An oft-repeated (and oft-misinterpreted) fact is that there are ten times more bacterial cells found in the human body than there are actual human cells. While this doesn't really make us "mostly bacteria" in the factoid sense pushed by cherry pickers like Michael Pollan, it does mean that our own health is impacted in powerful and poorly understood ways by the happenings of these colonies of non-virulent microorganisms. Collectively, these colonies are considered by some researchers to be a sort of forgotten organ or "virtual" organ, with gut flora doing some of the heavy lifting of (at least) the body's immune and digestive systems, while demonstrating metabolic activity roughly equal to a proper organ-organ.
It's tempting to look at bacteria as a kind of binary realm, with "good" and the "bad" sorts that have good and bad impacts on health, when it's really not that easy. Our own personal bacterial flora might help keep harmful bacteria at bay through competitive pressure, but the goodness of these tiny helpers is less a function of benevolence than geography—set them loose elsewhere in the body, beyond the inner-outside of the digestive tract, and very bad things will happen. A different set of bad things awaits a host with just a bit too much or too little friendly bacteria, ranging from cancer to inflammatory bowel diseases. While it's possible to live without gut flora, such an existence portends a wide variety of troubles.
For the rest of the story: http://motherboard.vice.com/read/when-bad-bacteria-make-good-bacteria-sick