Leaky Gut

Leaky Gut

Nikol Margiotta N.D.

Part 1:  Leaky Gut and Intestinal Permeability

This article discusses:

– Role of the digestive tract
– What is leaky Gut/IP

When it comes to the digestive health of my patients, there are days where I feel like I’m the hammer and all my patients’ are a nail! Metaphorically speaking, just about everyone I see has some sort of gut dysfunction and cleaning up the gut is where I tend to start — it’s the critical to all the other work that follows. And we see the gamut: patients with very straightforward complaints of gas, bloating, constipation or reflux and to those with symptoms not localized to the gut, but involve underlying GI dysfunction. What’s more, there is a growing body of research showing a strong correlation between compromised GI function and conditions as seemingly unrelated as: Rheumatoid arthritis, asthma and eczema. As a doctor practicing functional medicine, it is critical to assess, treat and support proper GI function.

A Little Background

GI complaints continue to be among the leading reasons people visit the doctor. In the U.S. alone, over 70 million people suffer some form of GI disorder — with symptoms ranging from mild to serious enough to interfere with normal day-to-day life. For some people, digestive disorders are so severe it will cause them to drastically limit their lifestyles, frequently miss work or quit their jobs altogether. It’s not uncommon for me to have a patient report that they map their travels based on rest stops available along their route.

Sadly, I expect to see GI issues continue to grow, especially as the population ages. Years of poor food choices, stress, lack of exercise, NSAID and antibiotic abuse, toxic environments and other lifestyle choices will take their toll. The good news is that many of these complaints can be significantly reduced with dietary, lifestyle and nutritional changes.

The Gastrointestinal Tract

Basically, the gastrointestinal tract, or gut plays a role in:

– Digesting foods – Absorption of small food particles to be converted into energy – Carrying nutrients like vitamins and minerals attached to carrier proteins across the gut lining into the bloodstream – Detoxification of the body – Providing immunoglobulins or antibodies (e.g. secretory IgA) that act as the first line of defense against infection

Leaky Gut Syndrome

LGS is poorly recognized by ordinary GI docs largely because you can’t see it on a biopsy, but nonetheless, the problem is extremely common. Essentially, it represents a hyper-permeable intestinal lining. In other words, spaces develop between the cells of the gut wall that allows bacteria, toxins and incompletely digested food to leak through. The official definition from Wikipedia is “an increase in permeability of the intestinal mucosa to luminal macromolecules, antigens and toxins associated with inflammatory degenerative and/or atrophic mucosal damage.” Ok, translation please…

The circled portion above shows areas of sparse microvilli where toxins and incompletely digested food particles can migrate across the epithelial barrier and enter the body. This action can cause the immune system to respond to these “invaders” by mounting an immune reaction — inflammation.

The Mucosal Barrier (The “Inner” Tube)

The mucosal barrier is essentially one long tube that starts in the mouth, down the throat, to the stomach, small intestine, large intestine, anus and then out. This tube, in theory, is the only thing in the body that comes in contact with the outside world. Its job is to keep the outside world out. However, the barrier created by this intestinal mucosa is, even in normal healthy people, an incomplete one. Small quantities of molecules of different sizes and types cross the intact epithelium by both active and passive mechanisms through the microvillus.

So, How Does The Gut Become Leaky?

The gut lining is pretty delicate and as I said earlier, subject to a variety of abuses — NSAID’s, antibiotics, poor gut flora, food poisioning etc. This leads to the tissue becoming damaged and inflamed, starting a chain of events that will decrease the overall functioning of the GI system. The cells that make up the GI are held together very tightly, but over time, these spaces open up and allow large food particles (antigens) to be absorbed into the body. Normally the body sees food particles that have been digested into their component parts: carbohydrates = glucose, fats = free fatty acids and proteins = amino acids. The body knows what to do with those particles. Is does not know what to do with particles of chicken or popcorn. The larger particles are foreign to the body’s defence system and create antibodies against what we believe to be harmless, even healthy foods — creating various levels of inflammation.

