More than a decade after the launch of the Human Microbiome Project, research in this field has grown exponentially, with studies associating microbial states or species with disorders including novel infectious etiologies and complex human disease. Scientists are searching for the potential utility of the microbiome (the community of bacteria, fungi, and viruses in an environment), with particular focus on manipulating microbial communities as novel therapeutic modalities. This Viewpoint highlights current applications of microbiome science to human health and examines successes and remaining challenges.