This chapter has highlighted the extraordinary advances in the molecular technologies that have substantially contributed to our knowledge and understanding of the human intestinal microbiota. The application of these molecular tools has greatly facilitated our analysis of the composition of the human microbiota. A picture of the "typical" microbiota for at least the northern European population of infants and adults is emerging, as are differences in individuals with intestinal diseases. The diversity is far greater than previously predicted from the initial culturing studies in the 1960s. Consequently, further technological improvements to perform the techniques at higher throughput, and for measurement of more subtle changes in the diversity of the microbiota due to, for example, specific dietary components, require further development. Microarray technology is amenable to both these requirements, and currently DNA microarrays are being constructed for the human microbiota using 16S rRNA sequences of microbiota (136); [Mirjana Rajilic and Willem M. de Vos, personal communication]. FCM with its unique capacity for quantitative and high throughput analysis is resulting in the development of an alternative type of array using beads with oligonucleotide probes on the surface that can be applied in hybridization assays in suspension (137-139).

The substantial impact of this highly diverse microbiota on the health of the human host is now well recognized, such as processing of undigested food, contributing to the host defense and regulating fat storage amongst others (6,140,141). It is a particular challenge to develop methods that allow monitoring of microorganisms according to their eco-physiological traits in situ. The application of cytometric protocols using fluorescent probes in combination with molecular techniques opens the potential for examining key microbial processes and community function in complex microbial ecosystems. Further efforts to determine the molecular foundations of the host-microbiota interactions will require multi-disciplinary approaches. The rewards of this research in terms of promoting host health via our microbiota and diet can be substantial, as well as novel approaches for treating intestinal diseases and infections caused by pathogens.

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