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The bacterial species that are most abundant in the gastrointestinal tract under normal conditions are anaerobic and have exacting growth requirements. As they display only a narrow range of biochemical activities, it is probable that the chemical transformation of metabolites in the gastrointestinal tract is less pronounced when these organisms predominate than when others gain the upper hand under pathologic conditions. In other words, the composition of the gastrointestinal flora determines the nature of the bioactive substances that are produced through metabolic transformation of amino acids, bile acids and other metabolites. Such biochemical activities may be as important as the orthodox pathologic lesions caused by pathogens.The microorganisms of the indigenous flora exert morphogenetic effects that are essential for adequate histologic development and for the healthy function of the gastrointestinal tract. The most important species of this flora are not necessarily those which multiply most abundantly within the lumen, but rather those which selectively become associated with the mucous layer in the different parts of the gastrointestinal tract.In brief, the microbial flora affects the histologic structure of the gastrointestinal tract and the kind of substances that are released from it into the general circulation. The different parts of the digestive tract, the various microbial species that they harbor selectively, and the physiologic conditions that govern the interplay between the host and its indigenous flora constitute a highly integrated ecosystem. Interference with any component of this system is likely to disturb its equilibrium and therefore to result in pathologic manifestations.