A stool culture is a test used to identify and locate the bacteria that infect the lower digestive system. The test distinguishes between bacteria that cause disease and those that are generally common in the gastrointestinal system (normal flora). In essence, a urine culture test is performed to determine whether any microorganisms exist in the urine that may cause an infection. No germs, microbes, or bacteria are present in urine on their own, but the bacteria usually enters the urethra from the urinary tract and causes an infection.