The Inflamed Gut

When most people hear the word “inflammation” they think of arthritis not the gut. What makes my job even harder, is trying to convince someone who doesn’t have GERD, gas or other GI symptoms (yet…) that there is a problem. But the kind of inflammation I am talking about goes far beyond reflux or acid indigestion — often it is the underlying source of many health complaints. Here’s what can happen:

  • When the gut is inflamed, it doesn’t absorb nutrients and foods properly and so fatigue and bloating can occur
  • Likewise when the detoxification pathways that line the gut are compromised, chemical sensitivity can arise. Also, the constant leaking of toxins overburdens the liver so that the body is less able to handle everyday chemicals
  • When the gut lining is inflamed the protective coating of sIgA (secretory IgA) is adversely affected and the body can’t fight off potentially harmful pathogens like protozoa, bacteria, viruses and yeast
  • When the intestinal lining is inflamed, bacteria and yeasts are able to trans-locate. This means that they are able to pass from the gut lumen or cavity, into the bloodstream and set up infection elsewhere in the body
  • When the intestinal lining is inflamed, bacteria and yeasts are able to trans-locate. This means that they are able to pass from the gut lumen or cavity, into the bloodstream and set up infection elsewhere in the body


GI and Chronic Disease

While the range of GI dysfunction varies, the underlying issue is the same: a compromised mucosal surface. The normal function of the gut may be even further compromised as seen in the increasing number of adults that “self-medicate” for heartburn with antacids or other medications. These drugs — Tums, Rolaids, etc. reduce or neutralize stomach acid (HCL), actually inhibiting the adequate digestion of proteins and key nutrients like B12. When stomach acid is reduced (hypochlorhydria), the patient is predisposed to an overgrowth in intestinal bacterial (e.g. candida albicans), H. pylori (the ulcer causing bacteria) and some parasitic infections (c.difficile, Giardia, Cryptosporidium parvum, etc).

Additionally, the over-prescription and self-medication of NSAID’s (i.e. Advil, Aleve) can lead directly to mucosal surface damage. The over-consumption of NSAID’s for anti-inflammatory purposes has been associated with increased incidence of upper GI complications, including gastric and duodenal ulcers, GI bleeds and GI mucosal lesions. Healthy GI function is key to overall health and its dysfunction is related to a multitude of diseases and conditions such as:

Diseases and Conditions Associated with GI Dysfunction:

Acne Dermatitis Herpetiformis Migrain Headaches
AIDS/HIV infection Diverticulitis Multiple Chemical Sensativities
Celiac Disease Food Alergies/sensativities Pernicious anemia
Childhood ear Infections Gastritis Psoriasis
Chronic yeast infection Rheumotoid arthritis Crohn’s disease
Ulverative colitis IBD w/food intolerance And more…

Now that you know what LGS/IP is — how do we find it and more importantly, fix it?

Part 2: GI Restoration: The 4 R’s of Functional Medicine

This article discusses:

– Digestion Processes – Detection of Digestive Issues – Repair of the Gut

The Digestive Process

A quick review of physiology…the body breaks down foods first by using mechanical means — chewing – which will then trigger a host of chemical processes (release of enzymes). Remember your mother telling you to chew your foods 50 times? Hate to say it, but she was right. It’s one of the second or third questions I ask patient with GI complaints — “How many times do you chew your food”? Sheepishly they will answer “not enough”. Ok, 50 times is excessive — but you need to get in at least 10 good chews before swallowing because digestion starts in the mouth with the action of chewing. Next is the release of a variety of enzymes which further aids in the breakdown of foods even before they get to the stomach, where more digestive enzymes and hydrochloric acid are released. Chewing only 3 or 4 times, while food is almost still whole and washing it down with large quantities of liquid is quickest way to bring the entire digestive process to a grinding halt.

The process is continued via the surface of thousands of finger-like projections, one cell thick called villi that are the primary tools of absorption. These sensitive finger-like projections can become “worn out” for all sorts of reasons and the area will actually become devoid of villi, creating issues of malabsorption or maldigestion. I tell my patients to think of these spots like potholes on Michigan Avenue waiting to be filled in. Luckily, the cells of the small intestine are one of the tissues that most rapidly renews every 2-5 days. The circular folds, villi and microvillus expand the absorptive area of the small intestine to approximately the size of a tennis court.

