Harnessing the global urban microbiome for the future of cities

Cities are as biological as they are architectural. Beyond the surface of each city lies an infrastructure of urban microbes and biology which play key roles in our health and development. However, these microbial ecosystems remain largely invisible to urban planners, designers, and public health teams. Rapid environmental DNA sequencing now enables us to monitor the microbial (and eukaryotic) life of cities in near real time, transforming our understanding of urban ecology and evolutionary dynamics, while providing novel tools for public health. Projects such as MetaSUB have revealed that each city possesses a distinct microbial fingerprint, with measurable implications for outbreak detection, infection control, and disease risk. Despite the insights gained to date, major gaps persist including inconsistent sampling methods across studies, geographic disparities, and a divide between environmental and clinical microbiology. Bridging these gaps requires a significant reframing of microbial life as a core asset of urban infrastructure in city design, healthcare systems, and sustainability initiatives. We outline a roadmap for building microbiome-informed cities, emphasizing routine microbial surveillance, clinical integration, while advancing microbial literacy among city planners, health professionals, and urban residents. Cities of the future will be judged not only by factors such as their air and water quality, but also by the sustainability of their urban microbiomes and by our ability to harness them to design healthy urban landscapes for both the microscopic and macroscopic residents.