New strategies for electrophoresis analysis of enterobacterial repetitive intergenic consensus PCR in animal intestinal microflora

Enterobacterial repetitive intergenic consensus–PCR (ERIC–PCR) is a molecular biological technology that can be used to study microbial community diversity and dynamics. In many reports, investigations of microbial diversity from environmental samples were based on the agarose gel electrophoresis (AGE) patterns of ERIC–PCR amplified products. This is not a sound practice, since bands with identical positions can contain different sequences; thus, this practice could possibly exaggerate the similarities or diversities among samples. To mitigate this issue, we employed a denaturing gradient gel electrophoresis (DGGE) strategy to explore DNA bands with the same size, between ERIC–PCR profiles of samples. DPS software was used with Shannon–Wiener diversity index (H’) to analyze ERIC–PCR fingerprint profiles. H’ revealed that the microbial community diversity at DGGE was higher than with AGE. The results of this study suggest that the ERIC–PCR assays with DGGE can provide a better assessment of electrophoresis pattern with regards to the structure of an intestinal microbial community.