Given that we swim in a sea of microbes, and there are approximately twice as many microbes as human cells in/on the average human, and we would get sick and die if this wasn't so, I don't worry much. There is no such thing as sterile anywhere near humans.

The key is to avoid colonies of disease causing microbes getting into or onto areas of the body where they might take up housekeeping and cause problems. One thing to remember is that microbes are very particular where they can live and thrive. The fungus that causes athlete's foot doesn't often take up resident in the crotch. And the fungus causing crotch corrosion doesn't like toes. And neither of them survive for long inside a healthy human body.

We have to keep in mind that long before humans understood germs and started to take steps to avoid contamination people lived pretty well and even when great diseases were around most people survived. Before the 1800s surgeons generally only washed their hands after surgery. For thousands of years people accepted, and most survived, even as a small proportion got sick, with a certain amount of raw sewage in their drinking water. Water was 'good' if it tasted and looked clean. For thousands of years people didn't understand disease and made up this deficiency with accusations of divine displeasure, witchcraft, and evil spirits.

The Greeks, Romans, Inca, and Chinese had functional knowledge of the need to keep sewage and contaminates away from drinking water. The western world forgot most of what it had learned from previous civilizations and started from scratch. It wasn't until 1854 for there to be an objective study of cholera to develop the modern understanding of epidemiology in relation to water supplies.

In a nutshell Snow noticed most cholera cases were in people who were getting their drinking water from a particular well. He stopped people from using that well by removing the handle and the number of cholera cases fell markedly. An experiment that showed that the prevailing view of the origins of cholera was wrong.

http://en.wikipedia.org/wiki/John_Snow_%28physician%29

This seems very old-hat, gee ... everyone knows you don't poop where you drink, but you have to remember that the germ theory of disease was not established at the time so if the water looked and smelled okay people assumed it was safe.

http://en.wikipedia.org/wiki/Germ_theory_of_disease