Investigating the mechanisms driving host-associated microbial community dynamics

PROJECT SUMMARY/ABSTRACT The gut microbiome is a complex ecosystem of microorganisms that live in the gastrointestinal tract. The gut microbiome and alterations to the gut microbiome, or dysbiosis, are linked to a number of human diseases. Variation in the gut microbiome plays a key role in microbiome-associated disease, but the rules governing microbial community dynamics are still being discovered. The composition and function of gut microbial communities change in response to variation in the host’s internal and external environment. While changes in response to antibiotics, disease, and diet are profound, gut microbiome changes associated with normal variation in host physiology or differences in host genetics are more subtle. Research in my lab focuses on understanding drivers of gut microbial community dynamics, particularly those related to changes in the environment or variation host physiology. Both environmental and host influences on the gut microbiome have been studied, but the relative contributions of each are still unclear and the mechanisms underlying these interactions have not been fully explored. My research program will focus on three main themes over the next five years: 1) examining how environmental and host factors interact to shape microbial community development and variation across an individual’s lifespan; 2) developing a more complete understanding of how normal variation in host physiology influences the gut microbiome; and 3) revealing the mechanisms by which host physiology contributes to variation in the gut microbiome. My lab uses metagenomics coupled with behavioral observations and non-invasive and minimally invasive methods to track hormones and immune activity to detect associations between environmental change, host physiological variation, and the gut microbiome in both wild animal systems and humans. Additionally, we pair this approach with cutting-edge computational tools and in vitro fermentation methods to determine the directionality and causality of relationships between the gut microbiome and host factors. This approach will allow us to understand the fundamental rules governing host-associate microbial community assembly and dynamics. This project will significantly contribute to our understanding of the range of normal variation in host-microbe interactions. The results of this project are key to predicting drivers of gut microbial dysbiosis and designing effect microbiome- targeted interventions and treatments.