Microbial programming of host physiology

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SUMMARY Much attention has been invested in cataloging the microbes that inhabit our bodies in various states of health and disease. Equally pressing is an understanding of the molecular pathways by which these communities of microbes (our `microbiome') program our physiology. This process occurs from the moment that the microbiome first colonizes the gut in early infancy. During this `critical period,' microbial input is required to complete development of the intestine, immune and nervous systems. When appropriate, these interactions provide a foundation for future health, but when it is disrupted, it predisposes individuals to disease. Thus, defining the genetic regulators of these events is one of the most fundamental questions in microbiome research today. Our goal is therefore to comprehensively identify the molecular pathways that govern microbiome programming of host physiology. Here, we propose a suite of innovative methods that will, for the first time, allow us to resolve microbial programming response networks in whole organisms—a veritable microbiome `moon shot'. This is made possible by employing a simple, exquisitely defined, and high-throughput amenable animal system, Caenorhabditis elegans. We have identified the C. elegans natural microbiome and characterized its wide breadth of influence on host physiology and development. We believe that the C. elegans system is ideal for interrogating the impact of microbiome programming for four main reasons. First, microbial exposures during larval development dictate adult physiology. Second, the intestinal niches that are available for bacteria are comparable to the infant gut structural, chemical, immune and digestive environment. Third, the potential host response pathways are well-conserved. Fourth, a majority of the types of microbes that are found in the infant gut also naturally colonize C. elegans. We propose to leverage this system to elucidate the networks of microbiome reprogramming by employing two complementary projects. In Project 1, we will generate the first complete map of the impact of microbiome programming on whole organism host physiology. These studies will use a new sequencing method that we are developing to quantify the impact of microbiome programming on all of C. elegans 959 cells in hundreds of animals at a time. In Project 2, we will identify the host genetic landscape that governs microbial programming using strategies that greatly enhance the throughput and phenotyping of targeted genetic disruptions. Based on preliminary data, we will first characterize the role of the highly redundant, receptor-mediated signaling pathways in this process. Results from these studies will identify host pathways that promote healthy microbial programming early in life, and will aid in the development of therapeutic strategies aimed at reopening this critical period to mitigate adult disease.