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9 Steps to Perfect Health: How to Heal Your Gut Naturally


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how to heal your gut naturally

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All disease begins in the gut. — Hippocrates

Hippocrates made this profound statement more than 2,000 years ago, but we’re only now coming to understand just how right he was. Gut health is critical to overall health, and an unhealthy gut contributes to a wide range of chronic diseases, including diabetes, obesity, autism, depression, and anxiety. Many researchers, myself included, believe that supporting intestinal health and restoring the integrity of the gut barrier are two of the most important goals of medicine in the 21st century.

If you’re experiencing issues, learning how to support gut health naturally could make a difference in your overall health and well-being. If you’re working in the health and wellness field as a nutritionist, health coach, or another allied provider, understanding gut health could help you support your clients as they work to restore and maintain a healthy microbiota. Read on to learn why a healthy gut is essential for creating a healthy body and how you can restore and maintain a healthy gut for life.

Finding natural methods to heal the gut can help you get relief from a wide range of distressing symptoms. Find out how to support a healthy gut through diet and lifestyle. #optimalhealth #changeagent #chriskresser

Health Coaches: Why Focus on Gut Health?

If you’re in the health coaching profession, you’ll undoubtedly encounter clients with existing gut problems and chronic diseases. Some may struggle with obvious gastrointestinal symptoms such as constipation, diarrhea, gas, or bloating that clearly point to gut issues. However, others may have extraintestinal manifestations, such as blood sugar dysregulation or mental health issues, that are also rooted in gut dysfunction. No matter who you’re working with, supporting your clients as they take steps to heal their gut naturally should be a priority due to the profound impact of gut health on overall health.

The idea of the gut affecting overall health may seem far-fetched to some people. Therefore, I recommend beginning any discussion of gut health by briefly describing the two related variables that determine gut health: the intestinal microbiota and the gut barrier.

Are We More Microbial than Human?

The human gut is home to approximately 100,000,000,000,000 (100 trillion) microorganisms, collectively referred to as the “gut microbiota.” (1) The gut microbiota harbors a gene set 150 times greater than that of the human genome. (2, 3)

These microbes aren’t just passively living their lives; they have a profound impact on our health. Within the GI tract, gut microbes promote peristalsis (the movement of food through the intestines), protect against infection, produce vitamins, and maintain a healthy gastrointestinal mucus layer.

Outside the digestive tract, gut microbes influence other organs and tissues through neural networks and signaling molecules. Through these complex communication networks, gut microbes regulate 70 to 80 percent of the immune system and influence blood sugar control. (4, 5) They also modulate the function of the brain, bone, heart, skin, eyes, and muscle tissue. (6, 7, 8, 9, 10, 11)

When the gut microbiome is disrupted, processes normally regulated by the gut microbiota, such as immunity and brain function, are impaired. This ultimately may lead to the development of chronic conditions such as autoimmune disease, metabolic dysfunction, and mental health issues, among many other health problems.

What Disrupts the Gut Microbiome?

There are many features of the modern lifestyle that disturb the gut microbiome. Exposure to these harmful factors is pervasive in our society.

Processed, Inflammatory Foods

The Standard American Diet, packed with processed, inflammatory foods such as refined carbohydrates and industrial seed oils, is an established risk factor for gut dysbiosis. (12) The Standard American Diet reduces bacterial diversity and induces inflammation in the gut, thereby contributing to a slew of downstream adverse health effects.

Low Fiber Intake

Our gut microbes ferment dietary fiber to fuel their activities. A lack of dietary fermentable fermentable fiber, which is quite common in the United States, deprives gut bacteria of this fuel and leads to reductions of beneficial bacteria. (13)


Chronic psychological stress alters the gut microbiota; in fact, this may be one of the critical mechanisms by which stress contributes to so many chronic health issues. (14)

Chronic Infections

Bacterial, fungal, and viral gut pathogens alter the composition of the gut microbiota. (15) Importantly, a gut infection does not need to be acute to cause problems in the gut microbiota; some infections fly under the radar for years. Stool testing is a valuable tool for identifying both acute and subclinical gut infections.

Antibiotics and Other Medications

Antibiotics and non-antibiotic medications such as birth control pills, proton pump inhibitors, and NSAIDs significantly alter the gut microbiota, according to research. (16, 17) Repeated rounds of antibiotics and the use of non-antibiotic meds are important risk factors to identify.

C-Section Birth and Lack of Breastfeeding

During vaginal birth, a baby passes through the birth canal and is “seeded” with a mother’s beneficial bacteria, setting the stage for optimal gut microbiota development. Babies born by Caesarean section, on the other hand, are first exposed to microbes present on the skin of those who touch them during the C-section delivery (doctor, nurses) and immediately after (mom), as well as whatever limited microbes are floating around a sterile hospital environment. A newborn’s lack of exposure to a mother’s beneficial vaginal bacteria alters the course of gut microbiota development in infancy and childhood and may be associated with future health problems, even into adulthood. (18)

Breastfeeding provides infants with breast milk rich in probiotics, prebiotics, and immunoglobulins, which facilitate the development of a healthy gut microbiota. (19) Infant formula lacks many of these nutritional factors and is associated with suboptimal development of the gut microbiota. (20)

Circadian Rhythm Disruption

Circadian rhythm disruption, induced by factors such as abnormal sleep/wake schedules and blue light exposure at night, causes imbalances in the gut microbiome. It also compromises the integrity of the gut barrier, the second essential variable that influences gut health. (21)

How Does the Gut Barrier Impact Our Health?

