Kiny says crohn's is not an autoimmune disease, but I was told by my Dr.'s that it was. (NOTE: My Drs. are very short on time and my GI Dr. is relatively uncommunative.) I was also under the impression that the problem with one's gut who has crohn's is that it lacks the proper bacteria to digest efficiently.
I think there are facts, which I and others put online many times:
http://www.ncbi.nlm.nih.gov/pubmed/19437144
http://www.ncbi.nlm.nih.gov/pubmed/20594136
http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2810%2960282-6/fulltext
And then there are the people and many GI who don't use facts and say things like "crohn's disease is a disease that attacks the intestine", which is completely wrong.
The inflammation is directed at gut lumen content, all tests, ASCA, AIEC, MAP, OmpC which is a reaction against E Coli outer membrane, all of them are directed at content in the intestine, none are directed at self-antigens. Autoimmune means they need to find autoantibodies, self-antigens, they have found NONE. What they do find is reactions against pathogenic and potential pathogenic bacteria, all the time, hell half the blood tests are looking for those things.
The immune system being overreactive is a nice theory but it's not founded in evidence, NOD2 and ATGL16 mutations results in a lowered initial immune response.
People talk about vitamin D all the time on the forum, if we have an overreactive immune system, vitamin D would be horrible for us, vitamin D stimulates human beta-defensin 2, it can partly correct issues with NOD2 and ATG16L1 and autophagy. Vitamin D helps the innate immune system and is able to stimulate NOD2, which is mutated in a number of crohn's disease patients. Even for the people without NOD2 mutation, vitamin D helps the innate immune system to deal with pathogens, which is why vitamin D and vitamin A are lauded for their antimicrobial properties.
Doctors and online resources have started to repeat this myth year after year, not a single study shows that's actually what's going on, in fact most studies if you actually start reading them, either never speak about autoimmune disease or point out that to this day there is no evidence that crohn's disease is an autoimmune disease, in fact the evidence there is, shows it's anything but an autoimmune disease. The best theory founded on evidence is that the body can not deal with gut lumen content because of macrophage deficiences, deficiencies in autophagy and bacterial recognition. It also easily explains why most crohn's disease patients with active disease have lesions in the terminal ileum, it's likely because bacterial load is extremely high there.
It also explains the high number of crohn's disease patients with terminal ileum involvement, who have strictures, don't respond to medicine anymore, called refractory patients, put them on antibiotics and many improve and even the strictures even improve in some, bacterial load increases in people with strictures, bacterial load becomes extremely high and they become refractory, give them antibiotics and they improve.
Which is also the reason why broad spectrum antibiotics that can penetrate macrophages like cipro, clarithromycin, rifampicin and others are able to induce short or long term remission, because they can correct where the immune system skipped a beat. If crohn's disease was an autoimmune disease directed at self-antigens, antibiotics would do literally nothing, that's not what happens at all, while antibiotics are not a cure, they do for a substantial amount of people result in temporary or long-term remission.