A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment
March 16 @ 1:00 pm – 2:00 pm
Statistical Bioinformatics Seminar
Speaker: Bokai Zhu, MIT
This is an online event held via Zoom: https://uni-sydney.zoom.us/j/85114748391
The intricate interactions between the host immune system and its microbiome constituents undergo dynamic shifts in response to perturbations to the intestinal tissue environment. Our ability to study these events on the systems level is significantly limited by in situ approaches capable of generating simultaneous insights from both host and microbial communities. Here, we introduce Microbiome Cartography (MicroCart), a framework for simultaneous in situ probing of host and microbiome across multiple spatial modalities. We demonstrate MicroCart by investigating gut host and microbiome changes in a murine colitis model, using spatial proteomics, transcriptomics, and glycomics. Our findings reveal a global but systematic transformation in tissue immune responses, encompassing tissue-level remodeling in response to host immune and epithelial cell state perturbations, bacterial population shifts, localized inflammatory responses, and metabolic process alterations during colitis. MicroCart enables a deep investigation of the intricate interplay between the host tissue and its microbiome with spatial multi-omics.
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Bokai Zhu
I am currently a postdoctoral researcher at MIT under the supervision of Professor Alex Shalek. I received my PhD from the Department of Microbiology and Immunology at Stanford University, where I trained with Professor Garry Nolan. My research focuses on integrating experimental and computational approaches in systems immunology to study tissue biology in disease contexts. On the computational side, I develop algorithms for cross-modality single-cell data integration; on the experimental side, I develop multiplex imaging assays to detect viruses and microbiota within complex host–tissue environments. This interdisciplinary training has equipped me with complementary skill sets spanning molecular method development, animal models, clinically relevant sample analysis, and rigorous statistical and mathematical modeling. Working at the interface of computation and experimentation has enabled me to initiate and lead collaborative projects across institutions including MIT, Stanford, Harvard, and Yale, collaborating closely with both early-career and established investigators.
Connect with Bokai
@ZhuBokai
https://bokaizhu.github.io/