The composition and metabolism of human gut microbiota play crucial roles in health. Microbial colonisation of the gastrointestinal tract varies widely, with the large intestine having not only the highest density of microbes in terms of bacterial cells per gram but also the most metabolically active microbial community. Genetics, mode of birth, infant feeding patterns, antibiotic usage, sanitary living conditions and long term dietary habits contribute towards shaping the composition of the gut microbiome. Diet clearly has a major impact on variation in the gut microbiota composition, and this can be detected in faecal samples after only a few days. The bacterial metabolism of dietary components produces much chemical diversity in the large intestine with protective or detrimental effects on disease development.