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How to Heal Your Gut Naturally With Functional Nutrition

Medically reviewed by 
How to Heal Your Gut Naturally With Functional Nutrition

The body depends on optimal gut health for more than digestion and absorption of nutrients. Looking closely at gut health to identify and correct imbalances can not only improve common digestive symptoms, but is also an essential aspect of many treatment plans for sleep disturbance, weight loss, skin issues, and cardiometabolic diseases. Making the right food choices is a primary step in treating the gut. This article will discuss common disturbances to good gut health and gut-healing nutritional interventions you can implement to better gastrointestinal health and function.


The Importance of Gut Health for Overall Well-Being

Greek philosopher Hippocrates was onto something when he said all disease begins in the gut. As science has turned more attention to the power of a healthy gut and microbiome, it becomes clearer that many diseases are fueled by intestinal inflammation, poor digestion, and imbalances in the gut microbiome. Aside from daily disturbances of unwelcome digestive and abdominal symptoms, an unhealthy gut is correlated to other systemic diseases, including cardiovascular and metabolic diseases, psychiatric and mood disorders, kidney disease, obesity, seasonal allergies, and autoimmune diseases. (1, 2)

Signs & Symptoms of an Unhealthy Gut

The most apparent symptoms of an unhealthy gut are related to gastrointestinal and digestive function. Signs and symptoms of digestive imbalance include (2, 3):

Because the gut plays such a pivotal role in overall health, symptoms outside of the digestive tract that seemingly appear unrelated to gut health may occur, including (2, 3):

Possible Causes of Unhealthy Gut

It's not always obvious to tell what affects the intestinal microbiome, permeability, and digestive function. Here are five factors that are disruptive to gut health.


Healthy, plant-based, and anti-inflammatory diets are associated with a high abundance of short-chain fatty acids (SCFAs) and a healthy microbiome, correlated with pathogen suppression, improved intestinal barrier function, and immune tolerance. Western dietary patterns, however, have the opposite effect, contributing to leaky gut, unfavorable shifts in the microbiome, systemic inflammation, and loss of self-tolerance. Western diets are characterized by excess intake of red meat, simple carbohydrates, saturated/trans fats, and alcohol, and insufficient fruits, vegetables, whole grains, lean proteins, and fiber. (3, 4)

Adverse food reactions, encompassing food allergies, intolerances, and sensitivities, can trigger localized gastrointestinal immune responses and disruptions in the gut barrier, translating to systemic inflammatory responses. IgE-mediated food allergies have been associated with the onset of inflammatory and functional gastrointestinal disorders. Food intolerances, like lactose or histamine intolerance, cause uncomfortable digestive and systemic symptoms of varying severity. IgA and IgG-mediated food sensitivities cause delayed systemic symptoms, leaky gut, and low-grade inflammation.


Stress is an often overlooked but relevant factor contributing to poor gut health and function. The hypothalamic-pituitary-adrenal (HPA) axis, the body's stress system, is responsible for sensing stress and ultimately stimulating cortisol release from the adrenal glands. Cortisol, especially when chronically elevated, suppresses the immune system and profoundly affects the gastrointestinal system, such as slowing intestinal contractility and motility, increasing visceral sensitivity, suppressing digestive enzyme secretions, and inducing dysbiotic patterns in the intestinal microbiome. (5)


Intestinal dysbiosis is an imbalance of the microorganisms in the human microbiome. Dysbiosis can occur when there is a lack of microbial diversity, a deficiency in beneficial bacteria, or an overgrowth of bacteria. Dysbiosis commonly causes and contributes to gastrointestinal symptoms (e.g., gas, bloating, pain, changes in bowel habits), pro-inflammatory cascades, immune dysregulation, interruption in the normal synthesis of vitamins and neurotransmitters, and autoimmunity (6).


The medications you take can suppress normal digestive processes and induce dysbiosis. Proton pump inhibitors (PPIs) and histamine blockers, commonly prescribed for heartburn and reflux, suppress stomach acid, predisposing an individual to infection and nutrient deficiencies. Chronic use of laxatives or antidiarrheals can create bowel dependence and irregular bowel movements. Antibiotics used to treat bacterial infections will also target healthy bacteria of the microbiome, causing dysbiotic patterns. Nonsteroidal anti-inflammatory drugs (NSAIDs) can induce irritation within the intestinal mucosal lining and increase the risk for inflammatory bowel disease (IBD) flares and peptic ulcers.

