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Boosting Your Patient's Immunity Through Gut Health: Testing, Nutrition and Supplements

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Boosting Your Patient's Immunity Through Gut Health: Testing, Nutrition and Supplements

According to a National GI Survey completed in 2018 of over 71,000 individuals, two-thirds experienced at least one weekly gastrointestinal symptom, and nearly 60% had at least two concurrent symptoms. Addressing these symptoms is important to functional health, as many people have these concerns. A healthy gut microbiome can improve gastrointestinal health, regulate immune response, and maintain proper daily body functions.

This article will provide insight into the gut microbiome and its relationship with the body's immune system. It will also provide the symptoms associated with an imbalanced microbiome, how to detect them through functional lab testing, and give various functional and integrative medicine approaches to maintaining a healthy gut microbiome and immune response.


What is The Gut Microbiome?

The gut microbiome, also called gut microbiota or gut flora, comprises trillions of microorganisms living in our gastrointestinal tract. The microorganisms consist of bacteria, viruses, protozoa, and fungi. These microorganisms are found throughout the body, but the largest numbers live in the small and large intestines.

The gut microbiota comprises both helpful and potentially harmful (pathogenic) microbes. Usually, in a healthy person, the gut microbiota is symbiotic with the human body, where both are beneficial to each other, and all the microbes coexist without issues.

Over the past decade, extensive research has been completed on the role of the microbiome and its effects on the body, including effects on metabolism, immune, and neuroendocrine responses. In impacting our metabolic functions, educating our immune systems, and communicating with our neuroendocrine system, the gut microbiota has the potential to have a major impact on our physiology, both in health and disease.

They play a role in nutrient absorption, including the function of enzymes, vitamins, and amino acids, along with the production of short-chain fatty acids (SCFAs). The gut microbiome plays many key roles in promoting the smooth daily operations of the body.

How Does the Gut Microbiome Affect Immune Function?

Researchers are finding that the trillions of microorganisms that comprise our microbiome play a key role in immune function. The immune system has a bidirectional relationship with the microbiota in which the immune system must learn from the microbiota in responding to pathogens, and the microbiota must educate the immune system to function properly.

One way the gut microbiota affects the immune system is that it can regulate the immune system's response to pathogens so it doesn't over or under-react to them. It has been shown to regulate the balance of the immune responses related to the T-cells (immune cells) TH1, TH2, and TH17. TH1 cell activity can lead to excessive immune or autoimmune reactions, while TH2 can lead to allergies or asthma, and TH17 is associated with autoimmune diseases such as rheumatoid arthritis. The gut microbiota is also linked to the lungs, to affect lung health. This is called the "gut-lung axis," in which the microbiota can impact the lung by regulating inflammation and its response to a pathogen.

The microbiota in the gut has also been shown to have downstream effects on the innate immunity (our first line of defense against invading pathogens). It can activate certain epithelial cells in the presence of bacteria overload. Epithelial cells are responsible for directly killing or inactivating bacteria. Another immune cell that the microbiota has a relationship with is regulatory T Cells or Treg Cells. Treg cells have a role in controlling inflammation, and a normal functioning gut microbiota has been shown to induce these cells in helping to regulate inflammatory responses.

Research is also showing a link between the gut microbiota and autoimmune and allergic immune disorders, inflammatory bowel disease, multiple sclerosis, and asthma, along with a link between the composition of the gut microbiota and being susceptible to immune disorders like Type 1 diabetes, rheumatoid arthritis, and allergic diseases. However, further research is indicated to explore this link fully. Overall, the studies show a complex interplay between the gut microbial makeup and its impacts on the immune cells and the immune system.

Symptoms of Imbalance Gut Microbiome

In a healthy person, the gut microbiome can help maintain the body's proper function. However, if an imbalance occurs in the microbiome, problems in the body can occur in which the normally unharmful pathogenic (leading to disease) microbes then become harmful to the body. This imbalance in the gut microbiome is called dysbiosis. When dysbiosis occurs, your body can become more susceptible to some stomach and other health conditions such as IBD (Inflammatory bowel disease), Irritable bowel syndrome (IBS), Diabetes, Obesity, Cancer, Cardiovascular problems, and Central nervous system disorders‌.

Dysbiosis can also lead to a variety of symptoms, and these can vary between individuals. Some of these symptoms include gas and bloating, constipation, acid reflux, diarrhea, bad breath, abdominal pain, and mucus in the stool, which are some of the most common symptoms. Anxiety, trouble with focus or concentration, depression, chronic fatigue, or brain fog can also occur, affecting the mental health of these individuals. Dysbiosis can also affect the skin resulting in acne, rashes, or psoriasis. These symptoms can become chronic if the imbalances in the microbiome are not addressed, and the dysbiosis continues. It's imperative to work with a qualified healthcare practitioner with experience in this area to assess for dysbiosis if you have any of these symptoms to prevent further impacts on your health.

