Denaturing Gradient Gel Electrophoresis (DGGE) for Gut Microbiota Research

For many years, descriptions of bacterial diversity in the gastrointestinal (GI) tract were based mainly on the use of anaerobic culture techniques which are usually very labor-intensive and time-consuming. Furthermore, comparisons with molecular methods suggest that culture-dependent approaches underestimate bacterial diversity in the GI tract. To analyze the composition and changes of the intestinal microbiota, population fingerprinting methods such as denaturing gradient gel electrophoresis (DGGE) are effective tools. Creative Biolabs, as an expert in live biotherapeutics products (LBP) development, has accumulated very deep experience in gut microbiota research. We are happy to discuss your objectives to determine the most effective techniques and methods.

Overview of DGGE

DGGE is a technique for separating short- to medium-length DNA fragments based on their melting properties. This depends on the fact that during electrophoresis, single-stranded DNA molecules migrate more slowly than equivalent double-stranded molecules. All rRNA gene sequences of bacterial species in mixed culture were first amplified using a conserved bacterial primer containing a hypervariable region of the rRNA gene, producing amplicons of the same length but with different sequences specific to a given species. DGGE isolates these amplicons, producing a "molecular fingerprint" of the bacterial species. DGGE fingerprinting has been widely used for its unique advantages in studying the genetic diversity and population differences of complex microbiota.

Principle of DGGE.Fig.1 Principle of DGGE. (Strathdee, 2013)

DGGE for Gut Microbiota Research

DGGE is an effective technique for microbial community analysis of human anaerobic feces. It is a molecular sequence dependent fingerprinting technique that allows characterizing the intestinal microbiota without pre-existing knowledge of its composition. DGGE using universal and bifidobacterial primers based on the bacterial 16S rRNA sequence has been applied successfully to monitor the development of the gut microbiota in infants. The use of the genetic fingerprint method based on denaturing gradient gel electrophoresis (DGGE) has become a popular method to use to study the gut microbiota in endothermic animals because it provides a rapid survey of the microbial community. This approach eschews bacterial culture and in principle provides information on all dominant bacteria, regardless of their ability to grow in culture medium.

Human microbiota: onset and shaping through life stages and perturbations.Fig.2 Human microbiota: onset and shaping through life stages and perturbations. (Ottman, 2012)

Applications of DGGE in Microbial Ecology

  • Studying Community Complexity
  • Studying Community Changes
  • Monitoring the Enrichment and Isolation of Bacteria
  • Comparison of Different DNA Extraction Protocols

To assess microbial community structure, DGGE provides an easy fingerprint of the community. By sequencing the bands in the gel, even species-level identification can be attained. Creative Biolabs is a leading LBP development company. Following the new drug development process, we meet requirements in different stages with rapid turn-around time and a 100% on-time delivery rate. If you are interested in our DGGE services for gut microbiota research, please contact us for detail.

References

  1. Strathdee, F.; Free, A. "Denaturing gradient gel electrophoresis (DGGE)". DNA Electrophoresis. Humana Press. Totowa, NJ, 2013: 145-157.
  2. Ottman, N.; et al. The function of our microbiota: who is out there and what do they do? Frontiers in cellular and infection microbiology. 2012, 2: 104.

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