Building the gut microbiome

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Bacteria hugely impact many aspects of our lives, including health, agriculture, industry, water treatment services, and the climate. Often, they live together in densely packed communities, where they can strongly interact with each other. In particular, the 'bacterial communities' living in our digestive tract are now known to be essential for our health and well-being, such as protecting us from harmful bacteria, improving our nutrition, and training our immune systems. Critically, changes in the community composition and structure can lead to chronic and life-threatening diseases. Therefore, we must understand how these bacteria interact with each other and ourselves if we want to unlock further health benefits available to us. However, it is extremely difficult to study and understand these bacterial communities, especially at the tiny scales at which they naturally occur. New methods are urgently needed to build simplified bacterial communities and their hosts, capturing the complex arrangements and interactions of different bacteria found within us. My goal is to build new tractable models - using 3D printing and flow systems - to study how the composition and structure of the community and the host determine how bacterial communities persist over time, and importantly, if they thrive or perish. I have chosen to work in this research area because I believe I can vastly improve our understanding of the link between the host, community structure, and community function by building simplified microbiome models. Importantly, the technologies and understanding I develop throughout this proposal will not only benefit human microbiome research, but microbial communities found throughout the environment.