The release of digestive enzymes allows the continued breakdown of large food molecules into smaller molecules that can be easily absorbed into the blood or lymph. If the digestive tract is intact there will be a minimum of GI problems. You know that is rarely the case.

The 4 R Program

In order to keep the body healthy, the gut must be healthy. Period. To do that, applying the following steps will significantly improve patient outcomes:

1). Remove
2). Replace
3). Repopulate
4). Regenerate


The first step in any GI restoration program has to focus on eliminating pathogenic bacteria, viruses, fungi, parasites and other toxic substances from the GI tract. There are a variety of tools to help determine the level of mucosal barrier dysfunction — e.g. comprehensive digestive stool analysis, parasite tests — available in both stool and blood tests — we use the Metametrix GI Fx test, which is based on DNA testing. It’s highly accurate and gives us lots of information about the “Inner” tube. Of equal importance is removing all offending foods — specifically those that create an immune response, which can be determined by a food allergy test — we use the LEAP test. Below outlines various symptoms and diseases associated with allergies/sensitivity:

Symptoms and Diseases Associated with Food Allergy/Sensitivity:

System Symptoms/Disease
GI Canker sores, celiac disease, ulcers, indigestion, constipation, gas, IBS, malabsorption, Crohn’s disease, colic (babies)
Genitourinary Chronic bladder infections, frequent urination
Immune Serous otitis media
Mental/Emotional Attention deficit disorder, depression, anxiety, memory loss
Musculoskeletal Joint pain, myalgias, RA
Respiratory Asthma, chronic or allergic sinusitis, nasal congestion
Cardiovascular Irregular heart rhythm, brusing
Skin Eczema, psoriasis, itchy skin and eyes
Miscellaneous Migraine Headaches

Studies have shown that significant improvement occurs in symptoms when patients follow this type of program, which is why it is a critical part of Remove. If a patient can’t or won’t give up problematic foods I delicately explain they will most likely not have any relief in symptoms, no matter how many supplements or prescriptions they take. Removing these foods is the quickest and least expensive route to regaining gut health. This is also the stage when many a resistant patient will tell me they are feeling much better because they have given up the culprit food(s). I do the secret “I told you so” dance.


Replace refers to the replenishment/replacement of enzymes and other digestive factors that are lacking in the GI system. Various GI enzymes that often need to be replaced include: Proteases, lipases, amylases, trypsin and chymotrypsin normally secreted by the pancreas. Another digestive factor that often needs replacement is hydrochloric acid. HCL is critical, especially in patients older than 60, since hypochlorhydria can cause a variety of GI symptoms, impair the absorption of nutrients — especially minerals and predispose a patient to opportunistic infection — particularly parasites. HCL production depends on zinc, so be aware that decreased stomach acid levels may also indicate a zinc deficiency. Hypochlorhydria is fairly easy to overcome, we carry a wonderful complete digestive enzyme complex on our website.


Enter the good bacteria, commonly referred to as “probiotics”, to the intestine to re- establish proper microflora balance. Probiotics are used for a variety of functions in the GI tract: helps production of SCFA’s (short chain fatty acids) necessary for colonic cell growth and function helps degrade toxins prevent colonization of pathogens aids with vitamin synthesis decreases inflammation

Probably the most important role probiotics play, is in keeping pathogens at bay. The following outlines just a few of the several varieties of probiotics and their use:

Bifidobacterium bifidum May inhibit the binding of pathogens to the intestial walls. Boosts immune properties
B. infantis Helps inhibit pathogenic bacterial invaders, including E.coli
B. lactis Resists acid digestion. Helps promote healthy bowel function. May help eliminate candida overgrowth
Lactobacillus acidophilus First line of defence against invaders and pooprtunistic organisms like yeast. Helps keep heart healthy. Helps keep pathogens from lining intestinal walls
L. brevis Decreases intestinal permeability and has a positive effect on the immune system

As stated earlier, supporting the Repopulation phase with the appropriate types and amounts of probiotics supports the regeneration and healing of the total intestinal tract.


