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Once the nutrients have been transported into the bloodstream they are ushered into a large vein called the portal vein which flows into the liver and branches out into numerous capillaries. From this blood, cells in the liver begin to filter out the nutrients, processing them either to be sent out to cells in the rest of the body or to be stored in the liver for future use. Amino acids are reformed into new protein configurations and rereleased into the blood. Sugars that are not needed by the body at the moment are hooked together to create huge storage molecules called glycogen. When the liver is in a healthy condition, sugars are readily processed then released or stored while sugar content of the blood remains at a constant level. If the liver is not functioning properly, however, sugars may not be modified appropriately and can flood into the bloodstream unprocessed.

The liver not only processes nutrients but must detoxify all the harmful substances the villi were unable to prevent from being absorbed into the bloodstream. Other situations that can tax the liver considerably include overeating and eating foods that are refined. Refined foods are missing the nutrients they need to be properly metabolized. If the liver can no longer filter and cleanse the blood, or properly metabolize nutrients, or take care of its own health, it is because liver cells are damaged or begin to die. Liver damage is not easily detected by conventional testing and its condition may not be known until dysfunction becomes apparent through illness. Symptoms may range from headache, diarrhea, constipation, food sensitivities, flatulence, sleeplessness, and aching joints to cirrhosis and hepatitis.

On the lower right-hand side of the abdomen, the small intestine ends and the large intestine, or colon, begins via the ileocecal valve. The colon is mainly for elimination and contains a thriving population of bacteria. Most nutrients have been removed and what remains is fiber and water, which is soon absorbed. Bacteria, while simultaneously feeding on the food mass, begin to break down the tough fiber molecules, creating an appropriate texture for elimination.

The kinds of bacteria found in the colon determine what effects the last stage of the digestion process will have on health. A predominance of beneficial bacteria will protect the lining of the intestinal tract from damage and irritation or infection that can be caused by undesirable bacteria, and will detoxify or neutralize any harmful substances. A diet that includes plenty of whole grains, legumes, fruits, vegetables, and fermented products like miso, soy sauce, and yogurt or acidophilus encourage growth of these beneficial bacteria. They in turn exert their considerable influence in keeping the colon in a healthy and vibrant condition.

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