Research into the gut microbiota and its role in health and disease has expanded rapidly in the past two decades. However, much of the early focus has been on cataloguing the microorganisms present, identifying correlations between microbial species and disease and using preclinical animal models to understand phenotypes. Now efforts are under way to provide functional insights into the gut microbiota and its mechanisms of action, improve understanding of the role of the microbiota beyond the gut and advance the development of microbiota-based therapeutics so that the microbiome can be harnessed in the clinic. In this Viewpoint article, we asked a selection of scientists and clinicians working in the gut microbiome field for their opinions on the major advances in and the challenges and solutions for translating gut microbiome research to the clinic, and where they expect progress to be made in the future.