The above factors change the percentile composition of the flora and changes the environment of the mucosa. The villi (small fingers in intestinal lining used to absorb nutrients) are destroyed quicker than can be generated. This results in the villi being shorter than normal, become atrophied and dysfunctional. As a consequence, the IgA production is reduced thus reducing the defense system.   

With reduction of defenses, perforation of intestinal walls occurs (leaky gut). The bacteria and toxins once contained in the gut pass thru the perforations into the blood stream unchecked by body's defenses. This is the onset for chronic diseases and dysfunction of various systems. 

Some indicators of dysfunction due to pathologically altered state occurs at these weakest links: tonsils, malpositioned teeth, rhinitis, bronchitis, eczema, lumbago, arthritis, ADHD, migraine. 

While the nutritional function of gut may still be intact, the immunological competence is reduced. The milieu found in intestine is the inter-cellular communication that floats the cells where functional reactions take place. The milieu composition (internal physical environment) determines whether physiological or pathological reactions will take place. Our organs' elimination and defense maintain the milieu and sphere of homeostatic tolerance of various tissues.

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