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

A healthy gut is essential to overall health, and a balanced gut microbiome influences every aspect of wellness. When your microbiome is weakened or damaged, it can trigger the onset of conditions that aren’t always obviously connected to your gastrointestinal health. 

As a functional doctor, educating patients about the connection between their gut and seemingly unrelated symptoms is a huge part of what I do. By understanding what can happen with an unhealthy gut, you can start learning about how to heal your gut in a natural, sustainable way.

1. Try An Elimination Diet

The fastest way to reset your gut is to start with your diet. I’m not talking about specialized diets or 7-day detox plans. It’s important to understand the foods your body loves and the foods it hates.

An elimination diet is my gold standard for uncovering hidden food intolerances and sensitivities. This approach involves removing potentially irritating foods from your diet and then slowly reintroducing them one at a time. Monitor your body’s reactions to each “new” food.  

Foods that cause any level of gastrointestinal distress or inflammation aren’t doing your gut health any favors. Focus on the foods that make you feel good for better digestion, nutrient absorption, and improved symptoms from common gut conditions. (1)

2. Rotate What You Eat

Variety is the spice of life and a salve for an inflamed gut. Eating many types of foods gives you a wide variety of much-needed nutrients. Rotating these foods to avoid having any one food too often helps you heal and keeps 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 than once every three days. For example, if you love leafy greens, have Romaine lettuce one day, kale the next, and collard greens the day after that before rotating back to Romaine.

3. Drink Bone Broth Regularly

Bone broth is full of collagen and minerals that can soothe and repair a damaged gut. Studies show it’s particularly good at reducing inflammation, which can mean relief from conditions like ulcerative colitis (UC). (2)

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 in a slow cooker or pressure cooker using bones from grass-fed cattle or organic chickens. 

If you don’t want to make it yourself, Fond and Kettle & Fire are both great options.

4. Take Probiotics

Your gut’s microbiome is a complex community of trillions of microorganisms living in your digestive tract. These microbes found in fermented foods play critical roles in digestion, immune function, nutrient absorption, and even your mental health. 

Probiotic foods and drinks like sauerkraut, kefir, kimchi, and kombucha introduce good bacteria that enhance your microbiome, especially after a round of antibiotics or chronic stress. (3) That gives your gut its best chance at preventing conditions linked to microbiome imbalances. 

Probiotic supplements like The Probiotic can support a healthier microbiome in the face of common gut stressors like toxins, stress, and dietary choices.

5. Manage Your Stress

If you’re feeding yourself a giant slice of stress every day,  all the healthy food in the world isn’t going to result in a healthy gut microbiome. Chronic stress can suppress the immune system, impair gut barrier function, and contribute to gut lining permeability. (4)

Make time to de-stress through pressure-relieving activities like tai chi, yoga, or meditation to reduce stress levels and reverse poor gut health.  

6. Try Intermittent Fasting

Going extended periods of time without eating gives your digestion a break, which can reduce inflammation and allow the gut lining to start repairing itself. During fasting periods, the body focuses on autophagy, a process that clears out damaged cells in support of healthy tissue. (5)

Intermittent fasting can also support a healthier microbiome, reduce bloat, and help you build healthier habits for sustained weight loss. (6)

There are many ways to try out the practice, such as fasting every night for at least 12 hours, alternating days, or fasting twice a week. Talk to your healthcare provider or a dietitian before trying out any new diet, especially if you’re currently taking medications.

7. Eat More Cooked Foods

Raw foods are packed with nutrients but can also be difficult to digest. Cooked foods decrease the amount of work your digestive system needs to do to break down food. Pureed foods like smoothies and soups are even easier to digest. 

Go easy on your digestion to reduce bloat and support a healthier gut. As you heal, you’ll be able to tolerate raw foods better.

8. Take Targeted Supplements

Nobody wants to take a fistful of vitamins every day, but there are a handful of gut-healing supplements I recommend often to help patients in digestive distress. These are my favorites for speeding up healing and improving symptoms of common gut conditions:

Colostrum: The lactoferrin in colostrum works as a prebiotic to feed good types of bacteria and fuel their growth. It also promotes cell growth in the intestines to repair a damaged gut and may reduce symptoms of inflammatory bowel disease (IBD). (7)

Slippery elm: This natural botanical works as a demulcent, or a protective film, to reduce inflammation in the gut. This could mean protection against heartburn and inflammatory gut conditions. You can find this in tea or supplement form. (8)

Turkey tail: This adaptogenic mushroom works wonders against conditions like small intestinal bacterial overgrowth (SIBO) affected by imbalances in your microbiome. (9) Try it in a warm drink.

Deglycyrrhizinated licorice (DGL): DGL is a type of licorice root with fewer side effects than other versions of the herb. It’s a common home remedy for treating peptic ulcers and gastroesophageal reflux disease (GERD). (10) Sip on licorice tea to soothe your gut lining.

Marshmallow root: This root contains a gelatinous substance called mucilage that can coat the stomach and offer some relief from IBD, leaky gut, and stomach ulcers. (11) Find it in tea or supplement form.

