leaky gut

Leaky Gut: a hidden solution for healing?

We’re always looking for these, aren’t we?

Those aspects of ourselves so pivotal to who we are and how we function, that with careful tending we unleash vast healing potential. To relieve all kinds of pain and suffering. To reverse chronic illness.

There is such a pivot point hidden within us.

Today I’m going to tell you about the gut mucosa, a powerful internal boundary between us and the outside world, and the ultimate integration point of body and mind.

More to the point, we’ll explore what happens when we lose the integrity of this boundary, a common condition called “impaired intestinal permeability (IP)”, often referred to as “leaky gut.”

Impaired IP is not a diagnosis you’ll hear in the realm of disease-focused conventional medicine. Diseases are downstream problems. They’re what happens when there is unaddressed dysfunction upstream to the symptoms you experience when the disease is diagnosed. That’s the focus of conventional medicine.

Impaired IP is the upstream problem to disease.

Impaired IP is one of the most common and insidious root-cause level biological dysfunctions in humans. When impaired IP and its risk factors are left unaddressed, it will lead to widespread damage that is the basis for chronic disease and suffering via gut-body-mind integration pathways.

Optimal gut structural and functional integrity is essential for healthy operation of all aspects of our bodies’ complex physiology. This includes brain function, cognitive capacity, emotional resilience, and experience of energy and wellbeing.

Common gut-body-mind integration problems associated with impaired IP:

  • Pain.
  • Autoimmune and inflammatory disorders.
  • Allergies.
  • Food sensitivities.
  • Mood and mental health disorders.
  • Sleep dysfunction.
  • Fatigue and exertional intolerance.
  • Neurodegenerative disorders.
  • Cognitive dysfunction and brain fog.

While focus is placed on the painful downstream manifestations of impaired IP—the joint pain, fatigue, or brain fog, for instance—and treated symptomatically, the smoldering dysfunction beneath the surface, “hidden” from our view, is often overlooked.

As we’ve discussed together extensively, only by addressing our problems at their root cause level, can we achieve optimal and sustainable healing.

Not only is impaired IP a causal culprit in these disorders, but its presence makes us more vulnerable to suffering and illness when triggering events come along.

For instance, my recent knee pain was clearly related to mobility issues and underlying abnormality of my patella, but impaired IP set me up for more pain as a result of increased inflammation bathing my tissues. A quick dietary reset (more on this in a bit) and pain decreased by 50% within a few days. Truly remarkable.

The primary functions of the gut.

The extensive surface area of our gut mucosa (about the size of a studio apartment!) is a primary interface between our interior and external worlds. As our chief boundary (in addition to skin, respiratory mucosa, and urogenital mucosa), the gut’s many functions are essential to survival and optimal health:

  • It carefully regulates what gets in (across the gut lining) and what stays out.
  • Nutrient management. It manages all the business of digestion and absorption of nutrients from our food.
  • Immune function. It is the primary site for immune perimeter protection and immune cell communication with the rest of the body.
  • It provides the foundation for a thriving microbiome, the trillions of micro-organisms that reside within us and influence all body functions including immunity, hormonal regulation, detoxification, gut barrier function, inflammation, brain function, energy production, and mood.
  • It releases a large array of communication molecules, hormones and neurochemicals (much like our brains) that play roles in vast aspects of physiological regulation.
  • It plays a key role in the elimination of toxins from the body.
  • Emotional wisdom. It is the source of “gut feelings” and emotions with powerful neurological inputs of information moving from gut to brain.

What goes wrong upstream in the presence of impaired IP?

When the gut becomes “leaky” it is no longer able to regulate what goes in and stays out and cannot provide consistent immune perimeter protection.

What does this mean for us?

Impaired IP causes localized (upstream) problems that lead to far-reaching (downstream) dysfunction:

  • Food sensitivities. Food proteins “leak” across and through gut lining cells, triggering immune cell activation that leads to increased inflammation and injury throughout the body.
  • Systemic toxicity. Transfer of environmental and microbial toxins from the interior of the gut into the systemic circulation, leading to widespread immune activation, inflammation, toxicity, and tissue injury.
  • Gut dysfunction. Gut lining inflammation can lead to mucosal injury and problems with digestion, absorption, motility, erosions, bleeding, and pain.

