Advances in genome sequencing technologies, like next-generation sequencing, provide powerful tools that have vastly improved the detection and classification of pathogens and disease outbreaks and support data-driven public health responses. In July 2024, the National Academies Forum on Microbial Threats hosted a public workshop to explore opportunities to advance the use of pathogen genomics and metagenomics data in the U.S. public health system. Speakers considered the application of these technologies to monitoring disease, characterization of emerging pathogens, rapid public health response to outbreaks, and biomedical research.