The urinary microbiome: the next frontier of bacterial ecology

The human urinary tract, once presumed to be sterile, has emerged as a new frontier of microbial ecology. Recent advancements in high-throughput sequencing technologies have revealed the complexity and diversity of microbial communities that reside within the urinary tract. This mini-review discusses the prominent bacteria identified in the urinary microbiome and their correlations with various urologic conditions. This review serves to summarize the current state of urobiome research and chart a path for ongoing discovery. Additionally, we address the methodological challenges in urinary microbiome research, emphasizing the need for standardization in study protocols and the refinement of bioinformatics tools. We highlight that although differences in urobiome composition have been described for various urologic diseases. Similarly, the pathophysiologic source and consequences of those differences remain uncertain. We outline the steps to move urobiome research from descriptive to mechanistic studies, emphasizing rigorous study design, integrating multi-omics approaches, and developing robust model systems for experimental investigation. Finally, we outline critical questions for future investigation aimed at elucidating the intricate connections between the urinary microbiome and host health.