Her research focuses on the complex community of microorganisms that inhabit the human body (the microbiota), particularly in the gastrointestinal tract. She has been heavily involved in the development of very popular computational tools for microbial community analysis, such as the UniFrac algorithm for comparing microbial diversity among many samples using phylogenetic information. Her substantial publication record in human microbiota research includes studies of the relationship between gut microbiota composition and age, culture, diet, obesity, and inflammatory bowel diseases.