How To Heal Your Gut: A Complete Functional Medicine Guide To Restoring Microbiome Health

Guide To Gut Health

Your gut’s influence over your health cannot be overstated. The trillions of microbes and colonies located in your microbiome are the manufacturers and managers of how you look, feel, and think. It makes up 70-80% (1) of your immune system, produces (2) a large amount of your “happy” neurotransmitter serotonin, and contains 10 times more bacterial cells than you have human cells!

You are, in truth, more bacteria than human. And researchers are quickly learning just how much it regulates all aspects of your health.

When your microbiome is healthy your overall health is likely to be quite good. However, many lifestyle behaviors, toxin exposures, and dietary choices can compromise gut health and lead to many downstream health issues. When your microbiome is weakened or damaged, it can “switch on” a number of potential disease processes throughout the body that may, on the surface of things, seem to have very little to do with your actual gastrointestinal system.

That is why it’s vital to educate yourself on the microbiome. By doing so you are taking back control of your health. Read on to learn more about what happens when your gut is unhealthy, what causes poor gut health, how to heal your gut, and more. This is your definitive guide to all things gut health.


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What are the signs of an unhealthy gut? 

Because your gut controls so many areas of your health, you don’t have to have typical gut symptoms to have gut problems. These are a few of the far-reaching health problems your gut has influence over. 

Your poor gut health may trigger conditions such as:

  • Autoimmune Conditions
  • Mental Health Disorders
  • Poor Immune Health
  • Heart Disease
  • Type II Diabetes
  • Skin Conditions
  • Weight Gain and Obesity
  • Acid Reflux or GERD
  • Cancer
  • Asthma or Chronic Sinus Infections
  • Constipation or Diarrhea

Types of gut problems

Gut problems don’t always look the same. Even if your symptoms look similar to another person, healing can only truly begin when you uncover what is happening underneath the surface.

1. Leaky gut syndrome

An intestinal lining damaged by years of unhealthy eating, food intolerances, stress, and toxins, can allow undigested food particles and bacterial endotoxins called lipopolysaccharides (LPS) to pass out of the digestive tract and into the rest of the body where they don’t belong. Sensing an “invader,” the body can react with systemic inflammation that can become chronic.

In functional medicine, leaky gut syndrome is considered a precondition for autoimmune diseases and many other health problems and requires intervention to heal the gut lining in order to stop the inappropriate immune reaction.

2. Bacterial imbalances

Your microbiome contains a delicate balance of bacterial and fungal species that live in symbiosis with you, but some of those species are pathogenic and can cause health problems if they are allowed to overgrow, crowding out more beneficial species – a condition called gut dysbiosis.

This can lead to health-damaging conditions like small intestinal bacterial overgrowth (SIBO) which in turn have been linked to a wide variety of health problems, from irritable bowel syndrome to autoimmune disease. For example, anxiety and depression have been linked to lower levels of Lactobacillus helveticus and Bifidobacterium longum, and weight gain was linked to higher amounts of Firmicutes.

Ironically, when someone with dysbiosis or SIBO starts to eat healthier, by increasing vegetable intake for example, it can cause an increase in gut symptoms like constipation and bloating. But it is the underlying microbiome issue, not the vegetables that is the root problem.

3. Histamine intolerance

Another issue I often discover in patients with leaky gut syndrome and bacterial overgrowths is histamine intolerance, which is a dysfunction or deficiency of the enzymes that break down histamines – the chemicals produced during an allergic reaction. In people with histamine intolerance, foods that naturally contain histamine or trigger the release of histamine in the body, become problematic. Without the enzymes to effectively get rid of excess histamine, the overflow can cause digestive problems like heartburn, acid reflux and stomach pain after eating, among other issues like anxiety, headaches, hives, and asthma.

4. Yeast overgrowth

We all have some yeast in our gut microbiome, but overgrowths of yeast such as Candida albicans can cause chronic low-grade inflammation and immune stress. People with an already weakened immune system or an autoimmune condition can find candida overgrowth to be a trigger for more health problems.

How do I know if my gut is healthy?

