A streamlined stack of supplements designed to meet your most critical needs - Adapt Naturals is now live. Learn more

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

by

Published on

how to heal your gut naturally

This content is part of an article series.

Check out the series here


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.

Like what you’re reading? Get my free newsletter, recipes, eBooks, product recommendations, and more!

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.

ADAPT Naturals logo

Better supplementation. Fewer supplements.

Close the nutrient gap to feel and perform your best. 

A daily stack of supplements designed to meet your most critical needs.

Chris Kresser in kitchen
Affiliate Disclosure
This website contains affiliate links, which means Chris may receive a percentage of any product or service you purchase using the links in the articles or advertisements. You will pay the same price for all products and services, and your purchase helps support Chris‘s ongoing research and work. Thanks for your support!

791 Comments

Join the conversation

  1. I are in my sixties, I get flatulence quite often. I have read articles about taking lemon juice with warm water to reduce acidity. I have been taking lemon juice with warm water. My urine ph was 8. I am not sure if my stomack is acidic or alkaline. What should I do to reduce gas production.

    • By 50 our enzyme production drops to ’bout half. A good multi-enzyme formula will help you digest proteins (protease), fats (lipase), milk (lactase), carbs (amylase) and fiber (cellulase). Complement with a good probiotic. 🙂

  2. Hi lo was born with poor digestive tract. Small intestine weak . Constipation jjoint pain suffer fatigue when I exercise I feel pain in my hip shoulders .lol experience poor concentration. I take probiotic, L Glutamine, gluten free . Rat green smooth I the morning. Eat veggies. Cutting Ogg wheat and yeast. No yellow cheese or eggs. Hopefully inflammation settles and gut improves. Ha en any suggestions?

  3. Question 1.

    If you could only eat 4 foods what would be the best for your digestive system.

    Question 2.

    Green tea is on all the must drink for best health lists. Is this because it helps the gut processes.

  4. I Accept the idea of the gut being the source of tons of health problems and how manufactured foods have raped America’s well being. I have several questions.
    1. Will cutting out manufactured foods greatly improve your health.
    2. Then will cutting that kind of foods intake in half or more improve your health even more. Less to digest or foods to cause problem so to speak.
    [email protected]

  5. C-section delivered – infant gut colonized by bacteria in OR suite/hands of surgeons and nurses, rather than mom’s vaginal canal. Not breastfed. Lots of genetic SNPs that could block methylation pathways. Symptomatic of many of these conditions all my life. Tried just about everything. Best solution for me is aggressive B12 replacement therapy with injections/patches/high dose sublinguals – but not cyano, or folic acid, since that seems to pool in my blood. Hydroxocobalamin/Megagolinic all the way for me baby. B12 Deficicency seems to be at the root of so many of these conditions, even hypothyroidism, since the body cannot detoxify the hydrogen peroxide byproducts of T4 to T3 conversion if there is not enough glutathione in your system, as manufactured by B12 and folates, among a few other things…….if I had to wait on an MD to help me get what I needed, at age 57, I am sure I would be inpatient for early dementia/Alzheimers…….stupid, stupid, stupid, unethical medical profession!!!!!

  6. I’m just starting this journey with the “5R” Gastro Plan, I have to start off slow with deleting things in my diet that I have been eating for years. I don’t want to give up so easy. today was pretty much ok, i’m a very picky picky eater, don’t like vegetables, but i do like fruits. .kind of lunch and dinner meals do you have in mind. i’m ok with drinking water all the time. trying to stop using milk or sweetened cereal for the and first week. I have to keep myself pre-occupied with things because i’m a sweet junky and a late night eater. but as of today. i’m starting to stop eating after 9pm and getting better rest. I set a new bed time too. PLEASEEEEE HELPPP

  7. so, on the list of what to do to fix gut issues, I have only 3 I can actively use. I am on a super limited diet due to food intolerances—only kale, meat, white rice, salt and olive oil. REALLY. What is my priority move then? first a parasite cleanse? Idid one, but had trouble getting to a full dose and feel I should redo it since parasites were found in my test…….. then probiotics? I would appreciate any advice.

    • As it was explained to me, the liver needs to be detoxed and to not worry about other types of cleanses for parasites, etc. That once the liver is cleansed the body then goes about cleaning house.

      Liver detoxing methods/protocols can take various forms – herbal cleanses, liver supporting supplements and/or tonics, cleansing foods, coffee enemas. Personally I lean toward liver supporting foods.

      My practitioners told me that once the liver is cleansed and strong the body is then freed up to heal the way it was designed to. Um, medically I have no idea how to define that any further, but I am following the guidance of these practitioners. They say no matter the issue, the body tackles it better with a healthy liver. The more liver supportive foods that worked for my body, the more foods I was able to eat. My hormones are balancing, as well as other improvements. But my inflammation from a lung infection and compromised digestive system, and my fatigue, are serious enough however that I have to take further cleansing steps. So I just thought I might share that liver health/liver strength appears to be a factor in the overall healing process. Apparently, we’re all bombarded with toxins on a daily basis. As we detox from wheat and dairy etc. with better nutrient rich foods we then release stored toxins. Help the body to clear them out via a liver detox protocol, and then the body can heal better.

