Dysbiosis Patterns

The four commonly recognized patterns of dysbiosis are putrefaction, fermentation, deficiency, and sensitization.


This is the most common type and occurs when food is not well digested, essentially rotting inside us. We may feel this as bloating, discomfort, and indigestion. The typical American high-fat, highanimal- protein, low-fiber diet predisposes people to putrefaction.

It causes an increase of bacteroides bacteria, a decrease in beneficial bifidobacteria, and an increase in bile production. Bacteroides cause vitamin B12 deficiency by uncoupling the B12 from the intrinsic factor necessary for its use. Other bacteria normally make vitamin B12 directly for their own purposes, but it too becomes unavailable to us.

The most common signs of B12 deficiencies are depression, diarrhea, fatigue, memory loss, numbing of hands and feet, sleep disturbances, and weakness. Vitamin B12 deficiency is commonly seen in older people because of poor hydrochloric acid (HCl) levels in the stomach.

Poor bifidobacteria levels decrease our body’s ability to resist infection, affect bowel health, and reflect a decreased production of B-complex vitamins. Research has implicated putrefaction dysbiosis with breast and colon cancer. Bacterial enzymes change bile acids into thirty-three substances formed in the colon that are tumor promoters.

Bacterial enzymes, such as betaglucuronidase, re-create estrogens that were already broken down. These estrogens are reabsorbed into the bloodstream, increasing estrogen levels and estrogen-dependent breast cancers. Putrefaction dysbiosis can be corrected by eating more high-fiber foods, fruits, vegetables, and grains and fewer meats and fats.


This is characterized by bloating, constipation, diarrhea, fatigue, and gas. People with fermentation dysbiosis have faulty digestion of carbohydrates: sugars, fruit, beer, wine, grains, and fiber. Fermentation of carbohydrates provides food for multiplying bacteria and produces hydrogen and carbon dioxide gases and shortchained fatty acids, all of which can be tested.

Fermentation dysbiosis is often characterized by flora that have been taken over by candida fungi or other disease-causing microbes. These microbes damage the intestinal brush borders (microvilli) and lead to increased intestinal permeability.

People with fermentation dysbiosis need to strictly avoid carbohydratecontaining foods. It is recommended that they receive therapeutic support to help regain bowel health. Up to 2,000 milligrams of citrus seed extract can be used daily. Use of probiotic supplements and repair of the intestinal mucosa are essential.


This is characterized by a lack of beneficial flora, such as bifidobacteria and lactobacillus. Use of antibiotics and low-fiber diets are the primary cause of poor flora. Deficiency dysbiosis is often seen in people with irritable bowel syndrome and food sensitivities.

Deficiency dysbiosis is often coupled with putrefaction dysbiosis, and the treatment is the same. To restore balance, supplementation with beneficial flora and fructooligosaccharides (FOS) is also recommended. Up to 2,000 milligrams of citrus seed extract may be used daily.


This occurs when the immune system reacts with abnormal or aggravated responses to the digestive process. Microbes in the gut and foods produce exotoxins that irritate the gut lining. Our bodies recognize these toxins as foreign substances and produce antibodies that signal the immune system to get rid of them.

Unfortunately, this local reaction might be the cause of some autoimmune diseases. Rheumatoid arthritis, ankylosing spondylitis, and perhaps skin diseases such as eczema and psoriasis are often the result. In this process, our body initially reacts to a “bug” of some sort, but the antibodies formed to fight it are the perfect keys that fit into gene markers.

These markers make us more susceptible to certain diseases. The mechanism by which these are turned on or off is unclear, but it appears that specific microbes cause disease only in people with specific gene markers who are exposed to specific microbes that are harmless in everyone else.

Our body senses that as a systemic problem rather than just some imbalanced microbes in our intestines. It reacts with an all-out antibody reaction, attacking the body itself—an autoimmune reaction. What originated as a local infection becomes an autoimmune illness.

For instance, rheumatoid arthritis has been linked to a prevalence of the bacteria proteus, which mimics gene marker HLA-DR4; 50 to 75 percent of people with rheumatoid arthritis have this gene marker. People with sensitization dysbiosis often have food intolerances, leaky gut syndrome, and increasing sensitivity to foods and the environment.

Symptoms may include acne, bowel or skin problems, connective tissue disease, and psoriasis. Sensitization dysbiosis may accompany fermentation dysbiosis, and similar treatments may be helpful. Replacing probiotic bacteria and repair of the intestinal mucosa are essential.