Fig. 1

A vision for the future: knowledge of the microbiome can lead to better predictions of drug response. a Currently, most medications are prescribed in a trial-and-error fashion. It has been estimated that only 30–65 % of patients respond to most drugs [5]. Non-responders need to undergo iterative rounds of trial-and-error treatments before physicians and patients arrive at an adequate drug regimen that treats disease. b Human genome sequencing has enabled physicians to predict responses to medication based on host genotype. However, this is routine clinical practice for only a few drugs and there is still considerable room to improve our predictions. c We envision a future where combined information from a person’s genome (or epigenome, proteome, metabolome) and microbiome will be used to predict the best treatment for patients. These predictions will enable tailored therapy that reduces the amount of time that patients suffer and likelihood of developing adverse effects from therapy