This refers to providing support for the healing and regeneration of the GI mucosa. Certainly, part of the support for healing comes from removing the offending foods, toxins and pathogens that continually re-injure or irritate the mucosa. By removing, replacing and repopulating, the following nutrients will help significantly when moving on to regenerating:

  • L-glutamine: Glutamine is a powerful amino acid that is the preferred fuel for the cells of the GI mucosa. Glutamine is believed to promote the production of glutathione, which provides additional protection from inflammation to help in healing. Clinically, dietary glutamine is important for the maintenance of GI mucosa during periods of stress, injury and of course, inflammation. Dietary deficiency of glutamine is associated with degenerative changes in the small intestine following intestinal injury, infection, stress, surgery
  • Aloe Vera: Use of Aloe Vera dates back as far as 6000 BC. Topical applications for fighting infection, healing cuts and burns, along with internal use for its digestive and laxative properties are touted in many books on natural healing. Aloe Vera is actually a succulent from the garlic family and not a cactus. When the entire leaf is processed, all 200 different nutrients found in the plant are available in just 1% of its juice. All together they promote healing on the inside as well as on the outside of the body.
  • Licorice Root: Licorice root is one of the most biologically active herbs in the world. Licorice root is an effective treatment for stomach ailments, because it exerts a soothing action on the mucosal surfaces of the GI tract and is frequently used to help these tissues heal. The licorice root has been proven to be among the best anti-ulcer medications available
  • Nutritional Anti-Inflammatories: To reduce GI inflammation quickly, several nutritionals come to mind: curcumin, EPA-DHA and GLA. For example, fish oils (EPA-DHA) are particularly effective in reducing inflammation and can be of great benefit to people suffering from Rheumatoid Athritits or ulcerative colitis (both often occur as a result of GI inflammation). Daily supplementation of EPA-DHA significantly reduces inflammation and severity of colitis, often allowing patients to discontinue anti-inflammatory medication and steroids

A Special Word About Enzymes

Aging causes most people to experience problems with digestion. It is estimated that after age 40 there is an approximate decrease in the body’s ability to produce enzymes by 20-30%. The use of specific enzymes can help to improve the efficiency of digestion. Enzymes are essential to the body’s absorption and full use of food. There are two primary classes of enzymes responsible for maintaining life functions: digestive and metabolic. The primary digestive enzymes are proteases, amylases and lipases. These enzymes function as a biological catalyst to help break down food. Metabolic enzymes operate in every cell, every organ and every tissue, and they need constant replenishment. Below is a quick guide to common digestive enzymes and their purpose:

Amylase Digests Starches
Bromelain A Proteolytic, anti-inflammatory food enzyme from pinapple. Aids Digestion of fats
Cellulase Digests cellulose, the fibrous component of most vegetable matter
Chymotrypsin Helps convert chyme
Diasteas A potent starch digestant
Lactase Digests lactose, or milk sugar, (almost 65% of humans are deficient)
Lipase Digests fats
Pancreatin A broad spectrum, proteolytic, digestive aid, derived from secretions of animal pancreas; important in degenerative disease research
Papain and chymopapain Proteolytic food enzymes from unripe papaya; a vegetable pepsin for digestion of proteins. These enzyme help loosen necrotic and encrusted waste material from the intestinal walls
Pepsin a proteolytic enzymes that breaks down proteins into peptides. Can digest 3500 times its weight in proteins.
Protease Digests proteins
Renin Helps digest cow’s milk products
Trypsin A proteolytic enzyme

Source: Ganoong WF: Review of Medical Physiology, Lange, et.al; 1987: 325

As a Functional Medicine doctor, I have the responsibility to look beyond the symptoms our patients present with. Our lives will always be stressful, our diets in need of improvement, our pace rushed and never enough sleep. If you have digestive issues or think you may have hidden sources of inflammation, call the schedule an appointment with Dr. Nikol at 312-366-8565. Your optimal health depends on it!


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Applying Functional Medicine in Clinical Practice Course Notes: November 2006

Special thanks to BioHealth Diagnostics for the use of their mucosal barrier slides

Page modified on 5/15/2011

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