Molecular Profiling of Bacteroides Spp in Environmental Water by PCR-Denaturing Gradient Gel Electrophoresis (DGGE).

Bacteroidales bacteria are deemed as a promising indicator of recent fecal pollution because they have been shown to correlate with the presence of fecal pathogen and also because they are anaerobic and their survival is thought to be restricted in extra-intestinal environments. Some microbial source tracking methods based on the detection of host-specific bacteroidales markers have been developed. The recent finding of the survival and persistence of fecal bacteroidales in freshwater environments challenges its suitability in this respect. As the first step to study the environmental behavior of bacteroidales, a fast and cost efficient method is required to characterize their population composition. In this study we therefore developed and validated a PCR-denaturing gradient gel electrophoresis method for the rapid and accurate investigation of bacteroidales in environmental samples. Different primer pairs targeting the 16S rDNA of bacteroidales were tested and the electrophoresis conditions, including gradient level, gel density and electrophoresis time were also determined. The results showed that under optimized conditions primers Bfr-F/Bfr-R produced sharp and well-separated bands in DGGE fingerprints. DGGE profile of environmental water samples was complicated but the band profile was unique and highly reproducible to each sample, indicating the application potential of this method in environmental studies.