The Gut Microbiome and Immune System Relationship

The relationship between the Gut Microbiome and Immune System is symbiotic, and, also very important to understand, which is what we cover in this article!

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We didn’t understand until recently the important connection between the bacteria in our gut and our health and well-being. We now know that as humans we have more than 10,000 different species of microorganisms in our gut. There are trillions of these microorganisms present at any given moment. We learn more and more about our gut, the bacteria that’s present and how it affects our health as time goes on and we invest in additional genetic sequencing and research. This allows for the development of different products and practices that benefit our gut.

Understanding the relationship between our gut microbiome and the immune system can allow us to alter how we take care of ourselves, so we feel better and our bodies function more optimally. Almost two-thirds of Americans experience some sort of GI issues on a regular basis. Many of these issues can be addressed with some minor dietary changes, like incorporating specific gut health superfoods, and the addition of supplements (probiotics, prebiotics). And, we have our recommended gut health tests from home to help you stay ahead of any potential issues.

The Gut Microbiome and the Immune System

immune system and gut microbiome

We’ve long known that bacteria live on surfaces, our skin, in our nose and in our ears. We pay close attention to the harmful bacteria that we potentially come into contact with that could make us sick, but there are also beneficial bacteria that we want to have in our body, especially the gut. Bacteria can negatively affect our immune system, but good bacteria can help our immune function. When the gut and microbiome changes drastically in an unhealthy way, this has the potential to lead to a variety of diseases.

Our immune system largely exists inside of our GI tract. We have cells all over the interior lining of our gut that release antibodies at frequent rates. We still need to learn more about what kind of antibodies are being released and how our gut facilitates that relationship between our body and bacteria that we come into contact with. However, we know a lot and we can make healthy changes to prevent disease, keep our digestive system functioning regularly and feel our best.

The Gut Microbiota

gut microbiota functionality

Our gut microbiome is a very diverse group of bacteria that exists in our gastrointestinal system. The state of this microbiome affects our brain function, mood, behavior, appetite, immune function and metabolism (just to name a few). We actually have 100 trillion microbial cells in our gut, which is 10 times larger than the amount of human cells that we have in the human body. Most of this bacteria is located in the GI tract, but it’s also on our skin and in different orifices. Our bacteria supports more genes than human cells. As we grow and develop throughout our lifetime, our body evolves to live in harmony with certain strains of bacteria that actually benefit us.

Researchers and scientists have only just touched upon how bacteria affects our health. We know it’s important to have a healthy level of bacteria in our gut to prevent disease, but there’s much to learn about how our microbiome affects our mood, concentration, energy levels and other physiological processes.

What we eat affects our microbiome. If you consume foods that you’re allergic to or have sensitivities to, this can lead to disturbances in your gut lining. Probiotics have the ability to heal this damage and strengthen the thin cells present at the epithelial level. There is a very specific balance of good to bad bacteria that should be maintained for optimal health. The more beneficial bacteria that you have in your gut, the healthier you will be by protecting your body from harmful bacteria.

The Immune System’s Basic Functions

basic functions immune system

The immune system in our body has a very important role. It is designed to protect us from harmful substances. Made up of different cells, proteins and organs, our immune system must be running smoothly in order to feel good each day. If our immune system falters, we’ll notice in a variety of ways from fatigue to illness. Even the healthiest immune system can be affected by germs that we’re not familiar with.

The immune system has two different parts. This includes the innate immune system which is our main defense from pathogens our body is not familiar with. Phagocytes attack these cells to kill them. We also have an adaptive immune system. This system reacts to pathogens that our body has encountered at one time or another during our lifetime. This phase of the immune system will actually adapt to the different strains, allowing our body to remain immune.

How Does the Immune System Trigger Activation?

Our body has the ability to recognize when it has come into contact with something that doesn’t belong there. The immune system kicks in and starts to fight back against these antigens that are binding to our cell receptors. Our immune system will take note of what it is coming into contact with, and it will be able to react accordingly the next time it sees a similar germ.

This process isn’t always perfect. If our immune system isn’t functioning at an optimal level, there’s the potential that we can become very sick or our body will actually see our own healthy cells as harmful antigens. Autoimmune disease, gut health issues and much more can result in an improper autoimmune response.

How Gut Bacteria Can Affect the Immune System

gut bacteria affects immune system

Our immune system works hard to protect our body from illness, but how is our gut bacteria involved in this process? The last few decades have brought about a new understanding of the gut microbiome / immune system relationship. The cells of the human body have evolved along with microbial units into a mutually beneficial relationship that helps us remain healthy. Interconnected with gut bacteria, our immune system has the potential to function quite effectively.

Most of the microorganisms in our body live inside of our gut. As much as eighty percent of our immune system exists here. Some of the relationship between these two systems takes place when we’re born. This is when a human will come into contact with bacteria for the very first time, as the birth canal has a high count of bacteria present in it. As time goes on, the immune system will build up a more diverse profile or bacteria in the microbiome. How healthy this system is really determines the efficiency of your immune system. You’ll find there are other situations in your life that will help this development as well. This can include your diet, exercise regimen, lifestyle and environment.

