The functions of our GI tract are accomplished through 4 main mechanisms:

1) The unique biochemistry of digestion, by which food is digested and absorbed:

  A lack of any of the digestive enzymes can seriously impair the health of our entire system as digestive enzymes have an effect on our nutritional status;

  One of the most important protective functions of a healthy digestive process is the protection from harmful substance introduced into the body.  If given a chance, these harmful substances will activate the immune system and cause a multitude of complaints throughout the body.

2) The complex barrier between the inside of the intestines and the rest of the body:

  This barrier protects the inside of the body from damaging stomach acid and it plays an important role in protecting the stomach from ingested toxins, drugs, alcohol, bacteria, and viruses.  It also aids in the digestion of nutrients.

  The barrier only allows the flow of certain materials from the inside of the intestines to the rest of the body (ie. beneficial nutrients).  In the unhealthy gut, however, this barrier is “leaky”, allowing molecules of all types (ie. bacteria, fungi, incompletely digested foods, food additives, over-the-counter drugs, etc) to get into circulation, potentially causing many problems.

3) An immune system, called the GALT (gut associated lymphoid tissue):

  Approximately 60% of the total immune system is located within the GI tract.  The primary purpose of the gut immune system is to provide a first line of defense against foreign invaders, such as bacteria or toxins.

  When invading material passes through the barrier into circulation, the immune system is activated and inflammation occurs.  The activation of the inflammation cascade can lead to damage of perfectly healthy tissue.

4) A beneficial, symbiotic relationship between the GI tract and the good bacteria in the colon:

  The colon houses beneficial bacteria (ie. “good” bacteria, aka probiotics) that have a direct impact on digestion and the development and support of the gut immune function.  

  Another clinically important function of the “good” bacteria is their ability to fight off the “bad” bacteria.

The 4R Gastrointestinal Restoration Program
I usually take a systematic approach to treating digestive disorders and you now know what some of functions of the GI system are but how do I treat digestive conditions? Well, this is where I use the 4R Program that I mentioned above. The way I go about this differs from patient to patient because it depends on symptoms, how aggressively they want their treatment to be, whether or not they are interested in doing any tests, etc etc but here’s the lowdown.

Step 1: REMOVE

The first step has 2 components: 1) Eliminate the bad bacteria, yeast/fungus, parasites, and other toxic substances that end up in the GI tract; 2) Remove problematic foods that your body is reacting to.

1) Many practitioners treat patients based upon the assumption that there is a yeast overgrowth, a parasite present, etc. I do not like making this assumption. The way I figure it, if you’re going to be eliminating a bacteria, yeast, or parasite, it’s best to figure out exactly what you should be eliminating. After all, various substances (just like antibiotics, fungicides, etc) work differently for different organisms. Whether or not you have a toxic substance in your gut can be diagnosed via a comprehensive parasitology test that detects for good and bad bacteria, yeast, and parasites.

2) Dietary modification is important since foods to which a patient is reacting to can exacerbate GI dysfunction and stimulate immune and inflammatory responses. Some symptoms and diseases associated with food allergies, sensitivities, and intolerances are as follows:

Gastrointestinal: Canker sores, celiac disease, chronic diarrhea, stomach ulcers, duodenal ulcers, recurrent mouth ulcers, indigestion, nausea, vomiting, constipation, gas, gastritis, irritable bowel syndrome, malabsorption, ulcerative colitis, Crohn’s disease, colic

Genitourinary: Bed wetting, chronic bladder infections, frequent urination

Immune: Ear infections

Mental/Emotional: ADD, depression, anxiety, memory loss, epileptic seizures, schizophrenia

Musculoskeletal: Joint pain, myalgias, rheumatoid arthritis

Respiratory: Asthma, chronic or allergic sinusitis, constant runny nose, congested nose, nasal polyps

Cardiovascular: Irregular heart rhythm, vasculitis, inflammation of the veins, spontaneous brusing, urticaria (hives), edema