 

LISTEN: Chinese Medicine Secrets For The Best Digestion, Nervous System & More | Dr. Chris Motley

9. Incorporate Coconut Oil

Studies show coconut oil may boost levels of beneficial bacteria in the gut on top of antimicrobial and antifungal effects that improve overall immune function. (12) This versatile superfood’s antioxidant effects may also benefit those with ulcers. 

Researchers say the presence of fatty acid components in coconut oil, like lauric acid, shows some gastro-protective activity that may soothe the gut lining. (13) Choose organic, extra virgin, cold-pressed varieties for maximum benefit.

10. Drink Lemon Water

Lemons contain phytonutrients, vitamin C, and fiber, all of which are needed for gut health. Vitamin C is a powerful antioxidant that helps lower gut inflammation and boosts the immune system. It also works as a natural antimicrobial for a healthier microbiome. (14)

Lemons are also high in a type of fiber called pectin, which helps balance bacteria and stimulate the growth of important probiotics in the microbiome. (15) The fusion of vitamin C, prebiotic fiber, and phytonutrients may create a cleansing effect, especially first thing in the morning.

I don’t suggest using lemon juice as a stand-alone tonic. For the biggest nutrient boost, try to keep as much of the pulp as you can. Drink lemon water, either warm or cold, not hot. Hotter water denatures the vitamin C.

11. Exercise Regularly

Exercise promotes a balanced gut microbiota, reduces inflammation, and improves digestion. (16) Regular physical activity stimulates your gut’s natural motility, which helps prevent constipation and improves nutrient absorption. It also increases blood flow to digestive organs. 

It’s important to consider the effects of movement on chronic stress, too, as stress can dramatically impact your gut health. If you’re new to regular exercise, start slow with walks, swimming, or yoga to get into the habit of daily movement for better health.

12. Increase L-Glutamine Intake

L-glutamine may improve gut permeability and prevent further gut deterioration by acting as a fuel source for cells in the gut. (17) Improved barrier function is essential in conditions like leaky gut syndrome and for better nutrient absorption. 

You can find L-glutamine in foods like grass-fed beef, bone broth, dairy, and red cabbage. Eating sauerkraut, the pickled version of cabbage, offers the added bonus of gut-healthy probiotics that may make the amino acid more bioavailable. 

Aside from whole foods, I advise supplementing anywhere between 2 and 5 grams of L-glutamine per day. Powder is generally easier for your gut to digest than capsules.

13. Try Apple Cider Vinegar

Apple cider vinegar (ACV) supports digestion by balancing stomach acidity and stimulating the production of digestive enzymes. Thanks to those gut-healing effects, I’ve seen quite a bit of success in patients using it for indigestion and heartburn. 

ACV’s antimicrobial and antifungal properties are also helpful in supporting immune balance and a healthier microbiome for a reduced risk of inflammatory gut conditions and leaky gut. (18)

I usually see the best results when using ACV in its raw, unfiltered form with the “mother” included. (That’s the byproduct of fermentation that looks like sediment in the bottle.) You’ll be able to see it, but it should also appear on the label.

ACV is very acidic. It can be hard to swallow and may cause damage to tooth enamel and your throat with prolonged use. Dilute up to 2 tablespoons in at least an ounce of water or juice for fewer side effects.

14. Eat Fiber-Rich Foods

Fiber is essential to a healthy gut. Not only does it help you build up good gut bacteria, but it also keeps you regular. Fiber adds bulk to stools, preventing constipation and promoting healthier bowel movements. (19)

Dietary fiber can be found in artichokes, carrots, broccoli, whole grains, legumes, nuts, and seeds. If you’re not getting enough fiber-rich foods, fiber supplements can help, but your diet should always be the first place to start when improving your gut health.

15. Take Digestive Enzymes And Bitters

Digestive enzymes are proteins that break down the food you eat into smaller pieces to make what you eat easier to absorb, use, and turn into energy. Some people have common food intolerances where they lack the enzymes to break down a specific protein or sugar. 

Others may not make enough digestive enzymes, resulting in slower digestion and uncomfortable symptoms like bloating, cramping, and gas. This is not uncommon, especially in people who are over 50 or those suffering from irritable bowel syndrome (IBS).

While digestive enzymes aren’t the go-to solution for every food sensitivity, they can be helpful to have on hand if you come in contact with a food you weren’t expecting to eat. Someone with a lactose intolerance, for example, might take a lactase enzyme. 

Digestive bitters are herbs like burdock root, bitter melon, and dandelion that stimulate the production of digestive enzymes. You can find digestive bitters in herbal tincture form, but I love adding bitter greens into soups, salads, and stir-fries.

16. Incorporate Ginger

Due to its anti-inflammatory properties, ginger has been used for thousands of years to soothe stomach problems like nausea, bloating, and indigestion. (20) It also helps alleviate heartburn and acid reflux by stimulating the production of stomach acid for smoother digestion. 

