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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

This content is part of an article series.

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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)

Stress

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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791 Comments

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  1. Hi there, I am from New Zealand, I recently had gastric sleeve surgery (bariatric surgery) I am very confused as to which probiotics/digestive enzymes to take, there are soooo many on the market and I really need and want top quality, could anyone give me any suggestions? I am able to get products from the states via Iherb. I will also be incorporating Coconut Kefir into my daily routine to help with gut etc, thanks 🙂

    • I too take coconut. I have been taking Probio5 daily. It has truly helped me. I am now an ambassador for Plexusslim because of the quality of our products. You can go to my website: http://www.plexusslim.com/cheryl56 to learn more about our Probio5 and other all natural products that are amazing. If you would like to contact me, please email me at [email protected]. I would love to help you find a great Probiotic. Probio5 is of high quality. Hope you can try it and hope you begin to feel better.

  2. Hi Chris

    When you have high traces of metals such as mercury, barium, aluminium and copper. And a unbalanced gut flora, which do you tackle first?

    • I’d also love to hear your thoughts on gut flora/permeability with respect to mercury. From what I’ve understood the mercury is taken up far more with a leaky gut, starting a cycle of mercury worsening the gut flora (& permeability?) – further increasing the mercury uptake..

      I was recently blood tested to > 60 ng / mL mercury.

  3. Hi Chris,

    Is there a way to heal a leaky gut when you suffer from histamine intolerance? I have been trying to heal my gut for a while now but recently found out that the foods I was using were actually making me worse. These foods (e.g. bone broth, fermented foods etc.) are the ones that are highly recommended by yourself and other experts on healing a leaky gut.

    Thanks

    • What an idiotic answer. The guy stated he has a problem with histamines, and you recommend the GAPS diet, one that is very high in histamines?

      Sheesh. I’m glad you’re not my ‘doctor’.

      • The Dr. was not responding to the message you think he was. Notice the dates…Peter Wright made his comment to no one in particular (simply to contribute to the conversation) on February 7. The comment you think he is responding to came in the NEXT DAY! Why would you speak to someone with that tone anyways? Very unkind.

        • Unkind seems to be an American condition these days. it’s horrible they way some of us treat each other. No wonder we have stomach issues.

  4. Hi, Chris,

    Microwave popcorn is my comfort food on bad days. Work is very stressful. The popcorn is organic and they use palm oil. I smother it in Kerrygold and sometimes grate Romano or Parmesan on it.

    How bad is it?

    Thanks,

    Wendy

    • Corn cooked in any method is usually not good for us. I would think twice about that snack. Read anything that Chris or Rob Wolf or Mark Sisson or any of the other leaders in clean eating have said about corn.

  5. Hi Chris,

    I am a type 1 diabetic and am working to heal my gut. To keep my blood sugars at the proper level, I eat close to a ketogenic diet (egg and dairy-free). You mentioned eating fermentable fibers. The ones listed spike my blook sugar too quickly to keep it below 120. Is there a good low carb source of fermentable fiber other than the ones you listed?

    • Try unmodified potato starch. Start slowly and build up to 3/4 tablespoons a day. You can add it to yoghurt, juices, etc. There’s lots of info on it out there. Think Chris has written about it before. Search under resistant starch. Best of luck!

  6. Chris – How damaging to the gut is alcohol like wine or distilled spirits? I totally see how beer and sugared drinks are evil due to the grains, gluten and sugar. But does alcohol itself cause/exacerbate leaky gut?

    • Hi Fredrick,

      There a quite a few studies that show alcohol will increase gut permeability in animals and humans. More specifically though, ‘binge drinking’ has been shown to cause leaky gut in humans. A recent study linked elevated blood alcohol levels with pro-inflammatory bacterial particulate (endotoxin). This bacterial-endotoxin is able to get inside the sterile compartments of the body through the leaky gut that Chris discussed in this great post.

  7. I notice lots of comments here,the only thing I did not notice is the mention of coffee enema.I was told by my homeopathic all those supplements or healthy foods would not help much if your liver or colon is congested and clog.It’s like applying supplements and foods on taferlone coating frying pan, it just slide off,and not able to be circulate to the systems to do it jobs.He said that we must do 4 steps in order to get better.First take out the trash ,second replenish,third able to digest foods,and fourth heal.Coffee enema remove trash,probiotic,fermented foods good bacteria,replenish and good enzymes to digest foods,fourth used high quality colostrum to heal leaky gut.

