Comparison of DNA extraction methods for polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of the infant fecal microbial communities

The study of the intestinal microflora has been developed mainly using conventional microbiological approaches. These studies have made ​​great progress, but it is imperative that new methods will be applied to facilitate scientific progress. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) has been used to study microbial communities in many environmental samples. So, we must do our best to enhance the quality and accuracy of upstream analyses, such as DNA extraction. In this study, the relative efficacy of four DNA extraction methods (QIAamp DNA stool mini kit method, Q; QIAamp DNA stool mini kit+ Bead beating method, QB; QIAamp DNA stool mini kit+ Frozen thawed method, QF; E.Z.N.A. Stool DNA Kit method, E) were evaluated. Further, PCR-DGGE technique was also assessed in detecting diversity in infant intestinal bacterial fingerprint profiles. The total DNA was extracted from the infant fecal specimens using four different methods, followed by PCR amplification of bacterial 16S rRNA-V3 region, and DGGE separation of the amplifications. The number of extracted DNA of the infant feces using the Q method was larger than the QB, QF and E methods, and the produced bands of its DGGE profiles were more than the other three methods, which was due to its cracking temperature (95°C). We concluded that DGGE of 16S rRNA gene PCR products was suitable for capturing the profiles of the infant intestinal microbial community and the QIAamp DNA stool mini kit method was appropriate for infant fecal DNA extraction. PCR-DGGE could be an important tool for DNA studies.   Key words: DNA extraction method, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), infant intestinal microflora.