Erwin G. Zoetendal and Roderick I. Mackie

It is now generally accepted in microbial ecology that cultivation-based approaches provide an incomplete picture of microbial diversity in the gastrointestinal (GI) tract because only a minority of microbes can be obtained in culture. Therefore, the application of molecular approaches, especially those focused on 16S ribosomal RNA (rRNA) sequence diversity, have become popular as they enable researchers to bypass the cultivation step. These approaches have provided considerable information about microbial ecosystems, including the GI tract. This article summarizes the different approaches and their impact on our knowledge of the ecology of the GI tract and provides guidelines for future research directions with a focus on pre- and probiotics. from Probiotics and Prebiotics: Scientific Aspects

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Molecular Methods in Microbial Ecology