Microbial Systems and Human Interfaces (MSHI) Lab

The challenge

Current microbiome research is largely descriptive and fails to capture the functional logic of microbial systems. Microorganisms act as coordinated communities that communicate through structured signaling networks – including quorum sensing molecules and bacterial extracellular vesicles (BEVs) – yet these signals remain largely undefined in human disease.

A key challenge is understanding how microbial communication interacts with host barrier interfaces and propagates across tissues to shape systemic outcomes, particularly in inflammatory bowel disease, early-onset colorectal cancer, and gut–brain disorders.

Our research addresses this gap by reframing the microbiota as microbiology at a different resolution. We focus on identifying, mapping, and ultimately reprogramming microbial signals to uncover causal mechanisms and develop actionable biomarkers and therapeutic strategies.

Main research areas

Human-centered multi-omics and microbial communication systems

We use deeply phenotyped clinical cohorts to identify microbial communication signals — including quorum sensing molecules, metabolites, and bacterial extracellular vesicles (BEVs) — associated with disease trajectories in inflammatory bowel disease (IBD), early-onset colorectal cancer (EO-CRC), and extraintestinal manifestations such as anxiety and depression.
We integrate multi-omics across compartments to define functional microbial networks beyond compositional descriptions.

Microbial signal tropism

We map signal tropism across tissues to define how microbial communication propagates systemically and influences brain and tumor responses.

Microbial rewiring of communication networks

We develop strategies to reprogram microbial communication by modulating quorum sensing, metabolism, and vesicle production.
Our goal is to shift microbial communities from disease-associated states to functional configurations with therapeutic potential.

BEVs as liquid biopsy of microbial functional states and biofilm dynamics

We investigate bacterial extracellular vesicles as accessible readouts of microbial communication and biofilm-associated states.
By capturing vesicle-derived signals in biological fluids, we develop liquid biopsy approaches to monitor microbial activity, detect functional dysbiosis, and track disease progression or response to therapy.