While you may suspect you have gut problems because of your symptoms, without running any labs, you won’t know for sure. These are the labs that I typically recommend to my patients, to determine if any of these gut problems are a factor in a particular health case:

1. Gut permeability labs

I always run tests for Zonulin and occluding antibodies. These two proteins control gut permeability, and the presence of antibodies can indicate damage to the tight junctions that keep your gut lining sealed. I also test for actomyosin antibodies, which can indicate destruction of the gut lining, and lipopolysaccharides (LPS) antibodies, which can also indicate leaky gut syndrome, if these antibodies are not contained within the digestive tract.

2. A comprehensive stool analysis

This test can uncover everything from the presence of parasites to bacterial imbalances to conditions like candida overgrowth or SIBO (small intestinal bacterial overgrowth) or SIFO (small intestinal fungal overgrowth)—any of which can negatively impact gut health.

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How long does it take to heal your gut?

Imagine the surface area of your gastrointestinal tract. If you spread it all out, it would cover about the size of a tennis court! This internal “court” is covered in special cells called enterocytes that constantly regenerate so that you get an entirely new gut lining every two to three weeks. (3) 

If you don’t have any chronic conditions or food sensitivities, you could heal a not-so-perfect gut in as little as two weeks or as long as 12 weeks. In fact, a study from Harvard, published in the medical journal Nature, found significant changes in gut bacteria actively happening just three days after a dietary change!

Unfortunately, most people who are trying to heal their gut do have other health issues that make healing happen more slowly. If you have chronic inflammation, Lyme disease, viral infections, blood sugar issues, adrenal fatigue, SIBO, an autoimmune condition, histamine intolerance, candida overgrowth, or leaky gut syndrome, it’s going to take longer to get you back on the right track. You are on what I call the autoimmune-inflammation spectrum, so you are going to have to come at your healing from multiple directions at once to get results.

How to heal your gut naturally

1. Elimination diet

An elimination diet is my gold standard for uncovering hidden food intolerances. In order to heal your gut, you need to stop eating foods that continue to damage your gut and increase inflammation, but you can’t know what foods are irritating to your individual gut until you remove all potential irritants for a certain amount of time and slowly reintroduce them one at a time, monitoring your body’s reaction. This will allow you to determine which foods your body loves and which foods your body hates. My mindbodygreen video class gives you step-by-step instructions on how to do an elimination diet the right way.

2. Rotating your food

Variety is the spice of life as well as the salve to an inflamed gut. Eating many types of foods will not only give you a wide variety of much-needed nutrients, and rotating these foods to avoid having any one food too often will help you heal and keep your immune system balanced. A good rule of thumb is to never have any one food more than once a day, or even better, no more often than every three days. For example, if you love leafy greens, have Romaine lettuce one day, kale the next day, and collard greens the day after that, before rotating back to Romaine lettuce.

3. Taking probiotics

Probiotic-rich fermented foods like sauerkraut, kefir, and kimchi will reinoculate your microbiome with good bacteria—especially important if you’ve recently had a round of antibiotics or been under a lot of stress. A probiotic supplement will also give your gut a much-needed boost of essential bacteria. 

4. Drinking bone broth regularly

This superfood brims with collagen and minerals that can soothe and repair a damaged gut. Sip it alone as a warm drink or use it as the base for soups and in other recipes. I recommend making bone broth yourself at home in a slow cooker or pressure cooker (it’s easy), using bones from grass-fed cattle or organic chickens. If you don’t want to make it yourself, Bare Bones and Kettle & Fire are both great options.

5. L-Glutamine

L-glutamine has been proven to improve gut permeability as well as prevent further deterioration of the gut. 

You can find L-glutamine in foods like grass-fed beef, bone broth, grass-fed dairy, and red cabbage. Eating cabbage in the form of sauerkraut will increase its gut-healing abilities since the fermentation provides your gut with probiotics that also help make L-glutamine more bioavailable. Aside from whole foods, I advice supplementing anywhere between 2 and 5 grams per day. Note that L-glutamine powder will be easier for your gut to digest than capsules.

