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Researchers are only now discovering the incredible array of bacteria that live in our mouths, our gut, our airways and on our skin. And then there are the fungi that normally live in our gut tube: apparently these self same fungi will "appear" in the vagina of pregnant women because there is a need for them in the soon-to-be-delivered baby who will need these "milk-splitting" organisms to help them absorb the proteins found in maternal milk. In non-pregnant women, these fungi are not found in the vagina.
Then there are bacteria teeming on our skin. These feed on the sebum produced by our skin cells and which then produce a film that helps to "water-proof" it. Meanwhile in the gut there are essential bacteria that help with the absorption of important vitamins and without which we'd all suffer serious deficiency syndromes. As for viruses, the experts are only now looking at what these "friendly" viruses do as they do invade our cells, but for what purpose is still not clear. They might have a role in priming our cell mediated immunity, but much more research needs to be done before the picture becomes clear.
The important point for this evolving field is that when we use "Broad Spectrum" antibiotics we actually destroy huge populations of these friendly bacteria and contrary to the long held assumption that they return after the antibiotics have been withdrawn, that might not actually be the case. Young children who have had repeated courses of antibiotics are at greater risk of developing immune system problems such as Eczema and Asthma - now thought to be associated with the loss of these gut based bacteria.
And in a quirky way of using this information to fight pathological infections, Doctors are already treating a nasty infection of the bowel caused by over use of antibiotics and and resulting in an "overgrowth" by a germ called C Difficile. They have found that the best way to treat this nasty bug is not with stronger antibiotics but to use a "Faecal Implant"! They take a sample of stool from a healthy person and give it via a suppository into the infected person and it "works like a dream". Now they are purifying the process to remove the "Yuk" factor, but the theory and practice are solid and so are the results!
The message here is that we need to think not twice, but long and hard every time we consider using antibiotics and what the collateral damage may be both in the short and in the longer term. We need to consider not only our biosphere, but the global biosphere too. You are more than you think you are!