Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography
<p>Abstract</p> <p>Background</p> <p>BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) is one of the most used techniques in biogeography studies of microbial isolates. However the traditional separation of BOX-PCR patterns by agarose gel electrophoresis suf...
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doaj-9732255167cd486ea0cef463a37ce6b12020-11-25T02:27:41ZengBMCBMC Microbiology1471-21802008-12-018122010.1186/1471-2180-8-220Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeographyMora DiegoChanishvili NinaMerabishvili MayaBorin SaraTamagnini IsabellaGtari MaherMalkhazova IanaBrusetti LorenzoCappitelli FrancescaDaffonchio Daniele<p>Abstract</p> <p>Background</p> <p>BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) is one of the most used techniques in biogeography studies of microbial isolates. However the traditional separation of BOX-PCR patterns by agarose gel electrophoresis suffers many limitations. The aim of this research was to set up a fluorescent BOX-PCR (F-BOX-PCR) assay in which separation of PCR products is automated in a capillary electrophoresis system. F-BOX-PCR was compared with the traditional BOX-PCR using bacterial strains with different G+C content (<it>Bacillus cereus</it>; <it>Escherichia coli</it>; isolates of the family <it>Geodermatophilaceae</it>). Resolution, discriminatory power and reproducibility were evaluated by assaying different electrophoretic runs, PCR reactions and independent DNA extractions. BOX-PCR and F-BOX-PCR were compared for the analysis of 29 strains of <it>Modestobacter multiseptatus </it>isolated from three different microsites in an altered carbonatic wall from Cagliari, Italy, and 45 strains of <it>Streptococcus thermophilus </it>isolated from 34 samples of the hand-made, yogurt-like product Matsoni, collected in different locations in Georgia.</p> <p>Results</p> <p>Fluorophore 6-FAM proved more informative than HEX and BOX-PCR both in agarose gel electrophoresis (<it>p </it>< 0.004 and <it>p </it>< 0.00003) and in capillary electrophoresis (compared only with HEX, <it>p </it>< 2 × 10<sup>-7</sup>). 6-FAM- and HEX-based F-BOX-PCR respectively detected up to 12.0 and 11.3 times more fragments than BOX-PCR. Replicate separations of F-BOX-PCR showed an accuracy of the size calling of ± 0.5 bp until 500 bp, constantly decreasing to ± 10 bp at 2000 bp. Cluster analysis of F-BOX-PCR profiles grouped <it>M. multiseptatus </it>strains according to the microsite of isolation and <it>S. thermophilus </it>strains according to the geographical origin of Matsoni, but resulted intermixed when a BOX-PCR dataset was used.</p> <p>Conclusion</p> <p>F-BOX-PCR represents an improved method for addressing bacterial biogeography studies both in term of sensitivity, reproducibility and data analysis.</p> http://www.biomedcentral.com/1471-2180/8/220 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Mora Diego Chanishvili Nina Merabishvili Maya Borin Sara Tamagnini Isabella Gtari Maher Malkhazova Iana Brusetti Lorenzo Cappitelli Francesca Daffonchio Daniele |
spellingShingle |
Mora Diego Chanishvili Nina Merabishvili Maya Borin Sara Tamagnini Isabella Gtari Maher Malkhazova Iana Brusetti Lorenzo Cappitelli Francesca Daffonchio Daniele Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography BMC Microbiology |
author_facet |
Mora Diego Chanishvili Nina Merabishvili Maya Borin Sara Tamagnini Isabella Gtari Maher Malkhazova Iana Brusetti Lorenzo Cappitelli Francesca Daffonchio Daniele |
author_sort |
Mora Diego |
title |
Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography |
title_short |
Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography |
title_full |
Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography |
title_fullStr |
Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography |
title_full_unstemmed |
Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography |
title_sort |
fluorescent-box-pcr for resolving bacterial genetic diversity, endemism and biogeography |
publisher |
BMC |
series |
BMC Microbiology |
issn |
1471-2180 |
publishDate |
2008-12-01 |
description |
<p>Abstract</p> <p>Background</p> <p>BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) is one of the most used techniques in biogeography studies of microbial isolates. However the traditional separation of BOX-PCR patterns by agarose gel electrophoresis suffers many limitations. The aim of this research was to set up a fluorescent BOX-PCR (F-BOX-PCR) assay in which separation of PCR products is automated in a capillary electrophoresis system. F-BOX-PCR was compared with the traditional BOX-PCR using bacterial strains with different G+C content (<it>Bacillus cereus</it>; <it>Escherichia coli</it>; isolates of the family <it>Geodermatophilaceae</it>). Resolution, discriminatory power and reproducibility were evaluated by assaying different electrophoretic runs, PCR reactions and independent DNA extractions. BOX-PCR and F-BOX-PCR were compared for the analysis of 29 strains of <it>Modestobacter multiseptatus </it>isolated from three different microsites in an altered carbonatic wall from Cagliari, Italy, and 45 strains of <it>Streptococcus thermophilus </it>isolated from 34 samples of the hand-made, yogurt-like product Matsoni, collected in different locations in Georgia.</p> <p>Results</p> <p>Fluorophore 6-FAM proved more informative than HEX and BOX-PCR both in agarose gel electrophoresis (<it>p </it>< 0.004 and <it>p </it>< 0.00003) and in capillary electrophoresis (compared only with HEX, <it>p </it>< 2 × 10<sup>-7</sup>). 6-FAM- and HEX-based F-BOX-PCR respectively detected up to 12.0 and 11.3 times more fragments than BOX-PCR. Replicate separations of F-BOX-PCR showed an accuracy of the size calling of ± 0.5 bp until 500 bp, constantly decreasing to ± 10 bp at 2000 bp. Cluster analysis of F-BOX-PCR profiles grouped <it>M. multiseptatus </it>strains according to the microsite of isolation and <it>S. thermophilus </it>strains according to the geographical origin of Matsoni, but resulted intermixed when a BOX-PCR dataset was used.</p> <p>Conclusion</p> <p>F-BOX-PCR represents an improved method for addressing bacterial biogeography studies both in term of sensitivity, reproducibility and data analysis.</p> |
url |
http://www.biomedcentral.com/1471-2180/8/220 |
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