Reference : High-throughput method for comparative analysis of denaturing gradient gel electropho...
Scientific journals : Article
Human health sciences : Gastroenterology & hepatology
High-throughput method for comparative analysis of denaturing gradient gel electrophoresis profiles from human fecal samples reveals significant increases in two bifidobacterial species after inulin-type prebiotic intake.
Joossens, Marie [> > > >]
Huys, Geert [> > > >]
Van Steen, Kristel mailto [Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Bioinformatique >]
Cnockaert, Margo [> > > >]
Vermeire, Severine [> > > >]
Rutgeerts, Paul [> > > >]
Verbeke, Kristin [> > > >]
Vandamme, Peter [> > > >]
De Preter, Vicky [> >]
FEMS Microbiology Ecology
Blackwell Publishing
Yes (verified by ORBi)
United Kingdom
[en] Adult ; Bifidobacterium/isolation & purification ; DNA Fingerprinting ; Denaturing Gradient Gel Electrophoresis/methods ; Feces/microbiology ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Intestines/microbiology ; Inulin/metabolism ; Male ; Polymerase Chain Reaction ; Prebiotics ; Statistics, Nonparametric
[en] Denaturing gradient gel electrophoresis (DGGE) is one of the most commonly used molecular tools to study complex microbial communities. Despite its widespread use, meaningful interpretative analysis remains a major drawback of this method. We evaluated the combination of computer-assisted band-matching with nonparametric statistics for comparative analysis of DGGE banding patterns. Fecal samples from 17 healthy volunteers who consumed 20 g of the prebiotic compound oligofructose-enriched inulin (OF-IN) for 4 weeks were analyzed before and after treatment. DGGE fingerprinting profiles were analyzed using bionumerics software version 4.6., which resulted in a data matrix that was used for statistical analysis. When comparing DGGE profiles before and after OF-IN intake with a Wilcoxon nonparametric test for paired data, two band-classes increased significantly after OF-IN intake (P<0.003 and <0.02). These two band-classes could be assigned to the species Bifidobacterium longum and Bifidobacterium adolescentis by band-sequencing analysis, and their significant increase was quantitatively confirmed with real-time PCR using species-specific primers (respectively P<0.012 and <0.010). Therefore, the nonparametric analysis of a data matrix obtained by computer-assisted band-matching of complex profiles facilitated the interpretative analysis of these profiles and provided an objective and high-throughput method for the detection of significant taxonomic differences in larger numbers of complex profiles.
(c) 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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