What happens when the microbes that keep us healthy disappear?

Source Scientific American

Bacteria, viruses and fungi have been primarily cast as the villains in the battle for better human health. But a growing community of researchers is sounding the warning that many of these microscopic guests are really ancient allies. Having evolved along with the human species, most of the miniscule beasties that live in and on us are actually helping to keep us healthy, just as our well-being promotes theirs. In fact, some researchers think of our bodies as superorganisms, rather than one organism teeming with hordes of subordinate invertebrates. The human body has some 10 trillion human cells"but 10 times that number of microbial cells. So what happens when such an important part of our bodies goes missing?