6. Trying intermittent fasting

By going extended periods of time without eating, you’re able to give your digestion a much-needed break. There are many ways to do this, such as fasting every night for at least 12 hours (many people do 16 hours) or fasting for one day every week.

7. Managing your stress

If you are feeding yourself a giant slice of stress every day,  all the healthy food in the world isn’t going to help heal your gut. Chronic stress can suppress the immune system, decrease blood and oxygen flow to the intestines, and contribute to gut lining permeability. Making time to de-stress through pressure-relieving activities like tai chi, yoga, or meditation can make a huge difference in your stress levels and in turn, your gut health.

8. Coconut oil

How did we ever live without coconut oil? This versatile superfood is full of the healthful saturated fats that are integral to gut healing, as well as lauric, capric, and caprylic acids that have important antimicrobial, anti-fungal, and antiviral properties. This real food medicine gently cleanses your GI system but is also great externally to nourish your skin. Choose organic, extra virgin, cold-pressed varieties for maximum benefit.

9. Eating more cooked foods

Raw foods are packed full of nutrients but they can also be difficult to digest. Cooked foods decrease the amount of work your digestive system needs to do to break down food because some of that has been done for you through the cooking process. Even easier to digest are pureed foods like smoothies and pureed soup. Going easy on your digestion can help reduce bloat and lead to a healthier gut. As you heal, you will be able to tolerate raw foods better.

10. Taking targeted natural supplements

Nobody wants to take a giant fistful of vitamins every day, but there are a handful of gut-healing supplements I often call upon to help my patients in digestive distress. These can help speed healing and make a big difference in symptoms:

  • Colostrum: The lactoferrin in colostrum works as a prebiotic to feed good bacteria and fuel its growth. It also promotes cell growth in the intestines to repair a damaged gut.
  • Slippery elm: This natural botanical works as a demulcent to reduce inflammation in the gut. You can find this in tea or supplement form.
  • Turkey tail: This adaptogenic mushroom works wonders against gut overgrowths like SIBO and candida overgrowth. Try it in a warm drink.
  • Deglycyrrhizinated licorice: Sip on licorice tea to soothe and heal your gut lining and ease digestive trouble.
  • Marshmallow root: This root supports the repair of a damaged gut lining by coating the stomach to protect it against increased inflammation. You can find this in tea or supplement form as well.

11. Lemon Water

Lemons contain ample amounts of phytonutrients, vitamin C, and fiber which are all needed for supporting gut health. Vitamin C is a powerful antioxidant that helps to lower inflammation in the gut and boost the immune system. It also works as a natural antimicrobial to bring balance to the bacteria in the microbiome.

Lemons are also high in a type of fiber called pectin. Multiple studies have shown that these particular fibers balance bacteria and stimulate the growth of important probiotics in the microbiome like Bifidobacterium. (4) The whole-food fusion of vitamin C, prebiotic fiber, and phytonutrients may create a cleansing effect, especially if drunk first thing in the morning on an empty stomach.

In order to really get the most positive impact on your gut health, I do not suggest using lemon juice as a stand-alone tonic. Try to keep as much of the pulp as you can with the lemon juice in your water since the pectin fiber and phytonutrients are mainly found in the lemon pulp. Also, make sure the water is either warm or cold, not hot, as the hotter water denatures the Vitamin C.

12. Apple Cider Vinegar

Research has shown that vinegar can mildly lower the growth of gram-negative bacteria like Pseudomonas aeruginosa and Staphylococcus aureus. (5) These bacterial colonies are higher in bacterial endotoxins called lipopolysaccharides (LPS). Higher LPS levels are implicated with a whole slew of inflammatory health problems as well as leaky gut syndrome.

Apple Cider Vinegar specifically has been shown to have anti-yeast, anti-fungal, and antiviral benefits which are all helpful at supporting the microbiome and immune balance. (6) Additionally, ACV has the ability to improve indigestion and heartburn, which I’ve found commonly in my patients to be caused by low stomach acid or hypochlorhydria.

I usually see the best results when using ACV in its raw, unfiltered form with the “mother” included. You’ll be able to see the mother as a sediment in the bottle but it usually will say so on the label. ACV is very acidic and may be hard to swallow as well as cause damage to tooth enamel and the throat. It is important to dilute 1 to 2 tablespoons in at least 1 ounce of water or juice. 

