The indigenous microflora of the upper digestive tract is poorly developed and consists of microorganisms in transit, originating in the oro-pharynx. Aerobic bacteria, mainly streptococci, predominate. In the normohydrochloric stomach, the mean fasting bacterial concentration is 10(3)-10(4)/ml gastric juice. In the small intestine, levels of up to 10(5) bacteria/ml contents are reached. The essential mechanism which maintains this relative sterility of the upper digestive tract is the gastro-intestinal transit and in particular the interdigestive migrating motor complex. In the terminal ileum, a zone subject to relative stasis, the intraluminal bacterial population rises to 10(8)/ml in one third of subjects, with the appearance of enterobacter and strict anaerobes. In the colon, a zone of physiological stasis, the number of microorganisms per ml of contents is 10(8)-10(9) on the right side and 10(10)-10(12) on the left side. The dominant flora is strictly anaerobic and the subdominant flora optionally aero-anaerobic, consist mainly of Enterobacter, Streptococci and Lactobacilli. The balance between the species of microorganisms in the colonic ecosystem and its stability results primarily from microbial antagonisms. The barrier flora, consisting of groups of anaerobes, either prevent the implantation of exogenous microorganisms (drastic barrier) or limit it to the subdominant flora (permissive barrier). The repression of the subdominant flora by the dominant flora prevents the subdominant flora from spreading to the mesenteric ganglia and then the whole body. Rupture of the barrier flora by a wide-spectrum antibiotic may permit the local multiplication of a pathogenic organism (C. difficile, Salmonella), or the spread of an opportunist organism (Klebsiella pneumoniae).