Defining a nutrient niche competed for by gut commensal bacteria and pathogens

University Of Michigan At Ann Arbor, Ann Arbor MI

Investigators

Linked publications, trials & patents

Abstract

Summary The ability to efficiently compete for available nutrients is a major determinant of success for both pathogenic and non-pathogenic bacteria in the human gut. In recent years, there have been monumental increases in our genomic and ecological understanding of the bacterial community (microbiota) that inhabits the human gut, as well as the pathogens that periodically invade this ecosystem. However, functional studies that define the competitive interplay between pathogens and the microbiota are still rare. Thus, there is a need to identify specific metabolites that are important for gut bacterial colonization, along with their sources, and to define how changes in the supply of these nutrients influences the balance between commensals and pathogens. The Bacteroidetes phylum represents a large percentage of the gut microbiota. A defining feature of many members of this group is the ability to degrade a vast array of host-derived and dietary glycans as nutrient sources. We have discovered that the model gut symbiont B. thetaiotaomicron (Bt) and members of many, but not all, other Bacteroidetes species possess the ability to utilize the five carbon sugar ribose a sole carbon source, along with various more complex sources like ribonucleosides. Using Bt as a model, we have identified the genes required for ribose metabolism and have discovered homologous gene clusters in other Bacteroidetes that use this sugar. Genetic dissection of the Bt ribose utilization system has resulted in a working model for ribose liberation and metabolism. However, many questions still remain, such as what dietary and endogenous sources provide accessible ribose for commensal bacteria in vivo? And, how does competition for ribose, or changes in its abundance, influence the competitive balance between the microbiota and invading pathogens? These questions are particularly relevant because the bacterial pathogen enterohemorrhagic E. coli (EHEC) has been shown to prioritize utilization of ribose in vivo. We hypothesize that ribose-utilizing commensal bacteria mediate colonization resistance (CR) against EHEC and that loss of these bacteria or disruptions in their physiology make ribose more abundant and promote susceptibility to EHEC. Our preliminary data reveal certain dietary conditions that exert positive selective pressure on ribose- utilizing Bt, while others do not. Extending from these data, we will identify the dietary and host sources of ribose, their concentrations in vivo and further define the mechanisms through which species like Bt metabolize this nutrient. Using competitive colonization experiments between wild-type and mutant Bt strains, we will test the role of Bt ribose acquisition in vivo and probe its mechanistic requirements. Through experiments with more complex synthetic microbiota, in which members can still be manipulated to alter ribose utilization, we will measure the impact of ribose availability on EHEC colonization. These experiments will provide needed functional insight into the pathways connecting diet with the gut microbiota and susceptibility to enteric pathogens and will yield knowledge about to treat or prevent diseases caused by EHEC or related pathogens.