Twiggs: You are right in the fact that there is a reason for everything, sometimes medical science just doesn't know what the reason is yet. You are wrong when you say that any time medical science doesn't know the why they just label it an autoimmune disease. There are many autoimmune diseases and they actually have scientific evidence for them that our immune systems begin attacking parts of the body that they shouldn't be. They have theories as to why but no hard proof. With this evidence they determined that weakening our immune systems with meds should help with the autoimmune disease and they were right because it does and there is proof of that. If it wasn't an autoimmune disease then weakening the immune system would probably not work. This could mean that in some UC cases and other "autoimmune diseases" where weakening the immune system did not work, it is possible that the disease is not autoimmune - like maybe our colitis is actually C-Diff instead and was misdiagnosed.
My first autoimmune disease was ITP. ITP is a disease where somehow your body has been tricked into forming antibodies to our blood platelets instead of to a virus. There is actually proof that these antibodies attach to the person's platelets, signaling the body's immune systems to attack and kill the platelets, causing seriously and extremely dangerous low platelet counts. They don't know why this happens, only theories, but they do have proof that this is what is happening. One of the leading theories is that you get a virus, and part of the virus's DNA closely matches part of the DNA of your platelets and your immune system gets confused and kills off both the virus and the platelets. When the virus has been killed off your body continues to fight the platelets in a never ending battle (sometimes the virus is never killed off). Your body makes thousands of new platelets every day but it does not make them at the same rate that your immune system is killing them off.
Now with actual UC cases they know that something similar is going on, but again don't know the why. There are several theories. I'll give you my thought process for my particular case. There may be different reasons for each person's individual case but I believe in my case that high dose antibiotics caused a virus or bacteria in my colon to create a biofilm to hide behind on my intestinal walls in order to avoid my immune system's attack. There is scientific evidence that this happens and that biofilms are very good at shielding the virus or bacteria from that attack. But, my immune system knows that the virus or bacteria is there and continually attacks the biofilm (unsuccessfully) in order to get to the virus or bacteria. Unfortunately for me that attack inflames my intestinal wall, causing my UC. One of the questions is which virus or bacteria is my immune system trying to kill? Is it one that if killed successfully, would my UC finally be over? And, if I ever get that same virus or bacteria again, will I get UC all over again? Or, is it a virus or bacteria that is always in my colon anyway (maybe even a "good" bacteria that is always present) and I have no chance of ever completely killing it off?
Mackster has a very good point about mutated viruses and bacteria.