As I mentioned earlier, two variables influence gut health: the gut microbiota and the gut barrier. But what exactly is the gut barrier and why is it essential for our health?

The gut is a hollow tube stretching from the mouth to the anus that passes out anything that is not digested. The gut barrier, a multilayer system made up of intestinal epithelial cells and proteins, prevents the escape of non-nutritive (and potentially harmful) substances from the intestine into the bloodstream. When the structural integrity of the gut barrier is compromised, large proteins and other molecules escape from the gut into the blood; this phenomenon is referred to as “leaky gut.”

The leakage of undesirable and incompatible substances from the gut into the bloodstream causes the immune system to launch an inflammatory response. The chronic inflammation resulting from leaky gut is an underlying cause of many chronic health conditions. Leaky gut could, therefore, be playing a role in many health conditions.

What Causes Leaky Gut?

We’ve learned that many of the factors that harm the gut microbiome, such as antibiotics and an unhealthy diet, also contribute to leaky gut, a predisposing factor in the development of many health issues.

In addition, there are particular substances that can compromise the intestinal barrier and cause abnormal permeability. Research has identified a protein called zonulin as one primary culprit.  

Zonulin increases intestinal permeability, including that of the tight junctions between intestinal cells. It has emerged as a critical link between leaky gut and adverse health consequences such as autoimmune diseases. (22) Gliadin, a component of the gluten protein, promotes leaky gut by increasing zonulin production. You can learn more about the connection between gluten, zonulin, and leaky gut in my podcast with researcher Dr. Alessio Fasano.

The Health Consequences of Leaky Gut

It is possible for someone to have leaky gut even if they don’t have gut-related symptoms. In fact, studies indicate that it can manifest as eczema, autoimmune disease, obesity, and many other chronic health conditions. (23, 24, 25)

If leaky gut is left untreated, it will be nearly impossible to improve other health issues, such as blood sugar control and cognitive function. That’s why it’s so important to focus on promoting a healthy gut barrier.

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Seven Ways to Heal the Gut Naturally

The first step in healing the gut is avoiding the disruptive factors I listed earlier that harm the gut microbiome and gut barrier.

While it’s not always possible to completely steer clear of those factors (an adult cannot control, for instance, whether he or she was born by C-section or breastfed), there are still many ways in which you can improve gut health.

1. Remove Processed, Inflammatory Foods from the Diet

Transition to a whole foods-based, nutrient-dense diet. Identify and remove foods that are causing inflammation, such as gluten and dairy. Inflammatory foods can be identified via food sensitivity testing or an elimination diet.

2. Add Fermentable Fibers

Eat plenty of fermentable fibers, found in foods such as artichoke, onions, garlic, and plantains. These fibers fuel the growth of beneficial gut bacteria and help heal leaky gut.

3. Add Fermented Foods

Fermented foods are rich in probiotics that help restore a healthy gut microbiota and intestinal barrier. Unpasteurized sauerkraut, kimchi, kombucha, yogurt, and kefir provide probiotics in abundance. However, make sure you’re not struggling with histamine intolerance before increasing your intake of fermented foods, as fermented foods can exacerbate symptoms.

4. Seek Treatment for Any Intestinal Pathogens

Gut infections are an important cause of gut dysbiosis and leaky gut. If you—or your clients—are currently seeking treatment from a Functional Medicine practitioner, ask about testing like the Genova GI Effects test or GI-MAP. These can identify specific bacterial, fungal, or parasitic imbalances causing gut dysbiosis.

5. Emphasize Healthy Sleep Habits

Get seven to eight hours of high-quality sleep a night to support your gut health. I recommend sleep hygiene practices such as maintaining a regular sleep schedule and avoiding blue light exposure at night. Blue light exposure can be minimized with blue-light-blocking glasses and the f.lux and Iris apps.

6. Develop an Exercise Routine

Develop a sustainable exercise program that will keep your gut microbes in shape. If you’re an endurance athlete, you may need additional gut support to mitigate the adverse effects of frequent endurance exercise on the gut microbiota, such as increased intestinal permeability. (26)

7. Manage Stress

Make stress-reduction practices, such as yoga or meditation, a part of daily life. Mindfulness apps such as Headspace or Calm can be helpful for people who are new to meditation.

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Join the conversation

  1. I’ve suffered with a leaky gut for a number of years now and have tried many things, including the things you recommend, to heal my gut. None of these natural remedies have worked. Only when I took the step recently of eliminating plants completely from an already very low carb diet have I found relief and healing. The effects have been speedy and dramatic: bloating and gut pain gone, along with improvements in mood, cold tolerance, energy, and more. I know you are not a fan of a carnivore diet, but for me, switching to this lifestyle has given me back my gut health – and my life.

  2. Hi Jo Grant, I also took the Elisa test and it saved me from heart palpitations and inflammation. I never knew I was allergic to so many foods I was eating. I suffer from Endometriosis and severe menstrual cramps. Avoiding the foods has helped a lot.

  3. multi-species probiotic,which ones and exactly howndo i fix a leaky gut I need a step by step.Anyone can you help.Having multiple issues

  4. I am intolerant to all fermented foods. Is there an alternative I can use to help heal gut?