How Impaired IP leads to downstream injury and chaos.

As you can imagine, there is the potential for extensive downstream problems relating back to the initiating events of immune activation to food proteins and toxins that leak across the gut barrier and generalized gut dysfunction. These include:

  • Inflammation injury. Direct injury to cells throughout the body from inflammatory cytokines and toxins.
  • Nutrient deficiency injury. Loss of nutrients associated with digestion and absorption problems leading to nutrient deficiencies and impaired function.
  • Toxicity injury. Increase in total toxic load, toxic injury to cells, overwhelm of detoxification pathways.
  • Energy deficit injury. Decline in energy production as a result of mitochondrial dysfunction from system-wide inflammation and toxicity.

What causes impaired IP?

Generally speaking, impaired IP is caused by common irritants, toxins, stressors, and loss of nutritional support to the mucosal surface that lines the gut. These include:

  • Anti-inflammatory drugs such as ibuprofen, aspirin, and steroids.
  • Antibiotics
  • Alcohol.
  • Acid-blocking drugs (like proton-pump inhibitors and H2 blockers).
  • Heavy metals (from the environment, food, dental amalgams, drugs).
  • Infections (pathogenic bacteria, fungi, parasites, viruses).
  • Food proteins (in the setting of food sensitivities or allergies).
  • Allergies.
  • Mast cell activation syndrome.
  • Environmental toxins.
  • Excessive exercise.
  • Excesses of stress.
  • Persistent sleep debt.
  • Nutrient deficiencies and nutrient-poor diets.
  • Microbiome imbalances.

As you can see, we risk gut injury from a wide variety of very common exposures. The more of these going on at the same time, the higher the risk of impaired IP, local dysfunction, downstream injury and chronic illness.

It is fair to say we’ve all experienced impaired IP at one time or another and very likely fall on the spectrum of some degree of impairment all of the time. Case in point: A single dose of Ibuprofen leads to measurable gut lining dysfunction. A single dose of antibiotics wipes out the microbiome and its contribution to the gut mucosal barrier. A brief exposure to high emotional stress can cause gut immune activation and acute gut dysfunction. A few molecules of a food allergen or toxin can lead to large scale immune activation.

What can we do to heal our guts?

Considering the wide and often devastating ramifications of impaired IP, my recommendations for gut healing are also excellent strategies for core daily healthy living to keep our guts and all of its downstream connections going strong, body and mind.

Because the gut mucosa consists of rapidly dividing cells, fully replacing itself every three days, the potential for healing is very high when all the sources of injury and toxicity are removed, while the gut is properly nourished.

Gut Healing-911.

You’ve got a problem that needs to be solved right now to relieve suffering or impending disaster. This might be pain, inflammation, persistent anxiety or depression (mood disorders have been shown to have a strong gut-brain relationship), gut symptoms, or signs of an autoimmune or neurodegenerative disorder (to review just a few).

Note: Even if your problem seems to have nothing whatsoever to do with your gut, I want you to assume that it does. Because it does. Inflammation, toxicity, and nutrient depletion absolutely participate in all your troubles.

How to support and de-stress the overwhelmed gut and reverse its downstream effects:

  • Remove all irritants, toxins, and stressors listed above. This must happen, or the injury will continue in spite of your best efforts.
  • Follow a strict nutrient-dense, anti-inflammatory food plan. My version is called “GRIN”—the Gut-Immune Restoration Intensive Nutrition food plan. Details
  • Support digestion. Take a full spectrum digestive enzyme supplement with betaine hydrochloric acid at each meal.
  • Support your microbiome. Eat fermented foods and take a multi-species probiotic (50 billion + lactobacilli, bifidobacterial, saccharomyces).
  • Support healing of your gut lining. Bath your gut mucosa with healing nutrients: l-glutamine 5 grams 1-2 x daily (see Resources) and Omega-3 fatty acids EPA-DHA 2 grams per day. Include bone broth in your daily food plan.
  • Modulate inflammation. Take curcumin (turmeric extract) 2 grams twice daily. Use anti-inflammatory foods and spices.
  • Relax: activation of the parasympathetic nervous system through deep breathing and meditation, moderation of stress physiology, and cultivating presence all assist in healing the gut.

