The commercial interest in functional foods that contain live microorganisms, also termed probiotics, is paralleled by increasing scientific attention to their functionality in the digestive tract. Most studies are focused on intestinal Lactobacillus species, which are part of the natural gastro-intestinal microbiota, and include analysis of colonisation factors and other interactions with the host, the design of novel or improved strains with specific health benefits, and the application of sophisticated molecular tools to determine their fate and activity in situ.