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Gut Health and Immunity

Updated: Jul 20, 2022

“All disease begins in the gut” - Hippocrates

Immune health and the ability of the body to adequately fight off infection without causing harm has been a topic in the forefront of many conversations of late. The current health crisis has provided a reminder to many people all over the globe to take time and reflect on necessary self-care behaviors to promote health and encourage protective immunity. Unfortunately, the general American population is overfed and undernourished. The devastating health consequences of the Standard American Diet (SAD) can be seen in the rising childhood and adult obesity rates, prevalence of inflammatory bowel disease, incidence of diabetes, rates of autoimmune diseases, rates of cardiovascular complications and even the death rate from Covid-19.

So, what does gut health have to do with immunity?

From the time we are born, the colonization of the gastrointestinal tract (GIT) stimulates immune system development by shaping which types of immune cells are generated. There are many different types of cells and signaling mechanisms involved in the immune response. A fascinating finding demonstrates that the immune system develops side by side with the microbial population present in the gut.

As colonization occurs, the body learns how to differentiate between helpful “commensal” bacteria and problematic “pathogenic” bacteria. Microbes teach the immune cells in the gut how to respond to varying stressors. As the GIT develops, the microbiome begins the important role of synthesizing essential nutrients such as vitamin B1, B2, B5, B6, B12, K, folate and biotin. These little organisms are power houses helping absorb nutrients, regulate metabolism, detoxification, provide protection against pathogenic bacteria and regulate the immune system (both local and systemic immune response).

The microbiota present in the GIT communicate directly with the cells lining the intestines, often directing different aspects of the cells and development of certain white blood cells. An abundance of data is being published about the link between the gut microbiome and many health conditions such as colon cancer, asthma, chronic sinus infection, irritable bowel syndrome, Crohn’s disease, high blood pressure, vaginal infections, colitis, obesity, neurological diseases, autism, liver disease and mental illness.

What does the microbiome have to do with the immune system?

The colon is designed to anticipate colonization from a variety of organisms which then take on the responsibility not only of producing essential vitamins, but also of creating a protective barrier which prevents direct contact of bacteria with the blood stream. A healthy GIT will have three distinct layers of microbes, each layer characterized by a unique microhabitat. An essential component necessary for the development of these distinct layers is the proper nutritional environment for the microbes themselves. While human preferred foods are trending toward processed food like substances filled with fats and sugars, microbiota preferred foods are the insoluble fibers present in vegetables, some fruits and true whole grains (not processed grains with a label stating “made from whole grains”).

How does gut health go wrong?

The key to gut health is diversity, meaning that health is characterized by having many different species of bacteria, protozoa, fungae and archaea. The greater the microbial diversity, the better the body can deal with stressors such as opportunistic pathogens. Biodiversity is affected by many factors including genetics, age, gender, lifestyle (diet, stress), early colonization (c-section, vaginal birth), medical practices (antibiotic use, hygiene), geographic region (sanitary conditions, rural/urban) and socioeconomic factors.

Dysbiosis occurs when the GIT microbiome is not in a healthy state. There are many factors which can lead to dysbiosis including the Standard American Diet (SAD) diet, broad spectrum antibiotics, chronic maldigestion, chronic constipation, stress, anger or fear. The SAD diet is high in animal fat, simple carbohydrates and sugars and low in indigestible fiber, fresh vegetables, fruits and legumes. This imbalance in diet promotes an overgrowth of opportunistic bacteria and fungi (yeast) which can lead to insulin resistance, chronic GI issues, poor concentration, poor sleep and other chronic symptoms.

Broad spectrum antibiotics can lead to dysbiosis by killing the beneficial bacteria along with the targeted bacterial infection. Chronic maldigestion can be caused by acid reducing medications which decrease acid production in the stomach. The GIT is designed to have stomach acid bathe the upper small intestines, preventing bacterial overgrowth in that area. Stress suppresses beneficial strains of bacteria and anger and fear increase a bacterial strain that can cause infections if it grows in abundance.

How do we keep the gut balanced and promote immune function?

The great news about the GIT microbiome is that it is very responsive to lifestyle change. By restoring balance among these symbiotic microorganisms, we can return the immune cells and signaling mechanisms back to working order. Changes in the microbiome can be measured in as little as 24 hours after making dietary adjustments.

Eat a variety of foods. Variety is truly the spice of life, and your microbiome as a whole thrives on digesting a wide range of foods. Every different species is going to have what it digests best. It is important to give each species a little something to work on, so that one species does not grow out of proportion to the others.

Eat plenty of insoluble fibers. Healthy bacteria thrive on indigestible fibers, fermenting them and turning them into short chain fatty acids (SCFAs), compounds which participate in communicating with the GIT cells and help maintain the protective barrier lining the colon. Great food sources of insoluble fiber includes vegetables, fruits with edible seeds, whole grains such as brown rice, wheat bran, couscous, and legumes.

Limit simple carbohydrate and sugar intake. Sugar is considered an inflammatory food. Consumptions of sugar and simple carbohydrates feeds the yeast and opportunistic bacteria in our GIT. This creates a significant imbalance in the microbiome, decreasing the body’s ability to fight infection and maintain the protective barrier. Sugar is hidden in many processed foods, since it is 10 times more addictive than cocaine. Foods to limit or avoid include flavored drinks (soda, Powerade, Gatorade), fruit juices (especially from concentrate), baked goods, fast food, alcoholic beverages, processed bread.

Manage stress. Stress has a profound impact on the health of the GIT. Stress can be directly linked to chronic constipation, irritable bowel syndrome, diarrhea, weight gain in the abdomen, increased cortisol levels and decreased immune function. Take the time to destress, recognizing that the microbiome literally changes in response to elevated stress levels, causing dysbiosis and allowing for the overgrowth of problematic bacteria.

Gut health is essential for a healthy immune system. It can be a challenge figuring out the healing process to revive the GIT and regain a healthy immune system from the inside out. It is best to start by following the simple guidelines discussed above. If a change in diet results in increased GI symptoms, or if GI symptoms persist, then visiting with a knowledgeable functional medicine provider familiar with GI health can be a great second step.

Gina Ditta-Donahue is a certified Family Nurse Practitioner and Anti-Aging Medicine provider with clinical experience working in Family Practice, Gastroenterology and Aesthetics.  She is also co-owner of Elevate Functional Medicine.


Lazar Veronica, Ditu Lia-Mara, Pircalabioru Gratiela Gradisteanu, Gheorghe Irina, Curutiu Carmen, Holban Alina Maria, Picu Ariana, Petcu Laura, Chifiriuc Mariana Carmen. (2018). Frontiers in Immunology (9). Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. URL=

Renan Corrêa‐Oliveira José Luís Fachi Aline Vieira Fabio Takeo Sato Marco Aurélio R Vinolo. 22 April 2016 Regulation of immune cell function by short‐chain fatty acids.

Wu, H. J., & Wu, E. (2012). The role of gut microbiota in immune homeostasis and autoimmunity. Gut microbes, 3(1), 4–14.

Science Nordic. (2018). Why gut bacteria are essential for a healthy immune system.

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