Community profiling of the urinary microbiota: Methodological considerations for low microbial biomass biological samples

Many recent studies have now shown that even under healthy conditions, the bladder and urinary tract harbors its own microbial community, collectively known as the urinary microbiota. This contradicts the long held notion that urine is a sterile environment in the absence of an acute infection. Given this relatively new discovery, many basic questions which are critical for our understanding of the role that the urinary microbiota plays in human health and disease remain unanswered. As this is an emerging area of study, optimized techniques and protocols to identify microorganisms in the urinary tract are still being established. This is made more challenging for the urinary microbiota given its low microbial biomass. A clear understanding of the unique technical considerations of low microbial biomass samples, as well the impact of key elements of experimental design and computational analysis on downstream interpretation will improve the interpretability and comparability of results across methods and studies both for the urinary microbiota as well as other sites of low microbial abundance.