Non-genetic inheritance: mechanisms of microbiome-mediated transgenerational change

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Project Summary The dense microbial communities associated with animals, referred to as the microbiome, can have an important impact on both host development and physiology. Yet, we are only beginning to understand the mechanisms by which the microbiome promotes these important functions. There is great interest to define and understand how these associations, such as changes in composition, or dysbiosis, are linked to a number of diseases. Moreover, the ability to manipulate or restore the microbiome is being pursued as a therapeutic target. While the success of fecal transplant therapy for acute and chronic Clostridium difficile infections highlights their potential, the broader applicability of such therapies to other maladies remains unknown. Consequently, there is great need to understand the relationship between a host and its microbiome with regards to its regulation and molecular signaling mechanisms. I propose to utilize the fruit fly, Drosophila melanogaster, to investigate mechanisms that contribute to the establishment of normal host physiological conditions, a critical step in developing strategies for microbiome therapy. My project will focus on the timing and establishment of normal parameters of host physiology and development. Specifically, I will study in germ-free flies and flies that have experienced early-life events that disrupt the microbiome, the latter of which has been linked to chronic diseases in other animal models. The specific goals of this proposal are to: a) Explore the trans-generational impacts of the microbiota on D. melanogaster. b) Identify host and microbiota factors that promote normal host physiology. c) Develop strategies to restore normal animal physiology through manipulation of the microbiome. I will use high throughput sequencing technologies in the form of transcriptomes, metabolomes, and epigenomes to investigate gene expression and metabolite production across fly development and through generations, coupled with traditional genetic approaches to characterize identified targets. My experiments will focus on comparisons with germ-free, gnotobiotic, and conventionally-reared flies to characterize the effects of host association with the microbiome. I will also identify microbial signals that induce changes in the host and will experimentally manipulate both the host and microbial recognition and signaling systems that mediate these associations. Given the high conservation of developmental and homeostatic signaling pathways between files and humans, and that 75% of known human disease genes have a match in the D. melanogaster genome, I anticipate that this work will identify conserved mechanisms that regulate host-microbiome interactions in all animals, including humans.