Research

Microbial regulation of intestinal epithelial gene transcription Mechanisms of intestinal repair and inflammation

Microbial regulation of host nutrient metabolism Developmental and environmental control of adipose tissue

Mechanisms underlying bacterial fitness in the intestine

Overview
Our research defines the integrative physiology of the intestine as a central organ system coordinating metabolism, immunity, and systemic homeostasis in response to microbial and nutritional inputs. Using complementary zebrafish and mouse models, we investigate how intestinal epithelial, endocrine, and immune programs are integrated to accurately interpret environmental cues. This work has uncovered evolutionarily conserved transcriptional regulatory networks that govern epithelial gene expression, nutrient absorption, bile acid metabolism, and inflammation, revealing how intestinal tissues integrate microbial signals to inform dietary nutrient assimilation, systemic innate immunity, and gut–brain communication. In parallel, we examine how intestinal physiology shapes microbial ecology, including genetic studies in prevalent gut bacteria to understand the genes, pathways, and metabolites that govern their colonization and fitness within the gut. Together, our research program is revealing how the intestine integrates microbial, dietary, developmental, and inflammatory signals to maintain organismal equilibrium. These insights are advancing our understanding of intestinal biology and host-microbiome symbiosis, and identifying novel therapeutic targets for human diseases ranging from inflammatory bowel disease to obesity to neurological disorders.