In this review, we report on the factors conferring a healthy microbiome, applications in the urinary tract with urgency, urge incontinence, and urinary tract infection and interactions of the Gut-Brain Axis as they apply to multiple sclerosis. Clinical applications in the use of probiotics are briefly reviewed.; Information from the Human Microbiome Project has spurred exponential studies which have opened up exciting possibilities in many fields. Of particular interest is how these concepts apply to the study of microbes in the urinary tract, vagina, and intestines and how they interact not only with each other but also the brain.; The ways that microbes affect the lower urinary tract as well as overall wellbeing are currently being explored.