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...
Velasquez-Manoff on Autoimmune Disease, Parasites, and Complexity: http://www.econtalk.org/archives/2014/03/velasquez-manof.htm...
http://www.amazon.com/Epidemic-Absence-Understanding-Allergi...
[1] http://www.amazon.com/Epidemic-Absence-Understanding-Allergi...
Podcast introduction from Chris Kresser: http://chriskresser.com/what-are-the-hidden-costs-of-modern-...
Amazon link: http://www.amazon.com/dp/1439199388?tag=chrikres-20&link_cod...
https://www.amazon.com/Epidemic-Absence-Understanding-Allerg...
Edit: I read a more recent article about the guy, and it said he subsequently backed off the idea after his allergies came back.