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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

Marie Joossens, Geert Huys UGent, Kristel Van Steen, Margo Cnockaert UGent, Severine Vermeire, Paul Rutgeerts, Kristin Verbeke, Peter Vandamme UGent and Vicky De Preter (2011) FEMS MICROBIOLOGY ECOLOGY. 75(2). p.343-349
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
analyses of complex profiles, denaturing gradient gel electrophoresis, 16S RIBOSOMAL-RNA, INFLAMMATORY-BOWEL-DISEASE, MICROBIOTA, HEALTH, COMMUNITIES, BACTERIA, FRUCTANS, FLORA, comparative analyses, prebiotic
journal title
FEMS MICROBIOLOGY ECOLOGY
FEMS Microbiol. Ecol.
volume
75
issue
2
pages
343 - 349
Web of Science type
Article
Web of Science id
000285877100015
JCR category
MICROBIOLOGY
JCR impact factor
3.408 (2011)
JCR rank
33/111 (2011)
JCR quartile
2 (2011)
ISSN
0168-6496
DOI
10.1111/j.1574-6941.2010.01008.x
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1203969
handle
http://hdl.handle.net/1854/LU-1203969
date created
2011-04-06 17:19:56
date last changed
2011-04-11 15:57:11
@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      = {analyses of complex profiles,denaturing gradient gel electrophoresis,16S RIBOSOMAL-RNA,INFLAMMATORY-BOWEL-DISEASE,MICROBIOTA,HEALTH,COMMUNITIES,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},
}

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.