Towards new approaches for studying personalized gut microbiota and host-microbe interactions

Human gastrointestinal tract is complex and highly dynamic environment, harboring trillions of microbes that collectively play a pivotal role in host metabolism, immune function, and the maintenance of general health. However, studying the gut microbes and their interplay with host requires measurements at multiple dimensions is challenging since we currently lack the tools to directly measure these microorganisms at many different levels, which hinders our ability to unravel the ecology of gut microbes and their mechanistic underpinnings in human health and disease. Here, I present a set of novel techniques to study gut microbe and host-microbe interactions at unprecedented resolution, providing tremendous innovative insights to comprehensively understand the gut microbes and their environment. First, I leverage a high-throughput automation system to build a machine learning guided culturomics platform, enabling rapid isolation and culturing of personalized gut strains. Second, to better characterize the functions of these non-model microorganisms, I describe a ribonuclease-based ribosomal RNA depletion approach for microbe, paving the way for high-throughput bacterial transcripto