The Poop Outlaws: At-Home Fecal Transplants to Cure Disease

"The human body, consisting of about 100 trillion cells, carries about ten times as many microorganisms in the intestines." http://en.wikipedia.org/wiki/Gut_flora

Since evolution shaped us this way I suggest these bacteria are important. I'm not surprised that there are negative side effects if antibiotics happen to kill some of the species.