The developing digestive system of the embryonic and larval zebrafish is a well-established model system for the study of vertebrate gastrointestinal physiology and metabolism. Metabolic and regulatory pathways for gastrointestinal system development, intestinal and liver cell differentiation, digestion, and nutrient uptake and transport are highly conserved between zebrafish and humans (1–7). The functional regionalization of the intestine also appears to be conserved among vertebrates including zebrafish with respect to transcription factor expression in epithelial cells over the length of the intestine (8). Additionally, the transparency of the developing larva makes it ideal for live imaging experiments: The larval zebrafish has a functional and visible liver, pancreas, gallbladder, intestine, and intestinal microbiota by 5 days post-fertilization (dpf) when it begins to feed. The zebrafish is also suitable for large-scale and high-throughput experiments due to its small size and high fertility (a single pair can produce hundreds of embryos in a day). Finally, as the importance of the gut microbiome to studies of nutritional physiology is becoming increasingly clear; the larval zebrafish microbiota are well-characterized, and germ-free and gnotobiotic models are available (9).