The Microbiota of the human gastrointestinal tract: a molecular view

The human gut microbiota represents a complex collection of microorganisms, which contribute considerably to host health. They occupy different ecological niches and habitats within the gastrointestinal tract and vary both in compositional make up and metabolic output at different sites along the gut. In this chapter, we describe the microbial “geography” within the human gastrointestinal tract and discuss available methods for studying the gut microbiota at both taxonomic and metabolic levels. Tremendous advances have been made in culture independent molecular microbiology over the past 20 years giving previously undreamt of insight into the architecture of the gut microbiota. Similarly, advances in “omics” technologies, especially metagenomics and metabolomics, are providing the tools necessary to give, for the first time, a real insight into both the gut microbiota metabolic potential (encoded by the genes of microbiota metagenome) and the metabolic kinetic (comprising the flux of microbially derived metabolites) and how these then interact with host physiology influencing health and disease risk