Environmental Toxins

Environmental toxins, including bisphenols, phthalates, heavy metals, and pesticides increase the body's chemical and toxic burden, increase oxidative stress, and induce inflammatory responses in every body system. They can directly cause digestive symptoms but can also induce neurological dysfunction, perpetuating poor digestion and intestinal motility. Toxic exposure can occur from almost any source: food, cosmetics, cleaning products, plastics, agricultural products, and industrial chemicals.  

Functional Nutrition Labs to Test for Root Cause of Unhealthy Gut

Functional medicine labs help practitioners personalize treatment options for their patients. Below are some of the most common labs ordered for patients suffering from digestive symptoms.

Inflammatory Markers

Inflammatory markers can be measured to quantify inflammation in the body objectively. Although many of these are nonspecific and can become elevated for reasons unrelated to gut health, biomarkers such as calprotectin and lactoferrin are more specific to inflammatory bowel diseases. They can indicate the presence of IBD, celiac disease, and colon cancer. Additionally, fecal secretory IgA (sIgA) is a first-line defense protein in protecting the body from intestinal pathogens and toxins. Elevations in sIgA can indicate increased intestinal permeability, inflammatory bowel diseases, infection, and food sensitivities. Alternatively, low sIgA can reveal the presence of chronic infection and poor immune resiliency.

Comprehensive Stool Test

A comprehensive stool analysis provides the most information regarding intestinal health and function in a single test. Comprehensive stool testing screens for gastrointestinal pathogenic infections, dysbiotic patterns within the microbiome, maldigestion/absorption, intestinal inflammation, immunological dysfunction, and imbalances in intestinal metabolic function. A stool analysis is a noninvasive test that provides invaluable diagnostic markers and defines treatment targets.

SIBO Breath Test

As valuable as a stool analysis is, it cannot diagnose small intestinal bacterial overgrowth (SIBO), known to cause digestive symptoms and contribute to other health conditions. The SIBO breath test measures gaseous metabolic products of bacterial fermentation within the small intestine. Overproduction of hydrogen, methane, and/or hydrogen sulfide gases is diagnostic for the various SIBO subtypes.

Adverse Food Reactions

There are various tests and panels that can be ordered to assess for adverse food reactions. A food allergy panel measures IgE antibodies against specific food proteins to diagnose food allergies, whereas panels that measure IgG and/or IgA antibodies can help to identify food sensitivities. Breath tests similar to the SIBO test exist for diagnosing lactose and fructose intolerance. Blood tests can also measure specific antibodies to aid in the diagnostic process of wheat and gluten-related disorders.


Functional Nutrition Treatment for Natural Gut Healing

When it comes to a thriving gut, what we eat matters. Making intentional food choices positively impacts intestinal permeability, inflammation, and the microbiome's health.

A plant-based diet is rich in prebiotics, fiber, and polyphenols. Together, these nutrients and compounds support healthy digestive function and the microbiome and reduce inflammation. Anti-inflammatory and gut-healing dietary guidelines suggest eating 4-5 servings each of fruits and vegetables daily. Specific fruits and vegetables beneficial for gut health include leafy greens, fennel, artichoke, beets, cruciferous vegetables, pineapple, papaya, and dark berries. Anti-inflammatory polyphenols are also concentrated in green tea, black coffee, and dark chocolate. (9, 10)

Fermented foods contain live probiotic cultures that can support the intestinal microbiome without taking supplements. Kefir is one fermented food that provides anti-inflammatory, antioxidant, antimicrobial, and anti-allergenic properties; it can also improve digestion and lactose intolerance. Sauerkraut, kimchi, and live-culture yogurt are other examples of probiotic fermented foods that can be incorporated into the diet. (9)

Miso is another probiotic food made from fermented soybeans. In addition, it contains digestive enzymes that assist in the breakdown and digestion of fats, proteins, and carbohydrates. (9)

Add spice to your food! Spices and herbs are rich in anti-inflammatory, antioxidant, and antimicrobial constituents and stimulate natural digestive processes and secretions. Commonly used spices and herbs known for their health benefits include turmeric, garlic, onion, chili pepper, cinnamon, ginger, and black pepper. (11)

Supplements and Herbs That Help Heal Your Gut

Sometimes, dietary interventions alone are insufficient in correcting pathologic inflammation and gastrointestinal imbalances. Natural supplements and herbs are available to supplement diet and lifestyle to heal the gut and optimize digestive function. Below are some commonly recommended gut-healing supplements.


