
A controversial, revisionist approach to autoimmune and allergic disorders considers the perspective that the human immune system has been disabled by twentieth-century hygiene and medical practices.
To learn more about auto-immune diseases and gut bacteria, I highly recommend the book An Epidemic of Absence [2]. It's an impressively well researched book that doesn't skimp on the science.
I managed to get my eczema under control by learning about the relationship between gut, food, inflammation, and auto-immunity.
[1]: https://scholar.google.com/scholar?q=multiple+sclerosis+gut+...
[2]: https://www.amazon.com/Epidemic-Absence-Understanding-Allerg...
My takeaway was that there's clearly stuff happening here, but the research is still very much in its infancy, so it's hard to be too confident about any one claim.
http://smile.amazon.com/Epidemic-Absence-Understanding-Aller...
[1] http://www.amazon.com/Epidemic-Absence-Understanding-Allergi...
There was a good discussion of "An Epidemic of Absence", a recent book on the topic, on EconTalk this week. The basic premise is that these disorders may be caused by a lack of microbes and parasites in the modern Western world. The lack of those microbes and parasites causes our immune systems to be overly aggressive towards harmless outside substances (peanut allergies, celiac disease) or mistakenly aggressive towards our own bodies (Crohn's disease, type I diabetes, etc.)
Sounds very plausible to me, but it lacks a villain, which I think makes it an unsatisfactory explanation for some.
http://www.econtalk.org/archives/2014/03/velasquez-manof.htm...
