Based on the research of others and my own amatuer research, I think the most likely culprit in many so called autoimmune diseases is the presence of one or more strains of mycoplasma. In particular mycoplasma fermentans and/or mycoplasma pneumonia.
While many people can have these bacterium in small amounts with no consequences, they are opportunistic. Under the right circumstances they can take off and invade different areas of the body in large numbers. When they take to the intestines then that starts an autoimmune type response in the normal defenses present are no longer effective due to the mycoplasma altering rhe immune response.
I think this starts the cascade of other pathogens to take hold and increase in large numbers such as MAP, H-Pylori, AIEC, and others.
Of course I could be wrong, but it is the hypothesis that makes the most sense to me.
Dan