13. Digestive enzymes

Digestive enzymes are proteins that break down the food you eat into smaller pieces that are easier for your body to absorb, utilize, and turn into energy. Some people have food intolerances (like lactose) where they lack the enzymes to break down this specific protein or don’t make enough digestive enzymes which can slow digestion and lead to uncomfortable symptoms like bloating, cramping, and gas. This is not uncommon, especially in people who are over 50, have low stomach acid, or you have IBS or IBD. 

While digestive enzymes aren’t the go-to solution for those with specific intolerances, they can be helpful to have on hand for when you come in contact with a food you weren’t expecting to eat or if you need a little help with enzyme production.

14. Eat more fiber

Fiber is essential for a healthy gut. Not only does it help you build up good gut bacteria, it keeps you regular and having healthy, solid bowel movements. Fiber can be found in vegetables like artichokes, carrots, and broccoli.

15. Exercise

Exercise is great for all areas of your health, but it can also increase beneficial bacteria in your gut and overall bacterial diversity. (7)

16. Digestive bitters

Digestive bitters are herbs that have a bitter taste including burdock root, bitter melon, and dandelion. Digestive bitters are taken with meals and work to stimulate the production of digestive enzymes that help break down food and make the digestion process easier on your gut. You can find digestive bitters in herbal tincture form but I personally love adding bitter greens into soups, salads, and stir-frys.

17. Ginger

Ginger has been used for thousands of years to soothe stomach problems due to its anti-inflammatory properties. It also helps to alleviate heartburn and acid reflux as well as stimulate the production of stomach acid. Try adding ginger to more recipes or cut up fresh ginger root to make a gut-soothing tea to sip on.

Seeking help from a functional medicine doctor

If you believe you are experiencing conditions caused by poor gut health issues, it is important to consult with a medical professional before trying any treatment plans. As an expert in gut health, my team and I provide you with the recommended testing and labs, followed by the right solutions for your health and its unique needs.

READ NEXT: The 14 Best Herbs For Intestinal Inflammation

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  1. Wiertsema, S.P.; van Bergenhenegouwen, J.; Garssen, J.; Knippels, L.M.J. The Interplay between the Gut Microbiome and the Immune System in the Context of Infectious Diseases throughout Life and the Role of Nutrition in Optimizing Treatment Strategies. Nutrients 2021, 13, 886. https://
  2. Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, Nagler CR, Ismagilov RF, Mazmanian SK, Hsiao EY. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell. 2015 Apr 9;161(2):264-76. doi: 10.1016/j.cell.2015.02.047. Erratum in: Cell. 2015 Sep 24;163:258. PMID: 25860609; PMCID: PMC4393509.
  3. M. Godlewski Michal, The Death Pathways in the Neonatal Gut, Current Pediatric Reviews 2011; 7(4) .
  4. Slavin J. Fiber and prebiotics: mechanisms and health benefits. Nutrients. 2013 Apr 22;5(4):1417-35. doi: 10.3390/nu5041417. PMID: 23609775; PMCID: PMC3705355.
  5. Johnston CS, Gaas CA. Vinegar: medicinal uses and antiglycemic effect. MedGenMed. 2006 May 30;8(2):61. PMID: 16926800; PMCID: PMC1785201.
  6. Visual inspection with acetic acid for cervical-cancer screening: test qualities in a primary-care setting. University of Zimbabwe/JHPIEGO Cervical Cancer Project. Lancet. 1999 Mar 13;353(9156):869-73. PMID: 10093978.
  7. Monda V, Villano I, Messina A, Valenzano A, Esposito T, Moscatelli F, Viggiano A, Cibelli G, Chieffi S, Monda M, Messina G. Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxid Med Cell Longev. 2017;2017:3831972. doi: 10.1155/2017/3831972. Epub 2017 Mar 5. PMID: 28357027; PMCID: PMC5357536.

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Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

Gut Feelings Dr. Will Cole 6

Gut Feelings

Healing The Shame-Fueled Relationship
Between What You Eat And How You Feel