L-glutamine is an amino acid that is the preferred fuel source for the cells that line the small intestine (called enterocytes). Glutamine can become depleted in times of chronic stress, so supplementation can be beneficial to support wound and intestinal healing. A significant body of evidence supports using glutamine to maintain intestinal integrity, heal leaky gut, and strengthen the immune system.


Probiotics are live microorganisms that confer many health benefits to the human body, including strengthening the intestinal barrier, synthesizing vitamins and neurotransmitters, and communicating with the immune system. Supplemental probiotics increase immune function and control inflammation. Probiotics effectively treat many gastrointestinal and extraintestinal diseases, including IBS, IBD, allergies, and autoimmune diseases. (7)

Zinc Carnosine

Zinc carnosine is a complex of zinc and amino acids that stabilizes small intestinal integrity and stimulates gut repair processes. Zinc carnosine is indicated for many gastrointestinal diseases, including GERD, peptic ulcers, and IBD. (8)

Vitamin D

Vitamin D deficiency is associated with increased intestinal permeability. Supplementation and optimization of serum vitamin D levels regulate intestinal mucosal homeostasis by maintaining the integrity of the epithelial barrier and suppressing pro-inflammatory immune responses. (3)

Deglycyrrhizinated Licorice Root (DGL)

DGL is a form of licorice root in which glycyrrhizin, a constituent that can increase blood pressure, has been removed. DGL is a demulcent and vulnerary herb, meaning it creates a protective film throughout the digestive tract to soothe irritation and encourage healing. Additionally, licorice has antibiotic properties, so it can be beneficial in treating dysbiosis or intestinal infections like H. pylori. (8)



Functional medicine doctors often look at the gut first when helping patients with complex medical conditions and symptoms. This is because the consequences of intestinal imbalances extend far beyond the intestinal walls. A food-as-medicine approach to gut healing can have profound effects on creating positive outcomes for intestinal integrity, microbiome composition, and immune function regulation. Dietary and herbal supplements can amplify nutritional intervention effects.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article


1. How Your Gut Health Affects Your Whole Body. WebMD.

2. Neibling, K. (2023, March 24). Why Functional Medicine Practitioners Focus on Gut Health. Rupa Health.

3. Cloyd, J. (2023, February 28). A Functional Medicine Protocol for Leaky Gut Syndrome. Rupa Health.

4. Ibragimova, S., Ramachandran, R., Ali, F., Lipovich, L., & Ho, S. B. (2021). Dietary Patterns and Associated Microbiome Changes that Promote Oncogenesis. Frontiers in Cell and Developmental Biology, 9.

5. Sweetnich, J. (2023, March 15). How Stress Affects Our Gut Health. Rupa Health.

6. Vazquez, K. (2022, August 22). How Gut Dysbiosis Negatively Affects Hormone Regulation, Immune System Activation, and Neurotransmitter Production. Rupa Health.

7. Cloyd, J. (2023, April 19). What's the Difference Between Prebiotics vs. Probiotics vs. Postbiotics? Rupa Health.

8. Sweetnich, J. (2023, Februrary 21). Top Gut Healing Supplements Used By Integrative Medicine Practitioners. Rupa Health.

9. Shemereko, L. (2021, January 20). Top 8 Best Foods For Gut Health. Fullscript.

10. Lauer, M. (2021, June 16). 5 Ways to Keep Your Gut Healthy. Fullscript.

11. Jiang, T.A. (2019). Health Benefits of Culinary Herbs and Spices. Journal of AOAC International, 102(2), 395–411.

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