      By the way, thanks to the reader for the wheat withdrawal link. It explained what happened to me when I quit gluten and all grains in late fall of 2012. Now I finally have an answer to the calve cramps.

      Best health to all.

  8. Hi, I have been recieving your emails and reading your very interesting articles and comments. I am in a bit of a quandary though. About 10 weeks ago I gave up ALL wheat products (to give up Gluten) and had the worst time with the withdrawal symptoms: (just a brief list)
    stomach in SUCH pain, bloatedness, all the aches and pains of flu without flu, stress, dramatic weight-loss 82 kilo to now 72.5K
    I had side pains and back pains, till finally I decided to go BACK to wheat. NOT in a big way, but bread, less slices, and some cerial, very little. It was WORSE!!! I had all the pains of withdrawing, with other stomach pains and pain under my lower ribs. I lost so much magnesium and salt that I had cramps permanently in my calves (I was quite heaklthy before this all happened and NEVER suffered from cramps).

    I had had enough, I went to the docter after I beleive my immune system went so low (apparently because of the wheat withdrawal), as I NOW had allergies to dust!!! NEVER had this in my life untill I gave wheat up. I now cough so bad and have to hoover every day. It was soo bad I went to the doctor for the respiratory prolem, where I almost choked from the coughing, I now have a “puffer” 🙁 and I find I may have a stomach ulcer or possibly kidney infection due possibly to the dramatic weightloss.

    I have just had a series of bloodtests then was urgent requested to go to the hospital for an ultra scan of my stomach and bladder.
    I am 56, I beleive this was alll a mistake at my age. I think most doctors have never heard of what you are talking about, especially in England, I had to complain about 2 doctors before I got a doctor who would give a dam to take the interest, and he is flumuxed!! I have given him printouts of your comments and of this page http://www.wheatbellyblog.com/2013/09/surviving-wheat-withdrawal/ but they look at me as if I am an idiot and how dare I research this myself.

    Personally I wish I had never given it up…. BUT I read articles like this one and it scares me that we are alll BASICALLY unhealthy!! And it is so hard to know what to do.

    Last comment: you mention antibiotics and ant-acids are bad for the gut. The doctor has given me antacids for my problem, and will likely need to give me a course of antibiotics if its an ulcer…… what is one to do???????

  9. Just thinking out loud here… But if the human gut holds 100 trillion bacteria, and those 400 species are specific to the environment of the human gut, would probiotics supplements make any real difference? After all, the species in probiotics are not cultured from the gut so how would they survive in the gut and what are they doing once they get there? Also, the billion or so that are in one supplement tablet is just a fraction of 100 trillion. The fraction is so small compared to 100 trillion it is hard to imagine having much if any impact.

  10. I am 50 years old and have never had any allergies but recently I have had allergic reactions to anything that has a seed in it. Tomatoes, avocados and mustered seeds to name a few. A friend told me to look into leaky gut. I think maybe that’s the problem. I have very poor medical insurance and I just don’t know what to do. Any help on were I could start would be great. Thanks danielle

  11. I am relatively new to the understanding that gut health leads to whole health and I have a lot of questions. Our children were all born naturally, and I breastfeed/breast all of them (until at least age 3). However, they all had eczema, the middle one self -clearing at age 2, but the oldest continuing still at 6, and the baby just developing it at 4 months this past week. We’ve been eating fermented foods for years, but recently upping the variety and quantity. We also follow the grain and nut protocols in Nourishing Traditions. I took probiotics during the pregnancies of our two younger children, though i had antiobiotics during delivering for the first two. I am heartbroken that child #3 has developed eczema despite a natural homebirth and no antibiotics. I think i must not have any decent flora to pass them. What else can I do to improve my flora? How can I get the baby’s flora to establish as healthy (and clear the eczema)? What about the 3 and 6 year olds? Can I shift their flora, and our family’s in a more positive way?

  12. A little help please! When trying to add digestive enzymes, what am I primarily looking for? It makes my head swim at the prospect of trying to understandings all the ” claims”!!!

  13. Great article Chris. I discovered that this was my problem after years of declining health and six months of constant colds/flu/viruses, aching joints and general lack of health. Having hit my “health bottom”, following the 2nd round of antibiotics in an inappropriate, but medically predictable response to chronic illness. Trying to treat the yeast infection that followed, I stumbled onto the answers you discuss.