  8. I have what has been diagnosed as chronic rhinitis and get a sinus infection almost every 60 days. My Dr. has been prescribing an antibiotic called Levofloxacin to treat my condition. It takes about two weeks of this anti-biotic to make the sinus infection to go away and then within 60 days it is back again. How can I break this cycle. I have cut out glutin, eat lots of fresh fruit with a concentration of bananas, apples and oranges and eat very little red meat. Any suggestions?

    • Hi Gary,

      Your situation is very close to my heart as my step-son has suffered from “nasomotor rhinitis” since he was a toddler. On his mother’s side, she chooses the western medicine approach which advocates for treating symptoms with sprays, pills and when the sinus infections come, and boy do they come, he is bombarded with antibiotics, killing off all of his good army of bacteria and leaving him more and more vulnerable with each and every (stronger) dose.
      My husband and I follow what his naturopathic doctor prescribed when his mother took him to her out of, I think, a moment of desperation (for her), nothing else was working. She had his food sensitivities tested with a blood draw, along with his immune system. He came back showing no allergies and a SEVERELY compromised immune system. The doc said that it was because his immune system was fighting so hard that it was too busy to recognize what he was sensitive to, and if we calmed down his immune system by modifying his diet, allergies / sensitivities would start coming up. Well, guess what? The next test after a couple of months of a clean diet he showed lots of sensitivities.
      Which led us to the next step. The sensitivities were potentially caused by a leaky gut and there was some kind of an infection that his body was fighting somewhere because the immune system still showed compromised. Unfortunately before we could get him well his mother switched back to a western doctor that gave him more sprays, pills, etc. If you put a picture of him side by side from the summer of 2011 (11 years old) when he was on a clean diet and thin, happy and active, to today (13) eating whatever he wants, he looks like a different person. In my mind he is the equivalent of a 60 year old man. He goes through at least a roll of toilet paper to blow his nose with every day, is borderline obese and on crutches because there is something wrong with his growth plate (gee, I wonder why??). The Naturopath warned that his body was so busy fighting off these perceived “invaders” (food sensitivities) that he had little left to do the growing that he was supposed to do.
      Sorry to go on so long, but the long and the short of it is that the best thing you can do for yourself is to follow a diet that Chris Kresser, Amy Myers, MD, Robb Wolf, Jordan & Steve (from SCD Lifestyle) or so many others that advocate a paleo-like, clean diet that is personalized to you, to get you free from reactions. Get serious about it. See a functional medicine doctor (www.functionalmedicine.org). Take the time, spend your money, don’t think twice. Listene to podcasts like crazy!! You think it’s bad now, but you may just may be at the beginning of the rat hole nightmare. Look down the hole, but turn around and run! You don’t want to do down there… diabetes, autoimmune disorders, migraines, the list just doesn’t stop.
      As a side note, I had my allergies tested when he did his second test just so he wouldn’t feel alone. Guess what? Tons of allergies – I had a leaky gut! Now after changing my diet and treating the fungal infection in my gut (thank you Peruvian jungle) I feel better than I EVER KNEW I could feel. You just don’t know bad until good comes along sometimes.

      All the best health to you…

      P.S. Oranges cause mucus, you might see what happens when you cut them out. And then read Chris’ book and I am SO interested to see how you feel after 30 days of a clean diet. I swear you will eventually not need antibiotics anymore. And that will be just the beginning…

  9. Can we really get our good condition back from leaky gut? cause I’ve been using supplement (contain l-glutamine), probiotics, and now I consume a spoon of VCO/virgin coconut oil (even i’m not sure bout this one, cause no one told me this could work to leaky gut but at some point i believe it could be, so i give it a shot and it has been 2 days since i consume it like 3 times a day as it recommended.)
    but all of them haven’t show a change in my body. so here i am, questioning whether i can be able to get rid of leaky gut or not?

  10. A good vegan diet with high percentage of raw vegetables can heal numerous problems and studies show you can become the healthiest in the population. By good I mean diversity and low / no sugar / wheat and processed foods. You have to be aware of the probable need for Vitamin B12 supplements due to sterility in the western food production system which prevents the vitamin produced by micro-organisms being transported to humans – however, this may be consumed with Algae, Sauerkraut, Miso-soup). Do the research (e.g. China Study), find out about the ignorance and myths still around (e.g. protein, calcium, iron – which are actually all available in sufficient quantities in the vegan diet) and I recommend it for the sake of your health, animal compassion and a sustainable future on Earth. It’s all connected, folks!

    • I feel so much better after going Paleo and making sure to have adequate amounts of fish/seafood, poultry and red meat in my diet. I wish I had done this years ago. A cascade of health problems have cleared up since I started, including a normalized digestive tract.

