You do realise that something like 50% of your gut contents is bacteria, don't you. And that the air we breath with every breath contains myriads of bacteria, fungus and protozoan spores. The surface of any food you eat is likely to have zillions of microbes in it.
The vast, vast majority of microbes are either harmless or beneficial. Only a tiny percent are harmful, and these ones are generally transmitted from person to person, such as influenza and gastro, and STDs.
The moral of the story is to wash your hands when you have been in public places, if your hand didn't touch anything that other people have put their germs on, then your water will be OK.