The gastrointestinal (GI) system in humans comprises the largest surface area of any organ in the body. The complexity of this system and its functions provides us with the ability to take in nutrition, selectively process it, assist in maintaining fluid and electrolyte balance, and offers a vehicle for excretion of waste while at the same time offering the first line of defense against toxins, pathogens, and other noxious agents. The indigenous gut microflora make up the complex ecosystem that inhabits the GI lumen, which mediates part of the interaction between the external environment and the host.

The basic development and makeup of the human intestinal microflora, and the metabolic, immune, and functional effects of the host are discussed below. The importance of maintaining a balance in this ecosystem, and the recent use of nutrition for providing beneficial microflora and the clinical effect this offers will be presented.

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