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Speaker: Katherine Xue, PhD
Postdoctoral Researcher
Stanford University


Talk title: Ecology of colonization in the human gut microbiome


Abstract: Humans constantly encounter new microbes, but very few of these new microbes become long-term residents of the human gut microbiome. To colonize the gut, new microbes must overcome barriers like environmental selection and ecological drift, and they must also compete successfully against resident microbes. These ecological barriers are poorly understood in the complex microbial communities of the human gut, making it challenging to predict the outcome of species introductions. My work investigates the ecological forces that shape colonization in the human gut microbiome by combining longitudinal, human studies with high-throughput experiments using in vitro gut microbial communities. First, I will discuss the results of a two-year study in which I used a controlled antibiotic perturbation to track the dynamics of colonization and transmission in human households. This work shows that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of ecological change in established communities. Next, I will discuss my development of a high-throughput platform of in vitro gut microbial communities, which I have used to conduct controlled colonization experiments. By combining these colonization experiments with consumer-resource models, I have shown that initial population size has stronger impacts on colonization outcomes in more diverse communities, when newly introduced species have high niche overlap with existing residents. This powerful combination of in vivo and in vitro approaches can shed light on fundamental questions in invasion ecology and accelerate the design of targeted microbiome therapeutics.

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