I'm no doctor but this is what I've learned by talking to doctors and doing my own research. As you already know, there's all different types of bacteria in the stomach/intestinal tract. Most of us have one bad one in our systems called Clostridium Difficile (aka C Diff). Our good bacteria keep this thing in line. However, over the last decade, this particular bacteria is becoming a problem in people for one very simple reason (which is precisely what happened to me). That reason is the rampant over use of powerful antibiotics. You go in to the doc with a simple sinus infection and get a script for Augmentin and take it for 10 days. Maybe it doesn't fully kick the infection so you get another 10 day script (entirely normal) and it's killing the good bacteria and, sometimes and in some people, the C Diff sees this as an opportunity and it rises up. It takes over. It causes the exact symptoms I had. The above scenario is exactly how I got in this situation.
Now I have all kinds of dietary issues to begin with. I'm diagnosed Celiacs, I'm highly allergic to dyes and certain additives that are in many foods, and high FODMAP food items (think very high fructose corn syrup) can really make me sick. If I eat an apple I'll be sick in 10 minutes. Certs breath mints (even two) make me sick for days (it's the dyes and additives in them). Minus the Celiacs, which I was diagnosed with about 4 years ago, I've had to figure this all out pretty much on my own over the last 3 years. I have very much become an advocate (for me) in the use of Eastern medicine (use of acupuncture and herbs to treat things as well as food). Eastern medicinal philosophy believes that the gut is the center for all good health. When the gut is in check, the rest of the body can fall in line but when it's not, you see other issues because it's all connected.
My primary care doctor (who I don't see very often at all anymore because I don't believe in his practices and I'm shopping for a new one if I go to one any longer at all) should have been telling me to overload my system with good bacteria while taking the antibiotics and that would have greatly reduced the likelihood of the C Diff going rogue. Since I've been out of the hospital, I take a particular capsule of probiotic twice a day that contains particular strains of bacteria that need to be in the body for the gut to be happy, and I intentionally eat foods such as ginger and sauerkraut (raw only as cooking it kills what I'm after) daily. Turmeric powder is also excellent and I use it on food like it's my job.
For someone who has already had a bout of C Diff, the risk of it happening again is huge. If I take another round of antibiotics (even two years down the road for a cut) I have a 33% chance for a relapse. After that it's 50%. It keeps going up from there. It's awful stuff and it's bad news. I'm gonna leave it at that because if I start talking more about what could happen I do tend to spin a bit. It's scary.