Joe Lim

I am a postdoctoral fellow at the Institute for Systems Biology (ISB). I earned my MS and PhD
in Environmental Toxicology in Dr. Julia Cui’s lab and an additional MS in Applied
Mathematics from the University of Washington (UW). My doctoral research investigated the
systems level interactions across metabolic organs (e.g., gut microbiome, liver). The goal of my
work was to understand how the exposure to certain persistent organic pollutants during critical
developmental windows affect liver cell types, and how this is modulated by the changes in gut
microbiome. I developed cell isolation methods and applied single cell RNA sequencing
methods for multiple organs (e.g., liver, large intestine, brain) and built in-house pipelines for
multiomics data integration to explore these topics.

Currently, my research centers around how environmental factors like diet shape the evolution of
commensal gut microbes across human populations. By integrating dietary and nutritional
information from gut metagenomes, along with microbial signatures of adaptation (e.g.,
horizontal gene transfer, selective sweeps), my work aims to test how dietary patterns exert
evolutionary pressures on gut microbes. Using a reverse ecology framework, I aim to uncover
how environmental pressures drive microbial evolution and how this knowledge can be applied
to promote microbial and human health in the face of environmental exposures.

Outside of the lab, I enjoy cooking various cuisines, beer tasting, biking, and spending time with
family.