1. How does an animal establish and regulate its gut microbiome? We recently identified a physical niche structure in the fly gut that houses specific bacterial symbionts. We examine the fly genetics of gut symbiosis including the construction of the microbial niche.
 
2. Gut microbial ecology modulates fly health. Using gnotobiotic flies and a battery of physiological and fitness assays, we study the effects of gut microbial community ecology on host cell physiology. 
 
3. Metabolic crossfeeding influences community ecology of the gut microbiota. Using both gnotobiotic flies and high throughput in vitro growth assays, we study the microbial interactions that shape the fly gut microbiota.
 
4. Real time study of colonization dynamics. We have developed single fly feeding and live fly microscopy techniques to measure microbial populations in the gut. These approaches allow us to visualize the process of gut colonization in real time to understand how the fly gut selects the correct bacterial species for colonization.