What Causes an Imbalanced Gut Microbiome?

A healthy microbiome consists of the right balance between protective microbes and pathogenic microbes. The balance of the microbiome keeps your GI tract and body functioning properly. This can occur because the different organisms in your gut aren't at the right levels, their production has changed, or there's a loss of diversity. Some known causes for these changes include diet, infections, antibiotic use, antacids, and certain lifestyle factors.

Diets have been shown to change the gut microbial flora. For instance, an inflammatory diet consisting of excessive refined sugar, processed foods, poor-quality fats, and lack of fiber can increase the growth of pathogenic microbes, further driving an inflammatory response in the gut and body. Infections such as those from food poisoning can also change the balance of the gut flora leading to more pathogenic microbes. These infections can be picked up through food and water sources.

Another common cause is the overuse of antibiotics or antacids. Chronic use of both has been shown to disrupt the important balance of the gut microbiome. Other factors include lifestyle factors such as chronic stress, poor sleep, excessive alcohol consumption, smoking, and poor dental hygiene. All of these contribute to imbalances in the gut microbiome by creating inflammation that can lead to intestinal permeability (leaky gut), allowing microbes in the gut to go into body circulation resulting in inflammatory responses.

How to Test the Gut Microbiome

Functional medicine labs can help assess the balance of the gut microbiome. Generally, these tests evaluate the presence of dysbiosis. Here are some of the functional labs to consider for testing the gut microbiome:

Comprehensive Stool Analysis

This test analyzes the makeup of the gut microbiome. The Gut Zoomer analyzes over 300 microorganisms to determine if dysbiosis is occurring that may cause chronic disease.

Intestinal Permeability

Imbalances in the gut microbiome are often associated with leaky gut or intestinal permeability. The Advanced IBA profile measures the levels of zonulin, DAO, and LPS. All of these are markers of intestinal permeability.

Organic Acid Testing (OAT)

This urine test can assess for dysbiosis by measuring the byproducts, or metabolites, produced from the intestine that can occur with dysbiosis. The OAT can also test for other sources of inflammation.

Breath Test

This is a non-invasive test that measures specific gases in the breath, specifically methane, that are produced with SIBO. SIBO is a small intestine bacterial overgrowth, another form of dysbiosis.

Additional Labs To Consider

Some additional labs to consider are the food sensitivity and the mold toxicity test. These are indirectly related to dysbiosis. In the case of food sensitivities, imbalances in the gut microbiome play a role in creating food sensitivities. Whereas mold toxicities have been shown to lead to microbiome imbalances.


Complementary and Integrative Medicine Approaches That Boost a Healthy Gut Microbiome & Immune Function

Complementary and integrative medicine approaches can help modulate the gut microbiota and improve immune function. These approaches can be classified into a few groups that include nutrition intervention, nutraceuticals or clinically relevant supplements, lifestyle approaches such as exercise and stress reduction, and other complementary approaches such as acupuncture therapy. These integrative approaches will be discussed in detail in the next sections.

Nutrition for a Healthy Microbiome & Immunity

Nutrition plays an important role in the microbiome's health and immune function. Utilizing clinical nutrition is one of the most important approaches functional medicine and integrative practitioners use to manage or improve health. There are certain nutrients found in a variety of foods that may better prepare the body for microbial attacks and excess inflammation, thus improving the microbiome and immune response. These nutrients include vitamins C, D, zinc, selenium, iron, and protein. These nutrients can be found in a low-processed, high-fiber, plant-rich, and prebiotic/probiotic-rich diet that includes diverse fruits, vegetables, whole grains, and legumes.

Incorporating these foods regularly is beneficial in supporting the balance of the microbiome and immune system. Having a diet high in fiber creates a symbiotic relationship between the microbes in the gut microbiome and the immune system as the microbes break down the fibers into SCFAs, stimulating immune cell activity. These SCFAs are considered postbiotics as they feed the microbes and are a product of prebiotics. Probiotic foods contain helpful bacteria responsible for maintaining a well-balanced microbiome. Besides eating a diverse amount of fruits, vegetables, beans, and whole grains, prebiotics can also come directly from garlic, onions, leeks, asparagus, Jerusalem artichokes, dandelion greens, bananas, and seaweed. Probiotic foods include kefir, yogurt with live active cultures, fermented vegetables, sauerkraut, tempeh, kombucha tea, kimchi, and miso.

