| Extended Bibliography: |
Show bibliography
| 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 #: |
95499 |
| Author(s): |
Ticknor,L.O.;Kolsto,A.B.;Hill,K.K.;Keim,P.;Laker,M.T.;Tonks,M.;Jackson,P.J. |
| Journal: |
Appl Environ Microbiol |
| Title: |
Fluorescent Amplified Fragment Length Polymorphism Analysis of Norwegian Bacillus cereus and Bacillus thuringiensis Soil Isolates |
| Volume: |
67 |
| Page(s): |
4863-73 |
| Year: |
2001 |
| Keyword(s): |
GENBANK/AF290545
GENBANK/AF290546
GENBANK/AF290547
GENBANK/AF290548
GENBANK/AF290549
GENBANK/AF290550
GENBANK/AF290551
GENBANK/AF290552
GENBANK/AF290553
GENBANK/AF290554
GENBANK/AF290555
GENBANK/AF290556
GENBANK/AF290557
GENBANK/AF290558
GENBANK/AF290559
GENBANK/AF290560
GENBANK/AF290561
GENBANK/AF290562
Bacillus cereus/*classification/*genetics/isolation & purification
Bacillus thuringiensis/*classification/*genetics/isolation & purification
Bacterial Typing Techniques
Base Sequence
DNA, Bacterial/analysis/genetics
DNA, Ribosomal/analysis/genetics
Fluorescence
Genes, rRNA
Molecular Sequence Data
Norway
Phylogeny
*Polymorphism, Restriction Fragment Length
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
*Soil Microbiology
Variation (Genetics)
|
| Remarks: |
We examined 154 Norwegian B. cereus and B. thuringiensis soil isolates (collected from five different locations), 8 B. cereus and 2 B. thuringiensis reference strains, and 2 Bacillus anthracis strains by using fluorescent amplified fragment length polymorphism (AFLP). We employed a novel fragment identification approach based on a hierarchical agglomerative clustering routine that identifies fragments in an automated fashion. No method is free of error, and we identified the major sources so that experiments can be designed to minimize its effect. Phylogenetic analysis of the fluorescent AFLP results reveals five genetic groups in these group 1 bacilli. The ATCC reference strains were restricted to two of the genetic groups, clearly not representative of the diversity in these bacteria. Both B. anthracis strains analyzed were closely related and affiliated with a B. cereus milk isolate (ATCC 4342) and a B. cereus human pathogenic strain (periodontitis). Across the entire study, pathogenic strains, including B. anthracis, were more closely related to one another than to the environmental isolates. Eight strains representing the five distinct phylogenetic clusters were further analyzed by comparison of their 16S rRNA gene sequences to confirm the phylogenetic status of these groups. This analysis was consistent with the AFLP analysis, although of much lower resolution. The innovation of automated genotype analysis by using a replicated and statistical approach to fragment identification will allow very large sample analyses in the future. |
| URL: |
11571195 |
|
| Ref #: |
95473 |
| Author(s): |
Nubel,U.;Schmidt,P.M.;Reiss,E.;Bier,F.;Beyer,W.;Naumann,D. |
| Journal: |
FEMS Microbiol Lett |
| Title: |
Oligonucleotide microarray for identification of Bacillus anthracis based on intergenic transcribed spacers in ribosomal DNA |
| Volume: |
240 |
| Page(s): |
215-23 |
| Year: |
2004 |
| Keyword(s): |
GENBANK/AJ841817
GENBANK/AJ841818
GENBANK/AJ841819
GENBANK/AJ841820
GENBANK/AJ841821
GENBANK/AJ841822
GENBANK/AJ841823
GENBANK/AJ841824
GENBANK/AJ841825
GENBANK/AJ841826
GENBANK/AJ841827
GENBANK/AJ841828
GENBANK/AJ841829
GENBANK/AJ841830
