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The Gut-Immune System Connection

Written by Dr. Group, DC Founder
A person handling lettuce with bowls of vegetables over a kitchen counter.

The digestive system doesn’t get enough credit. Not only does it break down the food you eat, but it also plays a major role in keeping you healthy. There’s a strong connection between your gut and your immune system. In fact, over 70 percent of your body’s immune system is in your gastrointestinal tract![1]

You've most likely heard of probiotics, the "good bacteria" many people take as supplements. Yet every person has a whole ecosystem of microbes in their gut. Known as the microbiome, it’s composed of bacteria, viruses, fungi, and bacteriophages. The microbiome is a fascinating place. Sometimes called "the last undiscovered human organ," scientists are still actively uncovering the many ways in which the microbiome affects health, from your skin to your mental wellness to your immune system.[2]

What’s clear is that a balanced gut strengthens your immune system, which helps ward off potential infections or concerns. "When there is an imbalance between good bacteria and bad bacteria in the gut, immune regulation is affected," explains Shezi Kirmani, MD, a functional medicine and natural health practitioner in Houston, Texas. "This makes it harder for your body to fight off infections."

So how exactly does the gut microbiome affect the immune system (and vice versa)? And what can you do to keep your gut — and your immune system — balanced, robust, and resilient? Read on.

How Are the Gut & the Immune System Connected?

Much of what you think of as your body’s immune response is actually controlled by groups of bacteria in your gut![3, 5] Besides the microbiome, your gut has tissue that is part of the immune system — together, these make up the gut-immune system connection.

What exactly does it mean that 70 percent of your immune system is in your gut? The answer is the gut-associated lymphoid tissue (GALT) lining your intestinal wall — this is the 70 percent of the immune system experts speak of. You may have heard of lymph nodes, which swell when you get sick. All lymphoid tissue contains lymphocytes (lymph cells) and produces white blood cells — key parts of your immune system. The skin lining the digestive tract (the gut epithelial cell lining) is where your GALT lives. Keeping your gastrointestinal tract healthy ensures that your immune system operates at full capacity.

Microbes also play a huge role in your gut immune system! Your gut microbiome — more than 100 trillion individual microbes of 2,000 species — send signals to and from the gut’s immune cells.[2] This microbial community produces hormones, antibodies, and other chemical compounds that break down cell walls of harmful organisms. So intricately are helpful microbes involved in your body’s innermost working — including the immune system — they are practically a part of you.

Interesting Facts About the Gut’s Immune System

  • The lamina propria, or mucosal gut lining, produces 80 percent of your immunoglobulin A — an antibody connected to a healthy immune response.
  • The gut lining produces antibodies in response to respiratory allergies, such as to pet dander and dust mites. This process starts when a child is in the womb.[1]
  • Vaginally-born infants have a gut microbiome similar to their mother’s. Those born by cesarean section have microbiomes rich in Propionibacterium spp. and Staphylococcus.[2]
  • Breastfeeding further nourishes the gut microbiome, which strengthens the immune system.[2]
  • Plasma cells in your gut produce antibodies. These antibodies neutralize sickness-causing pathogens (harmful microbes) and are central to a healthy immune system.[4]
  • The gut epithelium (lining) is very thin so nutrients from food can pass through to the bloodstream. If the gut lining gets damaged, often due to leaky gut syndrome, it can negatively affect the immune system.[2]
  • Short-chain fatty acids feed the gut epithelial cells lining the gut and strengthen the gut barrier. They also keep swelling down.[2]

How Your Microbiome Benefits Your Immune System

Why does your body tolerate all these non-human organisms in your gut? They provide many benefits!

  • Good gut microbes create an anti-infectious barrier. They inhibit harmful bacteria from sticking to the gut wall — helping them pass out of the body.[2]
  • Your gut microbes synthesize vitamins your body can use, including B1, B2, B5, B6, B12, K, folic acid, and biotin.[2]
  • Gut microbes can break down the cell walls of harmful gut organisms, and break down other substances, like xenobiotics, sterols (for example cholesterol), and more.[2]
  • Gut microbes interact with one another through cell-to-cell signaling. It’s well known that probiotic strains produce antimicrobial molecules in the gut.[2, 5]
  • Colonization by bad bacteria in the gut can lead to issues like small intestinal bacterial overgrowth (SIBO), chronic infections, autoimmune diseases, and even more serious terminal illnesses.[2]

What Causes Your Gut To Become Unbalanced?

When you’re healthy, there’s a balance between the good and bad microbes in your gut. When something upsets this balance, this can lower your immunity and make you vulnerable. Here are some potential causes of gut imbalance (below this section, we give solutions).

Poor Diet

It almost goes without saying that a diet heavy on junk food and light on nutrition leads to an unhealthy gut. Poor diet decreases the diversity of your microbiome, which can lead to conditions like diabetes, obesity, heart disease, and more.[6, 7] Eating processed foods can contribute to leaky gut — where a weakened intestinal barrier allows disease-causing microbes to enter the gut and nutrients to be lost.[2]


Antibiotics are used when you have an infection that needs intervention. However, they wipe out the good bacteria in your gut along with the bad. Without beneficial bacteria to offset them, harmful microbes can take over, leaving you vulnerable to illness.[7] Make sure to always take probiotics or eat probiotic foods anytime you take antibiotics to repopulate the gut.

Pushing Yourself Too Hard

The hectic pace of the world can lead to stress, too much fast food, and insufficient sleep. When we’re focused on the hustle and bustle of daily life, self-care isn’t always a priority. These choices catch up with us, leading to an unbalanced gut.[8]

Overindulgence in Alcohol

Chronic drinking causes unwelcome changes in gut bacteria and increases the risk of leaky gut. Alcohol may also throw off immune function in the gut and trigger an inflammatory response in the small and large intestines.[9]

Points to Remember

More than 70 percent of the immune system lives in the gut. That includes the mucosal lining of the GI tract, as well as the 100 trillion gut microbes living there. These gut microbes, your microbiome, play a key role in keeping you healthy. Not only do your gastrointestinal cells secrete antibodies and ward off unwanted invaders, but your healthy gut microbes (probiotics) do too.

References (9)
  1. Vighi G, et al. Allergy and the gastrointestinal system. Clin Exp Immunol. 2008;153 Suppl 1(Suppl 1):3-6.
  2. Lazar V, et al. Aspects of gut microbiota and immune system interactions in infectious diseases, immunopathology, and cancer. Front Immunol. 2018;9:1830.
  3. Abbas AK, et al. Cellular and Molecular Immunology E-Book, Elsevier Health Sciences, 2017. Accessed 9 May 2020.
  4. Wang X, et al. Function and dysfunction of plasma cells in intestine. Cell Biosci. 2019;9:26.
  5. Nicholson JK, et al. Host-gut microbiota metabolic interactions. Science. 2012 Jun 8;336(6086):1262-1267.
  6. Do MH, et al. High-glucose or -fructose diet cause changes of the gut microbiota and metabolic disorders in mice without body weight change. Nutrients. 2018;10(6):761.
  7. Karl JP, et al. Effects of psychological, environmental and physical stressors on the gut microbiota. Front Microbiol. 2018;9:2013.
  8. Tuck CJ, et al. Food intolerances. Nutrients. 2019;11(7):1684.
  9. Bishehsari F, et al. Alcohol and gut-derived inflammation. Alcohol Res. 2017;38(2):163-171.

†Results may vary. Information and statements made are for education purposes and are not intended to replace the advice of your doctor. If you have a severe medical condition or health concern, see your physician.


Restore Your Gut Microbiome