Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis

We describe the development and validation of a method for the qualitative analysis of complex bifidobacterial communities based on PCR and denaturing gradient gel electrophoresis (DGGE). Bifidobacterium genus-specific primer s were used to amplify an approximately 520-bp fragment from the 16S riboso mal DNA (rDNA), and the fragments were separated in a sequence-specific man ner in DGGE. PCR products of the same length from different bifidobacterial species shelved good separation upon DGGE. DGGE of fecal 16S rDNA amplicon s from five adult individuals showed host-specific populations of bifidobac teria that were stable over a period of 4 weeks. Sequencing of fecal amplic ons resulted in Bifidobacterium-like sequences, confirming that the profile s indeed represent the bifidobacterial population of feces. Bifidobacterium adolescentis was found to be the most common species in feces of the human adult subjects in this study. The methodological approach revealed intrage nomic 16S rDNA heterogeneity in the type strain of B. adolescentis, E-98107 4. The strain was found to harbor five copies of 16S rDNA, two of which wer e sequenced. The two 16S rDNA sequences of B. adolescentis E-981074(T) exhi bited microheterogeneity differing in eight positions over almost the total length of the gene.