Prostate disease is ubiquitous in aging men. Prostate disease includes BPH, PC, and prostatitis, and these diseases share many symptoms such as lower urinary tract symptoms (LUTS) and blood in urine. There have been efforts to develop better prostate disease tests, including interrogating the composition of bacteria in urine and in blood. In this dissertation, we evaluated the urinary microbiome and its relationships with LUTS and prostate disease in a large cohort of men, evaluated microbial DNA in fractions of blood of men with PC, and benchmarked microbiome analysis methods.