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Translating the human microbiome in health and disease requires detailed information about each microbial member—from individual annotated genomes to community functional dynamics to relationships with the host. Toward this goal, phylogenetic descriptions of the microbiome are evolving into mechanistic analyses. Recent years have seen a dramatic rise in metagenomic and metabolomic studies using microbial-driven pathologies as models to understand host–microbiome interactions. These studies are charting community-wide ecological maps that provide insight into microbial determinants of health and disease, layering in impacts of the microbiome at different life stages. Although much is known about early microbiome development, trajectories during aging and later in life require further characterization. The microbiome impacts every organ system and aspect of physiology, often through as-yet-unknown mechanisms. Moreover, the influence of the microbiome extends beyond the local environment: neuroactive molecules produced by gut commensals reach the brain to mediate mood, depression, and mental illness [1]. Understanding the principles that govern a healthy microbiome establishes a framework for interrogating perturbations associated with disease or diet and for developing interventional strategies. Unlike the genome, the microbiome is a dynamic reflection of health status that can be modified and, therefore, represents a largely untapped reservoir of opportunity to understand and exploit mechanisms that influence human physiology. This special issue of Genome Medicine highlights the advances made in understanding strain diversity, microbial biochemistry, disease risk, and clinical outcomes. In this Editorial, I highlight key areas and recent progress that has been made in the field toward translating the microbiome and defining the many pathways that modulate host biology.

Translating the human microbiome: a path to improving health