Skin: Eczema, psoriasis, urticaria, red itchy eyes, itchy skin

Miscellaneous: Migraine headaches

In general, this phase of the 4R Program is dealing with food sensitivities (not allergies or intolerances). According to one estimate, as many as 60% of the population suffers from undetected food sensitivities. These sensitivities may be overlooked because they are difficult to identify. Unlike the more obvious immediate allergic reactions, hidden food sensitivities can be delayed by many hours or even days. The foods most commonly associated with sensitivities are as follows: dairy products, wheat, eggs, corn, soy, citrus fruits, shellfish, nuts, tomatoes, and red meat. As you’ll read in my food sensitivity blog, I believe that there are only 2 effective ways of diagnosing food sensitivities: following an elimination diet, or having a blood test that assesses for your IgG immune reaction to 96 different foods. The route that I take with people is completely dependent on what they are interested in as both of these routes have their pros and cons.

Quite honestly, just taking this first step often reduces patients’ symptoms significantly. Sometimes we don’t even have to proceed into the next steps. This is my favourite place to start with GI dysfunction because if a certain bacteria/yeast/parasite is present or foods are causing the problem, then it’s easy to get rid of that problem. When you get rid of the problem, you get rid of the symptoms.


This next step refers to the replenishment of enzymes and other digestive factors lacking or in limited supply in an individual’s GI environment. Digestive enzymes enhance the breakdown of large substances, thereby preventing them from being absorbed into circulation and leading to problems. The common example I give is when you’re in a big hurry and you scarf down a meal really quickly (ie. A large sub from Subway) as you’re running out the door. Regardless of whether or not you typically have digestive issues, it’s going to cause some discomfort. Our body is designed to deal with food particles that are broken down into tiny tiny pieces and this digestion begins with chewing. If we don’t chew our foods properly or if we’re lacking in digestive enzymes, then it’s like we’re eating a large Subway sub in just a couple of bites – ouch!

Signs and symptoms of a digestive enzyme deficiency can be very vague, for example, they can include: bloating, belching, burning, and flatulence immediately after meals; a sense of fullness after eating; indigestion, diarrhea, or constipation; multiple food allergies; nausea after taking supplements; itching around the rectum; weak, peeling, and cracked fingernails; dilated blood vessels in the cheeks and nose; acne; iron deficiency; chronic intestinal parasites or abnormal intestinal bacteria; undigested food in stool; chronic yeast infections; upper digestive tract gassiness.

When it comes to replacing digestive factors that the body might be lacking in, there are a number of different things to consider. For example, one common digestive enzyme that tends to be lacking, especially in older persons, is hydrochloric acid. There are numerous other digestive enzymes that are necessary for proper digestion but for the sake of this blog, I will just touch on some of the main ones.

• Pepsin is the main stomach enzyme (it breaks down protein).
• Gelatinase is responsible for breaking down gelatin and collagen found in meat products.
• Amylase is responsible for breaking down carbohydrates and starch.
• Trypsin and chymotrypsin are secreted from the pancreas and break down protein.
• Lactase breaks down lactose and is deficient in people who are “lactose-intolerant”.
• Lipase breaks down fat.

So how do you know if you’re deficient in digestive enzymes? Well, you can take 1 of 2 approaches: treat based on signs and symptoms or do a comprehensive stool analysis that outlines how efficiently you are breaking down your foods (ie. Looks at a number of factors related to food breakdown). Ideally you would combine the comprehensive stool analysis with the parasitology (it’s much cheaper to combine these tests versus doing them separately) – this approach gives the most accurate information regarding the remove and replace phases, along with the next 2 phases, reinoculate and repair).


This step refers to the reintroduction of desirable bacteria (ie. “good” bacteria, aka probiotics) into the intestines to re-establish proper good/bad bacterial balance. Probiotics cooperatively maintain a delicate balance between the GI tract and the immune system. When this balance is disrupted, disease and inflammation result. A healthy GI tract prevents the overgrowth of bad bacteria, modulates disease processes, and prevents widespread inflammation throughout the body. Probiotics also synthesize various vitamins (Vitamin B12, folic acid, biotin, riboflavin, Vitamin K), produce fuel for colon cell growth and function, and degrade toxins.