GENBANK/AJ841831
GENBANK/AJ841832
GENBANK/AJ841833
GENBANK/AJ841834
GENBANK/AJ841835
GENBANK/AJ841836
GENBANK/AJ841837
GENBANK/AJ841838
GENBANK/AJ841839
GENBANK/AJ841840
GENBANK/AJ841841
GENBANK/AJ841842
GENBANK/AJ841843
GENBANK/AJ841844
GENBANK/AJ841845
GENBANK/AJ841846
GENBANK/AJ841847
GENBANK/AJ841848
GENBANK/AJ841849
GENBANK/AJ841850
GENBANK/AJ841851
GENBANK/AJ841852
GENBANK/AJ841853
GENBANK/AJ841854
GENBANK/AJ841855
GENBANK/AJ841856
GENBANK/AJ841857
GENBANK/AJ841858
GENBANK/AJ841859
GENBANK/AJ841860
GENBANK/AJ841861
GENBANK/AJ841862
GENBANK/AJ841863
GENBANK/AJ841864
GENBANK/AJ841865
GENBANK/AJ841866
GENBANK/AJ841867
GENBANK/AJ841868
GENBANK/AJ841869
GENBANK/AJ841870
GENBANK/AJ841871
GENBANK/AJ841872
GENBANK/AJ841873
GENBANK/AJ841874
GENBANK/AJ841875
GENBANK/AJ841876
GENBANK/AJ841877
GENBANK/AJ841878
GENBANK/AJ841879
GENBANK/AJ841880
GENBANK/AJ841881
GENBANK/AJ841882
GENBANK/AJ841883
GENBANK/AJ841884
GENBANK/AJ841885
GENBANK/AJ841886
GENBANK/AJ841887
GENBANK/AJ841888
GENBANK/AJ841889
GENBANK/AJ841890
GENBANK/AJ841891
GENBANK/AJ841892
GENBANK/AJ841893
GENBANK/AJ841894
GENBANK/AJ841895
Bacillus anthracis/*classification/genetics/*isolation & purification
Base Pair Mismatch
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal Spacer/*genetics
Molecular Sequence Data
Nucleic Acid Hybridization
*Oligonucleotide Array Sequence Analysis
Phylogeny
RNA, Bacterial/genetics
RNA, Transfer, Ile/genetics
Sensitivity and Specificity
Sequence Analysis, DNA
Sequence Homology, Nucleic Acid
|
| Remarks: |
We developed a DNA microarray for identification of Bacillus anthracis and other phylogenetic groupings within the "Bacillus cereus group". Nucleotide sequences of 16S-23S ribosomal DNA internal transcribed spacers containing genes for tRNA(Ile) from 52 B. anthracis strains were found to be identical to sequences from seven strains published previously and different from all other bacteria. When 42 oligonucleotide probes targeting polymorphic sites were immobilized on glass slides and hybridized to fluorescently labeled PCR amplification products, one or more mismatches could be discriminated in all but one cases. Hence, hybridization events were highly specific and identification of B. anthracis was straightforward. |
| URL: |
15522510 |
|
| Ref #: |
12211 |
| Author(s): |
Ticknor,L.O.;Kolsto,A.B.;Hill,K.K.;Keim,P.;Laker,M.T.;Tonks,M.;Jackson,P.J. |
| Journal: |
Appl Environ Microbiol |
| Title: |
Fluorescent Amplified Fragment Length Polymorphism Analysis of Norwegian Bacillus cereus and Bacillus thuringiensis Soil Isolates |
| Volume: |
67 |
| Page(s): |
4863-73 |
| Year: |
2001 |
| Keyword(s): |
GENBANK/AF290545
GENBANK/AF290546
GENBANK/AF290547
GENBANK/AF290548
GENBANK/AF290549
GENBANK/AF290550
GENBANK/AF290551
GENBANK/AF290552
GENBANK/AF290553
GENBANK/AF290554
GENBANK/AF290555
GENBANK/AF290556
GENBANK/AF290557
GENBANK/AF290558
GENBANK/AF290559
GENBANK/AF290560
GENBANK/AF290561
GENBANK/AF290562
Bacillus cereus/*classification/*genetics/isolation & purification
Bacillus thuringiensis/*classification/*genetics/isolation & purification
Bacterial Typing Techniques
Base Sequence
DNA, Bacterial/analysis/genetics
DNA, Ribosomal/analysis/genetics
Fluorescence
Genes, rRNA
Molecular Sequence Data
Norway
Phylogeny
*Polymorphism, Restriction Fragment Length
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
*Soil Microbiology
Support, U.S. Gov't, Non-P.H.S.
