labeled oligonucleotide probes. The probe-conferred fluorescence was quantified flow cytometrically. The brightest signal resulted from probe 23S-2018, complementary to positions 2018 to 2035. The distribution of probe-conferred cell fluorescence in six arbitrarily set brightness classes (classes I to VI, 100 to 81%, 80 to 61%, 60 to 41%, 40 to 21%, 20 to 6%, and 5 to 0% of the brightness of 23S-2018, respectively) was as follows: class I, 3%; class II, 21%; class III, 35%; class IV, 18%; class V, 16%; and class VI, 7%. A fine-resolution analysis of selected areas confirmed steep changes in accessibility on the 23S RNA to oligonucleotide probes. This is similar to the situation for the 16S rRNA. Indeed, no significant differences were found between the hybridization of oligonucleotide probes to 16S and 23S rRNA. Interestingly, indications were obtained of an effect of the type of fluorescent dye coupled to a probe on in situ accessibility. The results were translated into an accessibility map for the 23S rRNA of E. coli, which may be extrapolated to other bacteria. Thereby, it may contribute to a better exploitation of the high potential of the 23S rRNA for identification of bacteria in the future. |
| URL: |
21091995 |
|
| 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 #: |
4300 |
| Author(s): |
Jagnow,G.;Haider,K.;Ellwardt,P.-C. |
| Journal: |
Arch. Microbiol. |
| Title: |
Anaerobic dechlorination and degradation of hexachlorocyclohexane isomers by anaerobic and facultative anaerobic bacteria. |
| Volume: |
115 |
| Page(s): |
285-292 |
| Year: |
1977 |
|
|
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