His research has investigated the role of the intestinal microbiota in intestinal diseases such as irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD). Currently, with the mentorship of Dr. Cynthia Bulik his research focuses on the role the gut microbiome plays in the pathogenesis and maintenance of anorexia nervosa (AN). He and his research team aim to determine the mechanisms through which specific members of the intestinal microbiota influence gastrointestinal physiology, nutrition, behavior, and weight regulation. Through collaborations resulting in a multi-disciplinary approach to scientific inquiry, Dr. Carroll hopes to contribute to understanding host-microbe interactions, where the knowledge gained can be applied to enhance health and reduce illness.