Open AccessHigh‐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
Author(s) -
Joossens Marie,
Huys Geert,
Van Steen Kristel,
Cnockaert Margo,
Vermeire Séverine,
Rutgeerts Paul,
Verbeke Kristin,
Vandamme Peter,
De Preter Vicky
Publication year - 2011
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/j.1574-6941.2010.01008.x
Subject(s) - temperature gradient gel electrophoresis , biology , prebiotic , inulin , nonparametric statistics , bifidobacterium , metabolomics , gel electrophoresis , food science , bifidobacterium longum , computational biology , feces , genetics , microbiology and biotechnology , statistics , bacteria , bioinformatics , mathematics , 16s ribosomal rna , lactobacillus
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.