The GRIN food plan is designed to heal your gut, remove common triggers for inflammation, intensify nutrition, and reverse systemic symptoms related to gut-immune dysfunction and nutrient deficiencies.

But it is not meant to be a lifelong eating strategy!

Most people need to strictly adhere to the GRIN food plan for 6-12 weeks (minimum) to heal the gut, normalize gut permeability, and reverse the systemic injury due to inflammation and toxicity. The vast majority of people who use this plan go on to heal, then are able to successfully reintroduce food groups into their diet without recurrence of their symptoms.

Note: Be as strict as possible with this food plan for maximal benefit. Even a molecule of a culprit food or exposure can lead to a cascade of injuring events.

Long-term Gut-Body-Mind healing.

Whether you start with Gut Healing-911 to address a crisis or are interested in optimizing how you and your body feel and function, the strategy is basically the same, with variations to accommodate individual needs and preferences.

A nutrient-dense, low inflammation potential, whole foods food plan (like my “FINE” food plan—Foundational Intensive Nutrition Energy food plan) is essential. What this looks like will vary among us. Some very sensitive folks will stay on GRIN or something very close (based on the results of their food reintroduction challenge). I tend to eat according to FINE and hop on GRIN when I feel the need.

The basics of long-term gut-body-mind healing:

  • Optimal nutrition. Nutrient dense, irritant and toxin-free, low-inflammation potential food plan (FINE, GRIN, or your own variation that works) that optimizes amounts of healthy protein and fat
  • Avoid gut injury. Consistent avoidance of all irritants, toxins, drugs, stressors, and nutrient deficiencies that can lead to impaired IP (look back at the list).
  • Support digestion. Use digestive enzymes if needed.
  • Support your microbiome. Cultivate a healthy, robust microbiome by eating lots of plants (feeds the microbiome), fermented foods, and taking a multi-species probiotic daily.
  • Modulate inflammation. Liberally use anti-inflammatory food, spices, herbs, and practice healthy self-care.
  • Get consistent optimal sleep and relaxation practices.
  • Get consistent movement and exercise.

Gut-body-mind health supports our highest aspirations.

We forget, don’t we?

Sometimes we get so focused on nourishing our spirits, supporting our creative impulses, and elevating our minds, we forget to tend to our biology.

But there’s really no separation. We’re amazing beings of integrated body, mind, and spirit.

Now you know how the gut fits into the picture. We are as elevated as our guts are healthy.

In other words? Your meditation, yoga, and journaling practices (or whatever you do for your soul!) won’t take you quite as far if your body is struggling.

And sometimes it’s hidden.

Gut support fits right in there with our loftiest spiritual self-care.

If you’re not there yet, carve out some of your meditation, exercise, or contemplation time learning how to care for our gut.

Make the practice of gut-body-mind care part of your spiritual self-care (because it is).

Celebrate your renewed energy and wellbeing, and the reversal of pain and suffering—all because you healed your gut, the hidden key to your body-mind healing.

Did I leave something out you need to know? Hit “reply” and let me know!




Karyn Shanks MD. How to Reverse Autoimmunity with Optimal Energy Nutrition. 2019.

Karyn Shanks MD. How to Optimize Energy with the Foundational Intensive Nutrition Energy (FINE) Food Plan. 2019.

Designs for Health. GI Revive: this is a full-spectrum gut mucosal healing support preparation containing l-glutamine and a comprehensive array of nutrients and plant-derived compounds that soothe, protect, and heal the gut.

Karyn Shanks MD. How to Optimize Protein for Energy and Vitality. 2019.

Karyn Shanks MD. How to Heal Fatigue with Optimal Energy Nutrition. 2019.

Karyn Shanks MD. Wise Use of Supplements for Inflammation. 2016.


Karyn Shanks MD


Karyn Shanks, MD, is a physician who lives and practices in Iowa City. Her work is inspired by the revolutionary science of Functional Medicine, body-mind wisdom, and the transformational journeys of thousands of clients over her twenty-eight year career. She believes that the bones of healing are in what we do for ourselves.

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