    A mere 2 weeks into a repair regimen, I had regained vitality, had energy for the first time in years and was losing those impossible inches around my back and belly. I caution people who want to jump into a very strict regimen. For many, the inflexibility of some popular fad diets dooms them to failure, and is, honestly, unnecessary. You didn’t get this way overnight, and you aren’t going to fix it all in one day. I recommend just starting to look at sugars, alcohol, and anything “white” that converts into a sugar equivalent immediately (white starches) as “Poison”. Eliminate them. I add 2 glasses of my tonic: 8 oz of water with 1 tbsp Apple Cider Vinegar, a small drop of maple syrup, juice of 1 lemon and cayenne pepper. You get used to the taste and begin to like it. I munch on sunflower seeds to get me through the craving/manic urges to eat things I shouldn’t. Also, at the same time, I add 2 probiotics – a good, wide spectrum bacteria mix, and a quality yeast (good yeast) rebuilder, like Florastor, with Vitamin D, Magnesium, Calcium, and Fish Oil supplements morning and night.

    This has worked for me, without severe diet rules or complicated processes, and as such, can see myself maintaining these habits indefinitely.

    In Health –

  14. My son is 39 yrs.old and has had Colon Cancer.He was deemed cancer free in May 2013. He loves sweets and consumed alot of Butterscotch candy losenges over a 2-3 month period. He wound up with what the Dr.s thought was Crohn’s or Ulcertive Colitis. He has been on med.s for 3 months, has leaky bowels and a bad rash on his bottom. Nothing seems to be helping . We are open to any and all suggestions.I honestly think it had something to do with the large amounts of the candy, he wasn’t this way before.

    • He has a fungial infection. Sugar feeds it!Tell him no sugar for a while and start taking coconut oil everyday.When he first takes it he will feel bad because it’s killing it.tell him take some charcoal and keep taking the oil.stick with it it will heal him

  15. Thanks so much for the article. I have severe gluten sensitivities and wondered what you thing about using whey protein when doing body building. I am wondering if anyone has experience using whey and its impact on the gut.

  16. It is possible to acquire a leaking gut after hernia surgery with mesh in that some how the gut is permeated? My ex’s blood work has shown auto immune characteristics after mesh surgery along with peripheral neuropathy as a symptom.

  17. I’ve seen some research that shows wheat bran is a good source of food for bifidus strains of bacteria, boosting bifidus quite a lot. I seem to have much better stool quality since going on 1/2 cup of wheat bran daily (type4, good color and moisture content), before going on the bran I was stuck with slow transit and type one. I tried a number of alternatives such as Psyllium, ground flax, chia or hemp seed and more. Nothing seemed to help until I gave bran a try and I was back to my old regular self within 3 days.

      • While the bran may speed transit, I would think that it would have the same negative nutritional elements.

  18. I read allot about eating fermented foods to heal leaky gut…what’s an alternative if you can’t eat fermented food?

  19. My mom is in her 50s and was recently diagnosed with what her doctor is calling an extremely rare form of hypothyroidism. It’s NOT Hashimoto’s – he told her that the form she has afflicts 1% of those with hypothyroidism, and possibly fewer than that. Sounds like it’s genetic. She takes a little pill to help with her symptoms (mainly extreme exhaustion) but I refuse to believe that she can’t be helped by diet, especially recommendations mentioned in this post. She already kicked her diabetes to the curb by cutting out most gluten. Can you offer any insight? I’d love to help her, and also stave off any possibility of me inheriting this in the future. Thank you.

    • Hi
      I am on the search for anyone who has been diagnosed with diabetes and now through diet is no longer on medication. If I can find that person I’d like very much for them to share their story with my friend. My friend won’t explore this option unless I find someone its worked for.
      Thanks

  20. Leaky gut syndrome, carpel tunnel, soft bone density, weight loss, adrenal gland fatigue, constipation, hasimoto’s. low somach acid, sadness, lack of sleep, work place stress, pneumonia, that pretty much sums up my last year.
    I encourage you to never give up, keep looking and you will find the right answers that fit you or your loved one you are caring for.
    In the beginning I could only tolerate 10 foods: chicken and broth with garlic and onions, parsley sea salt, green beans, pears, pecans and quinoa. I missed 3 months of work. I was sensitive to salicylates ( natural inflammation foods there is a long list), night shades (tomatoes, potatoes, all peppers, eggplant) , proteins (brown rice, peas, dairy, eggs, red meat.)
    A natural path doctor encouraged me to go on an elimination diet.
    I eliminated corn, soy, wheat dairy, eggs, sugars/sweeteners, alcohol,
    Always wrote a food diary, compared it to symptoms, and how I felt. Adjusted my diet accordantly. When I started blended smoothies I had to cook any vegetable and greens. And rotated greens every 3 days or so. I can only tolerate swiss chard and all leafy greens, but spinach and kale will start getting brain fog, fatigue lack of sleep, all over again.
    She gave me probiotics, vitamin D3, Calcium/magnesium, multi vitamin and drink lots of water (non-chlorinated)
    In the last year I’ve had days with no symptoms. I look back at my diary to see what I did or did not do.
    Researching on the internet I learned I had to tailor the information for me. It;s been a trial and error process to understand the ever changing me.
    Acupuncture has helped. Heal your Body by Louise L Hay
    was another fascinating way of healing. It’s a mental approach to thinking about getting well.
    Keep researching, learn what foods do for you.