Variation (Genetics)
|
| Remarks: |
We examined 154 Norwegian B. cereus and B. thuringiensis soil isolates (collected from five different locations), 8 B. cereus and 2 B. thuringiensis reference strains, and 2 Bacillus anthracis strains by using fluorescent amplified fragment length polymorphism (AFLP). We employed a novel fragment identification approach based on a hierarchical agglomerative clustering routine that identifies fragments in an automated fashion. No method is free of error, and we identified the major sources so that experiments can be designed to minimize its effect. Phylogenetic analysis of the fluorescent AFLP results reveals five genetic groups in these group 1 bacilli. The ATCC reference strains were restricted to two of the genetic groups, clearly not representative of the diversity in these bacteria. Both B. anthracis strains analyzed were closely related and affiliated with a B. cereus milk isolate (ATCC 4342) and a B. cereus human pathogenic strain (periodontitis). Across the entire study, pathogenic strains, including B. anthracis, were more closely related to one another than to the environmental isolates. Eight strains representing the five distinct phylogenetic clusters were further analyzed by comparison of their 16S rRNA gene sequences to confirm the phylogenetic status of these groups. This analysis was consistent with the AFLP analysis, although of much lower resolution. The innovation of automated genotype analysis by using a replicated and statistical approach to fragment identification will allow very large sample analyses in the future. |
| URL: |
21455048 |
|
| 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 #: |
2358 |
| Author(s): |
Roberts,R.J. |
| Journal: |
Nucl. Acids Res. |
| Title: |
Restriction and modification enzymes and their recognition sequences. |
| Volume: |
13, |
| Page(s): |
r165-r200 |
| Year: |
1985 |
|
| Ref #: |
2422 |
| Author(s): |
White,P.J. |
| Journal: |
J. Gen. Microbiol. |
| Title: |
The nutrition of Bacillus megaterium and Bacillus cereus. |
| Volume: |
71 |
| Page(s): |
505-514 |
| Year: |
1972 |
|
| Ref #: |
3768 |
| Author(s): |
Fahmy,F.;Flossdorf,J.;Claus,D. |
| Journal: |
System. Appl. Microbiol. |
| Title: |
The DNA base composition of the type strains of the genus Bacillus. |
| Volume: |
6 |
| Page(s): |
60-65 |
| Year: |
1985 |
|
| Ref #: |
46 |
| Author(s): |
Lawrence,J.S.;Ford,W.W. |
| Journal: |
J. Bacteriol. |
| Title: |
Studies on aerobic spore-bearing non-pathogenic bacteria. Part I. |
| Volume: |
1 |
| Page(s): |
273-320 |
| Year: |
1916 |
|
| Ref #: |
6615 |
| Author(s): |
Heyndrickx,M.;Vandermeulebroecke,K.;Kersters,K.;DeVos,P.;Logan,N.A.;Aziz,M.A.;Ali,N.;Berkeley,R.C.W. |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (Nakamura 1984) as Paenibacillus lautus comb. nov. and of Bacillus peoriae (Montefusco et al. 1993) as Paenibacillus peoriae comb. nov., and emended description of |
| Volume: |
46 |
| Page(s): |
988-1003 |
| Year: |
1996 |
|
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