How do we know if there is a gut bacterial imbalance going on? Apart from signs and symptoms (similar to digestive enzyme deficiency), the only way to definitively diagnose a deficiency in beneficial bacteria would be to do the comprehensive stool analysis. It outlines your gut bacterial status (ie. Good bacteria, bad bacteria, and imbalances). If gut bacteria are out of whack for people, I am extremely picky about the probiotic supplements that I recommend. If you would like to learn more about probiotics, refer to my previous post called “Probiotics”.


The regenerate phase refers to providing support for the healing and regeneration of the gut – this means decreasing inflammation and/or resolving “leaky gut”.

Inflammation is a natural bodily process – it was designed to help our bodies heal. The problem is when inflammation becomes chronic. Think about acute inflammation – if you stub your toe, it becomes red, hot, swollen, and painful. Pain is often a byproduct of inflammation and this can happen in your gut! The problem is when there is prolonged, or chronic inflammation. Excess inflammation within the gut can be very difficult to diagnose based on signs and symptoms (unfortunately, it’s not as easy as looking at a swollen, red toe). If you have been diagnosed with inflammatory bowel disease, then, well, we know there is inflammation. Otherwise, we’re left thinking that maybe inflammation is a problem. If you want to find out for sure, you can do a comprehensive stool analysis. What exactly is the test measuring when it comes to inflammation? A number of things: 1) Lysozyme is an enzyme at the site of inflammation in the GI tract; 2) Lactoferrin is a quantitative GI-specific marker of inflammation; 3) White blood cells are elevated in areas of inflammation; 4) Mucous can be found in the stool when there is constant irritation to the area. Once again, if you’re interested in clearly determining what is wrong with your digestive system, you can perform the GI Effects Comprehensive Stool Analysis to determine the best treatment protocol possible.

And I mentioned “leaky gut”. What the heck is that? Well, I apologize because this explanation is fairly lengthy. Leaky gut is something that’s spoken about by different healthcare practitioners and internet sites but rarely, is a good explanation of physiology provided. Therefore, I’m going to do the best that I can to explain it adequately.

To start, we must examine the gut’s immune system. The normal immune system jumps into action only when it detects significant amounts of foreign proteins in the body. It reacts aggressively because these foreign proteins may signal the arrival of disease-causing microorganisms, such as bacteria or viruses. For example, when the body encounters a bacteria or virus, it mounts an immune reaction. And what’s a major way we encounter foreign proteins and substances? Through eating – immune soldiers sit under the cells that line the intestine, ready to pounce and call in reinforcements. This is called your GALT (gut associated lymphoid tissue). So, considering that we eat protein on a daily basis, how come our immune system isn’t constantly being activated? Well, there are 2 main reasons: 1) Before our defenses encounter anything that might trouble them, our digestive system usually breaks down most ingested proteins into its building blocks (called amino acids); 2) Cells within the GI tract are connected via “tight junctions”. The small intestine is a permeable pipe composed of cells that are connected with these tight junctions. These tight junctions are meant to keep all but the smallest molecules away from the immune system.

Problems arise when there are issues with these things. For example, if our protein-chopping machinery isn’t up to par (ie. Because we’re lacking digestive enzymes or we have certain intolerance to foods), then small protein fragments are left intact. In healthy people, most of these proteins are kept within the GI tract and are simply excreted before the immune system even notices them. In people with “leaky gut”, however, it’s a different story.

A protein in humans and other animals, called zonulin, was discovered to increase intestinal permeability. Intestinal permeability occurs when the tight junction connections between the cells are not so “tight”, meaning that more than just the small molecules leave the intestines. This enhanced intestinal permeability allows intact proteins and peptides to seep out of the gut and elicit an immune reaction. Just having a “leaky gut” by itself can activate the immune system, and if you happen to have issues breaking down your food into really small particles, then the immune reaction will become even greater. In fact, this leaky gut syndrome has not only been shown to be a root cause of many digestive disorders, but also many autoimmune conditions.