Mechanisms of Nutrient Competition in the Intestine

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PROJECT SUMMARY/ABSTRACT The World Health Organization classifies diarrhea as a significant worldwide health threat, killing thousands of children daily. Ingestion of a small number of infectious organisms can lead to trillions of pathogens being shed in the stool. Therefore, we postulate that enteric pathogens such as enterohemorrhagic E. coli possess potent mechanisms for obtaining nutrients that provide the energy needed to replicate rapidly in the intestine. While many of the nutrients that support intestinal colonization by model organisms are known, the mechanisms underlying competition for those nutrients are poorly understood. With NIH funding and a research strategy built on the streptomycin treated mouse model, we previously identified the nutrients that support colonization by six genome-sequenced, genetically tractable, prototypical pathogenic and commensal E. coli strains. While these bacteria essentially use the same growth substrates in laboratory culture, each uses a different subset of the available nutrients in the intestine. Indeed, different E. coli strains can co-colonize with one another, indicating that they occupy distinct niches. Two commensal E. coli strains were found to exert colonization resistance against E. coli O157:H7. On the other hand, two other pathotypes were able to overcome colonization resistance to co-colonize with the same commensals. According to basic ecological principles, the niches occupied by competing bacteria are defined by nutrient availability. An important prediction of the nutrient-niche hypothesis is that resistance or sensitivity to invasion depends on nutrient consumption by the resident microbiota, but there is little supporting evidence. Importantly, we recently proved that colonization resistance is imparted by the facultative anaerobes. The question is: how do pathogens overcome colonization resistance to initiate infections? In the streptomycin treated mouse model of competitive colonization, the facultative microbiota can be manipulated to consist of carefully chosen, well-characterized commensal E. coli strain(s) that either exert colonization resistance, or not, against selected pathotypes. The proposed research strategy tests the hypothesis that successful invasion by enteric pathogens depends on potent mechanisms to compete for the nutrients needed to replicate in the intestine. In Aim 1 the competitive colonization model will be used to measure the nutrients that are available to invading pathogens and genome-specific RNA sequencing will determine the catabolic gene systems that are induced in the competing E. coli pathogens and commensals in the intestine. Aim 2 will focus on the mechanisms of nutrient competition between E. coli pathogens and commensals by direct measurement of nutrient consumpition in vivo. To identify allelic differences in catabolic genes that confer fitness advantages, catabolic operons will be swapped between strains and their competitive fitness will be assessed in animals. These experiments are designed to elucidate the mechanisms of nutrient acquisition that are critical to establishing infection. A better understanding of how enteric pathogens compete with the microbiota for nutrients is needed to prevent intestinal infections.