The human microbiome consists of hundreds of thousands of bacteria (called microbes) that reside in the body and all over the surface of the skin.  Different areas of the body have different bacterial colonies that have a multitude of functions to keep our bodies functioning optimally.  The digestive tract is lined with epithelial cells that make up the gut lining (gut epithelium) and on top of the lining is a thick layer of bacteria that provides a natural defense against pathogens, parasites, toxins, undigested food, and other invaders.

Dr. Campbell-McBride states the bacteria that protect the gut wall “produce antibiotic-like substances, anti-fungal volatiles, anti-viral substances, including interferon, lizocym and surfactins, that dissolve membranes and viruses and bacteria; they engage the immune system to respond appropriately to invaders” as well as reduce the pH near the surface of the lining to create an uncomfortable, acidic environment for pathogens.

Gut bacteria is absolutely essential for proper digestion and providing energy and nourishment to the cells making up the gut lining.  Gut bacteria are also involved in the following functions:

  • produce immune system cells including lymphocytes and immunoglobulins
  • produce enzymes necessary for breaking down food
  • release vitamins, minerals, and nutrients through the gut wall for other cells in the body
  • produce and release B vitamins
  • Balance TH1 and TH2 immunity arms (auto-immunity is contributed from this imbalance)
  • Produce humic acid – needed to take and transport inorganic minerals to other cells
  • Assist in detoxification by neutralizing toxins (acts as a “second liver”)
  • Involved in controlling inflammation
  • produce neurotransmitters – plays a major function with the endocrine system, influencing cortisol (stress-hormone), mood, weight, sleep patterns, energy levels, etc.

brainClearly, the condition of our gut flora and intestinal lining influences not just digestion and the immune system, but our brains.  Clinical and experimental studies suggest gut microbes impact the gut-brain axis significantly.  According to preclinical trials from Oppenheimer Center for Neurobiology of Stress, Division of Digestive Diseases, David Geffen School of Medicine at UCLA concluded:

“Emerging data support the role of microbiota in influencing anxiety and depressive-like behaviors, and, more recently, of dysbiosis in autism. In fact, autistic patients present specific microbiota alterations according to the severity of the disease.”

Damaging the precious gut lining and destroying beneficial gut microbes can wreak havoc on all areas of the body.  A diet high in processed carbohydrates, refined sugars, and denatured/oxidized proteins and fats, excessive antibiotic and steroid use, contraceptive pills, alcohol/drug use, environmental toxins, heavy metals, chronic stress, and over-the-counter pain medications are only a few of the things that contribute to a damaged gut.  Gut bacteria is highly sensitive to dietary changes.  The GAPS Diet provides the digestive tract with essential nutrients to feed and rebalance the beneficial bacteria and heal the gut lining.

Probiotics (beneficial bacteria) are an essential part of the GAPS protocol and can be found naturally in fermented foods and in supplements.  Dr. Campbell-McBride recommends consuming both forms to get the most beneficial bacteria as possible to populate the GI tract and balance the bacterial ecosystem.   Probiotics go to work in the body by controlling inflammation, supporting the immune system, protecting and repairing the gut lining, regulating proper body pH, serve as natural antibiotics, and support proper digestion and nutrient absorption.  Please refer to Dr. Campbell-McBride’s book Gut and Psychology Syndrome or Gut and Physiology Syndrome for an extensive discussion on probiotics and her specific recommendations.


  • For those on the GAPS diet, it is recommended to build your dose of probiotics gradually.  Start with a very small amount (example 1/4 capsule or less for 3-5 days) and see how your body responds.  Guidelines for choosing a therapeutic probiotic will vary for each person depending on health concerns, however, Dr. Campbell-McBride has provided specific things to look for in a probiotic in her book Gut and Psychology Syndrome .
  • Observe for “die-off” reactions when introducing probiotics.  These symptoms may include, but are not limited to, fatigue, nausea, bloating, diarrhea, constipation, low grade fever, headache, and flu like symptoms.  If there are none, the patient may increase the dose gradually.  If there is a reaction, the patient should settle on the current dose until symptoms subside or move back to the previous dose.  Some patients may need to temporarily stop the probiotic until symptoms subside if experiencing extreme die-off.
  • It may take patients a few weeks to a few months to reach their individual therapeutic dose.  It is important to remember the patient is also receiving probiotics from fermented foods.  Although you can not “overdose” on probiotics, it is important to listen to your body and adjust your commercial probiotic and fermented foods accordingly to control die-off.
  • If you take the probiotic powder out of its capsule, it is important to remember the temperature of the food/drink is not too hot, as this could destroy the bacteria.