  11. Love your blog Chris.

    Please i’d like to know what someone suffering from hidradenitis suppurativa can do to control or manage it. I’ve been suffering from HS for 8 years now and it keeps getting serious. All the doctors do is give me antibiotics which i’ve stopped taking when i found out about the side effects. I’m suspecting that probably it’s caused by this gut issue. I don’t know what to do because it’s affecting me pretty badly.

    • The Hidden Plague – by Tara Grant is specifically about healing HS, and contains a ton of information about dealing with the misery of the condition, the general lack of information in the medical community about how to treat it effectively.
      Tara has HS and has managed to put into remission.

      A very tough health problem to deal with. Best of luck to you.

  12. My 7 yr old daughter has been having stomach pains for 2 months now and we have no answers. Have tried prevacid and levsin with no success. She is now on Klaire labs probiotic (ther biotic complete, 25+ CFU) once daily. She has a dairy and nut allergy. The assistant from Klaire labs told me that the probiotic should be ok for her even if she has a dairy allergy bc it does not contain milk/casein. She hasn’t gotten better and has missed 25+ days of school. We’ve also started her on a Chinese herbal tea to aid digestion. We are trialing her on a specific carb diet excluding grains from her diet. Today we will be seeing a dietician who will go over blood lab results. She has had blood work done testing for h-pylori (?), pancreatitis, and other inflammatory conditions. She was originally taken to the ER where they did an x-ray and diagnosed her with constipation. That has since cleared up but she is still having abdominal pains, complains of weakness, and sometimes that her head hurts which she states is “nausea”. She is on a calcium/magnesium/Vit D3 supplement bc of her dairy allergy. Is there anymore I can do for her?

  13. Hi! I’ve just had to give my daughter, 2 1/2 yrs antibiotics for the first time as she has a chest infection. As I have my own issues with leaky gut, this is a concern to me. What can I do for her, being so young, to help restore gut flora? TIA

  14. Hi Chris,
    I was diagnosed with Crohn’s 11 years ago but i’ve been lucky enough that my illness is pretty mild. A recent colonoscopy showed that I have a small area of inflammation which is bleeding a little and my doctor wants to put me on medication. I have followed the SCD diet on and off since being diagnosed but I have been on it strictly for 3 months now. Do you have any advise on how I might be able to deal with this issue in a natural way? I have no other symptoms at the moment and I would rather not take medication if avoidable. Any advise would be really appreciated.
    Kind Regards
    Rebecca.

  15. Hi Chris,
    I’m in the UK – a very small little island within the UK to be exact. My access to cutting edge, or even accurate medical assessments is limited to say the least.
    I’ve started following a LCHF type diet, with some paleo and bulletproof type principals (including the coffee each morning)
    I have been eating a lot of eggs and I think I may have developed at the very least a sensitivity to them.
    There is a local Chinese medicine practice that say they can measure my sensitivity / allergy to food. They take hair samples and send them to lab. Is this a viable and accurate measure, or simply a waste of money?
    How do you suggest I get my allergy/sensitivity and gut health tested reliably?
    Kindest regards
    Thomas

  16. Hi tania. Ive read oregano oil for blasto can help 6/8 weeks. Look it up on internet . Best of luck , im in same situation

    • Hi Kevin,
      I just posted a reply to Tania’s giardia problem. I had the same problem when I was pregnant and couldn’t take antibiotics. I researched and found that raw garlic is the best natural treament for giardia and it works. 3-4 large cloves of garlic, 3 times a day, for 5 days. It is much faster than 6-8 week treatment you mentioned. Just read what I wrote to her above. I hope you are feeling better.

  17. I heard about leakygut recently and thought it is a new type of sickness. After that I searched the net and found this video ( http://t.co/gLqFqWDBw2 ) which describes most of the symptoms I have. One of the mmost frstrating problem for me is the sound my belly makes when I refuse to pass wind. It is almost unbearable especiallyin class. But does this all natural approach work? Thx.

    • I don’t have any experience with her program but I did watch the video. My thought is that you could probably find a very similar gut restoration program in a book at the library. Off my head, here are two: Clean Gut by Alejandro Junger and Gut and Psychology Syndrome by Natasha Campbell-McBride. I’ve read both. My library always has quite a waiting list (popular subject) for them but they are worth it. Each of these folks have a website with alot of help…for free. I’d suggest saving the $40 for now and checking out the Clean Gut site as it has a free pdf that states his recommendations for supplements (here’s where your $40 could go!) and another with recipes. Also, Clean Gut can be purchased in audio format from Audible.