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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

(2011) FEMS MICROBIOLOGY ECOLOGY. 75(2). p.343-349
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Abstract
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.
Keywords
HEALTH, COMMUNITIES, MICROBIOTA, INFLAMMATORY-BOWEL-DISEASE, 16S RIBOSOMAL-RNA, denaturing gradient gel electrophoresis, analyses of complex profiles, BACTERIA, FRUCTANS, FLORA, comparative analyses, prebiotic

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Chicago
Joossens, Marie, Geert Huys, Kristel Van Steen, Margo Cnockaert, Severine Vermeire, Paul Rutgeerts, Kristin Verbeke, Peter Vandamme, and Vicky De Preter. 2011. “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.” Fems Microbiology Ecology 75 (2): 343–349.
APA
Joossens, M., Huys, G., Van Steen, K., Cnockaert, M., Vermeire, S., Rutgeerts, P., Verbeke, K., et al. (2011). 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. FEMS MICROBIOLOGY ECOLOGY, 75(2), 343–349.
Vancouver
1.
Joossens M, Huys G, Van Steen K, Cnockaert M, Vermeire S, Rutgeerts P, et al. 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. FEMS MICROBIOLOGY ECOLOGY. 2011;75(2):343–9.
MLA
Joossens, Marie, Geert Huys, Kristel Van Steen, et al. “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.” FEMS MICROBIOLOGY ECOLOGY 75.2 (2011): 343–349. Print.
@article{1203969,
  abstract     = {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 {\textlangle} 0.003 and {\textlangle} 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 {\textlangle} 0.012 and {\textlangle} 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.},
  author       = {Joossens, Marie and Huys, Geert and Van Steen, Kristel and Cnockaert, Margo and Vermeire, Severine and Rutgeerts, Paul and Verbeke, Kristin and Vandamme, Peter and De Preter, Vicky},
  issn         = {0168-6496},
  journal      = {FEMS MICROBIOLOGY ECOLOGY},
  keyword      = {HEALTH,COMMUNITIES,MICROBIOTA,INFLAMMATORY-BOWEL-DISEASE,16S RIBOSOMAL-RNA,denaturing gradient gel electrophoresis,analyses of complex profiles,BACTERIA,FRUCTANS,FLORA,comparative analyses,prebiotic},
  language     = {eng},
  number       = {2},
  pages        = {343--349},
  title        = {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},
  url          = {http://dx.doi.org/10.1111/j.1574-6941.2010.01008.x},
  volume       = {75},
  year         = {2011},
}

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