Another way of looking at this gut / immune system relationship is considering your gut to be like a teacher. Your microbiome will teach your immune cells what it needs to know in order to fight off foreign pathogens (or invaders). When our antibodies are not able to keep us healthy, our immune cells will intervene to destroy infected cells in a process called cell-mediated immunity.

Does a Healthy Gut Help Your Immune System?

Now that we clearly understand the relationship between the immune system and your gut, it’s easy to understand how important your gut microbiome is. There is a level of communication that must exist between these systems in order for our bodies to feel their best and function optimally. On a day to day basis it’s likely that this system is running smoothly. This means your gut is boosting the development of a healthy immune response through beneficial microbes. When this system breaks down, there is the potential for disease and illness.

The body is inevitably exposed to things like bacteria, viruses, chemicals and other invaders throughout our lifetime. There are other things that can reduce our beneficial bacteria, including antibiotics, chemotherapy and surgery. Reduced immunity occurs when our microbiome isn’t in tip-top shape. This system is efficient but it’s also very delicate. Our whole body can be affected by just a slight shift in our good versus bad bacteria lineup.

Steps to Take to Improve Your Gut Microbiome

One person’s gut microbiome is very different from another person’s. However, there are steps that you can take in order to improve your microbiome. Research is determining that we have quite a bit of control over this system. If we adopt a very healthy diet, we have the ability to change our gene expression by adding more diverse microbes into our microbiome. The best way to do this is by increasing your probiotic and prebiotic intake, eating more fiber and eliminating processed and fatty foods. Probiotics and prebiotics can be taken in supplement form but they are also naturally found in foods like kefir, yogurt, sauerkraut and other fermented foods.

If you would like to learn more about your microbiome, you can figure out how to test your gut health, or, there are gut health tests that you can invest in. After providing a stool sample to the gut health company that you’ve chosen, they will study the different bacteria and microbes that are in your gut. You’ll be provided with an intricate report of what’s present, what’s missing and what you can do to change your gut health for the better. Some companies even tell you what foods you should avoid and what you should increase in your daily diet.

Learning what shape your gut health is in is critical to your health. By following this plan, you can now plan accordingly, some have even restored a healthy gut flora after knowing they weren't in great shape.

Foods That Can Improve the Gut Microbiome and Immune System

foods to improve gut health and immune system

The food that we eat can directly affect the microbiome, which is why we should pay close attention to our diet each day. Let's take a look at some tips for improving your gut health simply by way of your diet.

Pay Close Attention to Diversity

Hundreds of different bacterial species live inside of our intestines and gut. The more diverse your microbiome is, the healthier your gut will be. Eating a diverse diet can help you develop a healthier microbiome. Unfortunately, many Americans are living off a diet that is high in fat and refined sugar. It’s ideal to eat as many different fruits and vegetables as possible, but you should also work in lean protein like chicken and fish, whole grains, cultured dairy products, fermented foods and healthy fats like avocado and olive oil.

Learn More about Fermented Foods

Fermented foods have gone through a process where the sugars in that food have been broken down by bacteria or yeast and a large amount of the bacteria lactobacilli is present. Commonly consumed fermented foods include yogurt, kefir, soy, kimchi, sauerkraut, tempeh and kombucha. When you consume a healthy amount of fermented foods on a regular basis, this can boost the amount of beneficial bacteria that you have in your gut. This can decrease inflammation and prevent disease.


Understanding how the body works can provide some very insightful information that allows us to better care for our body. With all that we know about the relationship between our gut and our immune system, we’re able to make healthy choices that will assist our body with protection against harmful bacteria and pathogens. We’re even able to utilize at-home gut health tests to learn what’s going on inside of our gut.

If you experience health issues related to your gastrointestinal system or you’re dealing with autoimmune issues, your gut may very well be to blame. You can speak with a doctor about your situation, but you may also want to think about changing up your diet and lifestyle. There are healthy choices that you can make to develop a more diverse microbiome that will boost the function of your immune system.

Tips for Success from the RD

If you're interested in improving your microbiome to boost your health and immune system, here are some tips for success.

Purchase a Gut Health Test (Get the data)

There are numerous gut health tests that you can purchase online to learn more about your own personal gut health. Many of them also sell supplements that you can use to address the deficiencies in beneficial bacteria that may be found in your results. I highly recommend Ombre's at-home gut test, Viome or Flore – all of these brands are leading the charge by offering an at-home test and customizing your probiotics / prebiotics based on your test results.

Consider a Supplement

Directly adding probiotic and prebiotic supplements into your daily routine is a fast way to boost the beneficial bacteria in your gut. Not everybody feels like they have enough room in their diet to include fermented foods and foods that are high in probiotics into what they eat every day. You can take a high-quality supplement that will help to boost your immune health and regulate your gut. Supplements to consider are ONNIT Total Gut Health and Primal Harvest Gut Restore, which we covered in full detail.

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Courtney D'Angelo, MS, RD

Courtney D'Angelo, MS, RD, earned her masters degree in Nutrition and Foods from the University of Georgia. She's a Registered Dietitian at Morrison Healthcare and has a strong passion in helping people improve their wellness!

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