Through enzyme secretions, bacteria transform metabolic and microbial wastes before they are discharged by the body. These wastes include cellular debris, hormones, chemical wastes, bile, pus accumulations, viral toxins, bacterial toxins, etc.
For example, the body creates bile not only as a lubricant to flush wastes out of the liver, but also, to detoxify many of the poisons accumulating in the liver. Bile however is extremely damaging to large intestine epithelium.
When bile enters the small intestine via the common bile duct, beneficial bacteria break the bile salts down into a less toxic compound, making it non-dangerous by the time it reaches the large intestine.
When you take antibiotics you destroy these bacteria and the bile salts freely enter and damage the large intestine. I believe this contributes significantly to the high incidence of colon cancer plaguing today's society.
Beneficial bacteria also break down hormone secretions that are discharged from the liver to the small intestine. If you lack the bacteria to break down estrogen and the intestinal permeability has been altered, the patient is now reabsorbing estrogens in their original state.
The body will deposit these in estrogen sensitive areas such as the breast, uterus, or ovaries, contributing, if not causing, fibroids and tumors. The same scenario is responsible for premenstrual syndrome as well.
Healthy mucosa allows nutrients to pass the barrier while blocking the entry of toxins.
With leaky gut, the barrier is dysfunctional, blocking nutrients at the damaged villi while permitting toxins to enter the blood stream.