To colonize an animal host, bacteria must acquire nutrients for growth. However, despite extensive research, next to nothing is known about the nutrients and metabolic pathways used in situ by the 400-500 species which inhabit the mammalian large intestine. The proposed research uses functional genomics technology to investigate the acquisition of nutrients by enteric bacteria during the colonization process. Specifically, we will test the hypothesis that induction of the pathways used for catabolism of mucus-derived sugars is essential for colonization of E. coli. Global transcription assays will be used to identify regulons induced for growth on the complex mixture of nutrients present in intestinal mucus. Probes prepared from cells grown on minimal media containing cecal mucus will be hybridized to DNA arrays of all E. coli genes. Pathways induced in situ for growth on mucus will be identified by analyzing global transcription patterns of E. coli cells in the ceca of experimentally colonized germ-free mice. Pathways which contribute to the ability of E. coli to successfully compete with the 400-500 other species in the large intestine will be examined. Mutant strains selectively blocked in specific catabolic pathways will be tested for their ability to colonize mice and green fluorescent protein reporter fusions will be used to determine the temporal and spatial expression of these regulons in individual bacterial cells during colonization. These experiments will identify the distinct physiological roles of individual mucosal sugars in colonization of the large intestine by E. coli, providing knowledge important for addressing the more general question of whether or not metabolic diversity allows pathogenic E. coli strains to colonize in the presence of precolonized strains, thus leading to their ability to cause disease. Knowing precisely which nutrients are essential for colonization should lead to improved strategies for combating infection.
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