Mice deficient in interleukin-2 are well suited for use as an animal model for inflammatory bowel disease. Raised under specific-pathogen-free conditions, interleukin-2-deficient mice develop an inflammatory bowel disease resembling ulcerative colitis in humans. The finding that colitis was attenuated when the mice were kept under germfree conditions implies that the resident intestinal flora is involved in the pathogenesis of colitis. The present study addresses the composition of the mucosa-associated bacterial flora in colon samples from interleukin-2-deficient mice that developed colitis. This was investigated by comparative 16S ribosomal DNA (rDNA) sequence analysis and fluorescence in situ hybridization using rRNA-targeted fluorescent probes to quantify the bacterial populations of the mucosa-associated flora. The investigations revealed distinct differences in the bacterial composition of the mucosa-associated flora between interleukin-2-deficient mice and healthy controls. Fluorescence in situ hybridization identified up to 10% of the mucosa-associated flora in interleukin-2-deficient mice as Escherichia coli, whereas no E. coli was detected in the mucosa from healthy wild-type mice. This finding was consistent with the results from comparative 16S rDNA analysis. About one-third of the clones analyzed from 16S rDNA libraries of interleukin-2-deficient mice represented Enterobacteriaceae, whereas none of the clones analyzed from the healthy controls harbored 16S rDNA from Enterobacteriaceae. The abundance of E. coli in the colonic mucosa of interleukin-2-deficient mice strongly suggests a participation in the pathogenesis of colitis in the interleukin-2-deficient mouse model for inflammatory bowel disease.Ulcerative colitis and Crohn's disease are chronic diseases of the intestinal tract which are characterized by a strong activation of the intestinal mucosa-associated immune system due to a complex interaction of genetic, immunologic, and environmental factors. Despite numerous investigations over the last half-century, the etiology of inflammatory bowel diseases (IBD) remains unknown (32). Today several animal models for IBD are established and allow the investigation of factors which are involved in the pathogenesis of the disease (6). Interleukin-2 (IL-2)-deficient mice represent an animal model in which mice develop a colitis resembling ulcerative colitis in humans (4). Colitis developed spontaneously when the mice were kept under specific-pathogen-free (SPF) housing conditions but was greatly attenuated when they were raised under germfree conditions (29). This finding is consistent in various rodent models of IBD and demonstrates the pivotal role that the endogenous intestinal bacterial flora plays in the initiation and perpetuation of the chronic inflammation (23, 27, 36) Results from studies of T-cell-receptor-deficient mice and of rats with induced experimental colitis indicate that the species composition of the microbial flora, rather than the intestinal flora per se, seems to be of particular...