A complex community of microorganisms inhabit the gastrointestinal tract throughout its length. The colon is the main site of microbial colonization and, typically, the indigenous microbiota are considered to be made up of more than 500 different species of bacteria. Recent molecular studies have confirmed this view of microbial diversity within the gut [1]. The gut microbiota plays an important role in both human health and disease [2]. The main function of the gut microbiota, from the host's point of view, is to prevent colonization by potentially pathogenic microorganisms. It does so efficiently by outcompeting invading pathogens for ecological niches and metabolic substrates. Microbial metabolism also serves as an important source of energy for the gut wall, providing up to 50% of the daily energy requirements of colonocytes by fermentation of carbohydrates to organic acids, mainly butyrate. The gut microbiota acts as an important modulator of the immune system, not only educating the naı̈ve infant immune system but also serving as an important source of noninflammatory immune stimulators throughout life in healthy individuals. However, these health-promoting aspects of the gut microbiota are not infallible and can be overcome by pathogens specifically evolved for gastrointestinal infection (e.g. Salmonella spp., attaching and effacing Escherichia coli strains and Campylobacter jejuni). Similarly, the defence mechanisms afforded by a healthy gut microbiota might be overcome when compromised by chemotherapy (especially antibiotics) or chronic disease [e.g. colon cancer and inflammatory bowel disease (IBD)]. This realization has lead to the development of foods specifically designed to fortify the gut microbiota.