The Microbiome Diet may be another excellent option for those hoping to improve their overall health. This diet recommends foods that support a healthy microbiome, like prebiotics, probiotics, and fiber-rich foods. It also includes foods low in processed sugars and refined grains.

Supplements and Herbs for a Health Microbiome & Immunity

Reducing inflammation and re-establishing the balance in the gut flora are both important aspects of maintaining the microbiome's health, thus improving immunity. Here are some of the supplements and herbs that are utilized by functional medicine and integrative practitioners:


Glutamine is the preferred fuel source for specific cells called enterocytes and colonocytes. Both cells are located within the GI tract. Glutamine has been shown to protect the gut barrier and prevent permeability to toxins and pathogens, thus improving the microbiome's health and immunity.


Curcumin, a compound found in turmeric, helps reduce inflammation, improves immune response, and modulates the gut microbiota. A study where participants consumed 500 mg of curcumin for 28 days showed gut microbiota metabolic activity, suggesting the gut microbiome's modulation with curcumin consumption.


Probiotics help re-establish the microbiome and maintain its balance. They can reduce inflammation while enhancing immune function by promoting the production of certain immune cells.


Butyrate is an SCFA (short-chain fatty acid) and is fuel for the microbiota. This can be taken as a supplement, typically in the form of sodium butyrate, and plays an important role in regulating immune responses. Sodium butyrate can also be used in a colonic enema for a more direct approach.


Ginger is antioxidant, anti-inflammatory, and supports gastrointestinal motility. Ginger is also commonly used to symptomatically treat gas, bloating, abdominal pain, and nausea, all symptoms associated with SIBO.


Zinc, selenium, iron, copper, folic acid, and vitamins A, B6, C, D, and E can protect healthy cells and support the activity of immune cells. Deficiencies in these nutrients can alter immune responses.

Acupuncture for a Healthy Gut Microbiome & Immune Function

Acupuncture is a complementary therapy typically associated with reducing musculoskeletal pain. However, it's also been shown to improve the microbiome's health and immune function. Studies show that acupuncture can regulate inflammation and modulate certain immune cells, such as TH1, TH2, and TH17 cells. Acupuncture has also been shown in research to be effective in managing Crohn's Disease by increasing intestinal anti-inflammatory bacteria, enhancing the intestinal barrier, and regulating cytokines, all of which help maintain a balanced and healthy gut microbiome and immune function.

Exercise for a Healthy Gut Microbiome & Immune Function

Studies show that exercise is a lifestyle factor that can influence the composition of the microbes in the gut microbiome. A diverse and stable microflora is crucial to maintaining homeostasis and healthy gut physiology, contributing to appropriate signaling along the brain-gut axis and overall individual health. Exercise may enhance microflora diversity which may help with reducing weight and gastrointestinal disorders while modulating immunity. This can ultimately lead to a reduced incidence of obesity and metabolic disease and improve immune function. Exercise can also promote SCFAs helping to rebalance the microflora. Therefore, exercise can be used as a treatment to maintain the gut microbiome and improve immune function, improving overall health.

Stress Reduction Techniques for a Healthy Gut Microbiome & Immune Function

Scientists have long been aware that our gut and brain are connected and work together to manage how we react to stress. Recently, they've discovered that the microbiome plays a role in how we process stress. The microbes throughout our gut can talk to our brain through things such as the vagus nerve, hormones, and chemicals. When we're young, the bacteria in our gut can also affect how we react to stress as we grow older. Studies show that changes to the gut flora, caused by things like antibiotics or stress, can lead to anxiety, depression, digestive problems, and decreases in immune function. Mind-body techniques such as meditation, mindfulness-based practices, tai chi, yoga, qigong, hypnosis, guided imagery, relaxation therapy, biofeedback, and breathing exercises can all be beneficial in maintaining stress levels, thus improving our gut microbiome and immune function. More studies in the future will help to understand the full impact of the gut microbiome on stress-related disorders in humans.



The gut microbiome has a myriad of effects on the human system. It has been shown to affect metabolism, immune, and neuroendocrine responses. It also contributes to nutrient absorption and synthesizing enzymes and vitamins. Imbalances in the gut microbiota can have detrimental effects on overall health and lead to decreased immune function and increased risk for conditions such as diabetes, obesity, gastrointestinal issues, and cardiovascular problems. Functional medicine and integrative approaches such as personalized nutrition, nutraceuticals, acupuncture, exercise, and stress reduction have been suggested to help maintain the balance of the microbiome while improving immune function, making these approaches a viable option in managing symptoms or diseases associated with an imbalanced gut microbiome. It's crucial to work with a licensed healthcare provider, such as a functional medicine doctor, for proper evaluation if you suspect that you have an imbalance in your gut microbiome.

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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