Recently, increasing evidences have shown that the abnormal inflammatory response, which can be from chronic gut dysfunction, chronic infection other toxic exposures or sometimes genetics are closely associated with many chronic diseases, especially autoimmune diseases, including rheumatoid arthritis (RA), inflammatory bowel disease (IBD), systemic lupus erythematosus (SLE), gout, and diabetes to name a few.

Thus, the gut pyramid obviously plays a large role in inflammation and autoimmunity.  A huge proportion of your immune system is actually in your GI tract.  The interaction of the gut and immune cells causes a secretion of massive of quantities of antibodies into the gut over time creating immune regulation issues and auto immunity.

The longer chronic inflammation and auto immunity are allowed to go uncontrolled, according to the studies and data, the risk seems to increase of other chronic diseases as listed above as well as being linked to some cancers. 

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