Try adding ginger to more recipes or cut up fresh ginger root to make a gut-soothing tea full of health benefits. 

17. Prioritize Sleep

Sleep supports a balanced gut microbiome and the health of your digestive system. (21) While you sleep, your body kicks off repair processes that strengthen the gut lining and reduce inflammation, helping prevent a variety of gut-related conditions.

Good sleep supports healthy immune function for protection against harmful bacteria and infections that can have long-lasting impacts on your gut. It also regulates the release of stress hormones like cortisol that contribute to obesity and worsened outcomes of issues like IBD. (22)

Aim for regular, high-quality sleep by introducing good sleep hygiene habits, like sticking to a schedule and reducing the use of devices before bed.

18. Decrease Your Sugar Intake

Reducing your sugar intake promotes a balanced microbiome and reduces inflammation. Too much sugar, especially from refined sources, feeds harmful bacteria and yeast that can contribute to dysbiosis. (23) This imbalance contributes to digestive issues, bloating, and poor immunity. 

Cut back on sugar and carbohydrates to allow beneficial bacteria to thrive and reduce your risk of obesity and conditions that can happen as a result. That includes diabetes, reduced kidney function, and high cholesterol.

19. Eat Slowly

Eating slower supports better digestion and nutrient absorption. When you chew your food thoroughly and break it down into smaller pieces, digestive enzymes can process it more easily. This can mean reduced stress on your gut and better gut motility. 

Slowing down at mealtimes also gives the body time to recognize fullness. This can prevent overeating and associated discomfort from bloating or indigestion. 

Signs Of An Unhealthy Gut

Signs and symptoms of an unhealthy gut include:

Bloating

Gas

Constipation

Diarrhea

Heartburn

Food intolerances

Sugar cravings

Unintentional weight changes

Fatigue

Skin issues (e.g., acne, eczema)

Frequent headaches

Brain fog

Mood changes

Joint pain

Frequent infections

Your gut controls so many areas of your health, so you don’t have to have typical gut symptoms to have gut problems. Poor gut health can trigger conditions such as:

Autoimmune conditions

Mental health disorders

Poor immune health

Heart disease

Type 2 diabetes

Cancer

Asthma or chronic sinus infections

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.

Bacterial Imbalance

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

This can lead to health-damaging conditions like SIBO, which in turn is linked to digestive health problems like irritable bowel syndrome and autoimmune disease. 

The causes of these imbalances can vary. Antibiotic use, a diet high in processed foods and sugar, and chronic stress are common culprits. For example, anxiety and depression have been linked to lower levels of Lactobacillus helveticus and Bifidobacterium longum.

Ironically, when someone with dysbiosis starts to eat healthier, it can cause an increase in gut symptoms like constipation and bloating. That’s the underlying microbiome issue at play, not the vegetables. A functional medicine provider can help you get to the root of the issue.

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Yeast Overgrowth

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

Leaky Gut

Leaky gut syndrome occurs when the lining of the small intestine becomes damaged, creating gaps that allow undigested food particles, toxins, and bacteria to enter the bloodstream. This can trigger inflammation and immune responses, potentially contributing to digestive issues.

Damage to your intestinal lining can happen due to years of unhealthy eating, food intolerances, chronic stress, and regular exposure to toxins. In functional medicine, leaky gut is a precondition for autoimmune diseases and requires intervention to stop the inappropriate immune reaction.

Histamine Intolerance 

Histamine intolerance 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 its release 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. This is on top of other issues like anxiety, headaches, hives, and asthma.

How To Test Your Microbiome Health

Without running labs, you may not be able to confirm gut problems. I typically recommend gut permeability labs and a comprehensive tool analysis to get a better understanding of patients’ gut health. 

Gut permeability labs test for zonulin and occluding antibodies, proteins that control gut permeability. I also test for actomyosin antibodies, which can indicate destruction of the gut lining, and lipopolysaccharides (LPS) antibodies, which can point to leaky gut syndrome.

A stool analysis can uncover the presence of parasites, bacterial imbalances, and conditions like candida overgrowth or SIBO.

Your Gut-Healing Timeline

If you don’t have any chronic conditions or food sensitivities, you could heal a not-so-perfect gut anywhere from 2-12 weeks. Unfortunately, most people have other health issues that impact healing and act as a barrier to restored gut health.

If you have chronic inflammation, Lyme disease, blood sugar issues, adrenal fatigue, an autoimmune condition, or leaky gut syndrome, it’s going to take longer to get you back on track. 

You’re on what I call the autoimmune-inflammation spectrum. Any healing will need an individualized approach to see lasting results to your gut health and overall well-being.

Restoring Your Gut Through Functional Medicine

If you believe you are experiencing conditions caused by poor gut health, it’s important to consult with a medical professional before trying any treatment plans. 

As an expert in gut health, my team and I provide our patients with individualized solutions based on recommended testing and labs, your health history, and existing conditions. That ensures your treatment plan is tailored to your health needs and gets to the root of your gut issues.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe. Schedule your consultation today.