The human large intestine is a complex anaerobic ecosystem, composed of numerous different species, which degrade and ferment substrates that have either escaped the digestion in the upper digestive tract or are produced by the host. It is recognised that a significant daily quantity of undigested dietary carbohydrate enters the colon (Edwards and Rowland, 1992; see Chapter 2). In contrast, the amount of carbohydrate fermented from endogenous sources like mucus remains undefined (Cummings and Macfarlane, 1991; Flourie et al.,1991). The microbial degradation of this organic matter in the colon constitutes a fundamental process which requires the contribution of different groups of microorganisms linked in a trophic chain (Wolin and Miller, 1983). These food-chain reactions break macromolecules such as complex polysaccharides down to short-chain fatty acids (mainly acetate, propionate and butyrate) and gases (H2, CO2 and in some case CH4). Polysaccharide degrading bacteria hydrolyse polymers into smaller fragments that can be used by saccharolytic bacteria. This cross-feeding allows maintainence of bacterial diversity in the ecosystem. The fermentation products of hydrolytic and saccharolytic bacteria include intermediates, such as lactate or succinate, that are metabolised by other species and do not accumulate to any significant extent in the colon. Hydrogen, which derives enterely from these fermentative processes, can be re-utilized in situ by hydrogenotrophic microorganisms.