DGGE of PCR-amplified rRNA gene amplicons offers
several potential advantages over culture techniques as
a method to monitor mixed bacterial populations.
The development of molecular techniques based on
sequence variability in 16S and 23S rRNA genes has
led to an improved understanding of the microbial
communities present in a variety of ecosystems,
including the intestinal tract.59–61 Although more than
400 different species of anaerobes may be present in
the human colon, phylogenetic analysis of 16S rRNA
gene sequences has revealed that most of these organisms
could be categorized into merely four phylogenetic
clusters.60 These clusters included the genus Bacteroides,
the genus Bifidobacterium, Clostridium coccoides and
relatives and a cluster including Clostridium leptum and
relatives, fusobacteria and the Atopobium group.60
Others have used similar techniques to identify many
anaerobic species in the colon that have not previously
been cultured.6