Questions and challenges associated with studying the microbiome of the urinary tract.

Urologists are typically faced with clinical situations for which the microbiome may have been a contributing factor. Clinicians have a good understanding regarding the role of bacteria related to issues such as antibiotic resistance; however, they generally have a limited grasp of how the microbiome may relate to urological issues. The largest part of the human microbiome is situated in the gastrointestinal tract, and though this is mostly separated from the urinary system, bacterial dissemination and metabolic output by this community is thought to have a significant influence on urological conditions. Sites within the urogenital system that were once considered "sterile" may regularly have bacterial populations present. The health implications potentially extend all the way to the kidneys. This could affect urinary tract infections, bladder cancer, urinary incontinence and related conditions including the formation of kidney stones. Given the sensitivity of the methodologies employed, and the large potential for contamination when working with low abundance microbiomes, meticulous care in the analyses of urological samples at various sites is required. This review highlights the opportunities for urinary microbiome investigations and our experience in working with these low abundance samples in the urinary tract.