We are all covered in bacteria. (You could even say we are all contaminated.) Bacteria and other microorganisms live in our gut, in our mucous membranes such as our nostrils, on our eyelashes, and in our bellybuttons. We do not consider ourselves infected, however, because these organisms have not crossed the barrier of our skin to enter our tissues, muscles, bones, and body cavities. These deep parts of our bodies are basically sterile - no microorganisms live there at all. As long as our protective barriers are not breached, we remain healthy. The "contamination" is just part of our microbiome, our own personal little collection of life that we carry around with us all the time. This microbiome is made up of colonies of bacteria, groups of same-species bacteria that live and die without our even being aware of them.