Methods for analysis of the intestinal microflora.

The concept of probiotics has been around for about 100 years. Yet its impact on human nutrition is still an emerging concept. Lack of convincing scientific validation for the efficacy of any ingested probiotic bacterium on intestinal health, has been a major reason for the low impact of probiotics on human nutrition. Obtaining positive scientific validation requires the use of suitable probiotic strains and also the necessary tools to monitor the performance of these bacteria in the intestines of individuals. To date, selection of strains for probiotic purposes has not been based on a scientific directed approach, primarily because it is not yet fully known what specific traits a desirable probiotic strain should possess. Filling this knowledge void will depend largely on furthering our understanding of the human intestinal ecosystem and the functional role of specific bacteria for intestinal health. Traditional approaches for studying this ecosystem have provided a good foundation in this knowledge base. Complementation of the traditional approaches with the emergence of sophisticated molecular tools shows enormous promise for obtaining the necessary insight into the intestinal microflora. This review will cover the traditional methodologies which have been used to analyze the human intestinal microflora. It will also reveal the development of modern molecular approaches for studying the diversity and phylogeny of its flora, and the rapid molecular tools for monitoring the presence of specific strains in the intestine. Finally, it will address the advent of in situ analysis of individual microbial cells, which promises to provide tremendous advances in our understanding of the microflora and their metabolic activities in the human intestine.