Molecular Ecology and Diversity in Gut Microbial Ecosystems

The microbial community inhabiting the gastrointestinal tract is represented by all major groups of microbes and is characterized by high population density, wide diversity and complexity of interactions. Resident microbial populations have been described as herbivores, omnivores, carnivores, and in a wide range of zoological classes where they contribute to the nutrition, physiology, immunology and protection of the host. Despite this vast amount of knowledge, the basic prerequisites for ecological studies, namely enumeration and identification of all community members have tremendous limitations.
These limitations can be overcome using molecular ecology techniques based on sequence comparisons of nucleic acids (DNA and RNA) and can be used to provide a molecular characterization, while at the same time providing a classification scheme that predicts phylogenetic relationships. The use of nucleic acid-based techniques to detect, identify and quantify microbial populations in the gastrointestinal environment will be briefly reviewed. Some key discoveries revealed by application of the rRNA approach to characterization of morphologically conspicuous but as yet uncultured bacteria are described. The use of molecular ecology techniques will lead to major advances in our
knowledge and provide the first complete description of gastrointestinal ecosystems.