Did you know that the composition of your gut microbiome – aka your gut health – can impact several body systems? Scientists have discovered that gut microbiota can impact your nervous system, metabolism, immune system, and more. 

Today we’ll look at some studies that link the gut microbiome to the immune system. We’ll also talk about ways to improve your gut health for the sake of your immunity. Let’s jump in!

Recap: Balancing the Gut Microbiome

You might already know a bit of microbiome science, but here’s a quick recap. 

The microbiome is an ecosystem of millions of microbes – like bacteria, yeasts, and even fungi – living within or on the human body. The term “gut microbiome” refers to the microbes inhabiting the GI tract. 

At first glance, microbes living in the body might sound pretty gross – but it turns out they’re necessary for our survival. Many of the microorganisms living within us benefit our bodies by regulating our metabolism, helping us absorb vitamins from food, supporting our immune system, and much more.

The thing is, not all of the microorganisms in our microbiomes are helpful. Some are harmful. These harmful microbes can damage the gut barrier, increase inflammation, and wreak havoc on our metabolisms, hormone production, immune systems, and mental health. 

Plus, they can cause uncomfortable digestive issues like gas, bloating, and stool irregularity – no fun. 

To minimize the gut damage and annoying symptoms the harmful microbes cause and maximize the benefits helpful microbes confer, we want many beneficial microbes and very few harmful microbes to live in our guts. 

There are typically too many harmful microbes and not enough helpful microbes in an unhealthy microbiome. This state of imbalance is called dysbiosis.

Many scientists argue that dysbiosis, an imbalanced gut microbiome, is likely the culprit of most digestive health issues in America. Dysbiosis can lead to a variety of other health conditions, aside from digestive distress. Today, we’ll look at how it can impact the immune system. 

Gut Microbiome Composition and Immunity

There are tons of studies that have highlighted the importance of gut microbiome composition for adequate immune function. One way it does so, according to a study published in the journal Cell, is by influencing the development and maturation of immune cells in the gut. 

The study found that certain species of bacteria in the gut stimulate the production of immune cells known as T cells, which are critical for fighting infections and diseases. Cool, right?

Another study published in Nature showed that the gut microbiome helps to regulate the body’s inflammatory response. We often think of inflammation as bad. Indeed, it’s bad when we experience chronic inflammation. But we rely on short-term inflammation to fight off invaders and heal injuries. 

In short, inflammation is an essential component of the immune response, but chronic inflammation can lead to a host of health problems, including autoimmune diseases, metabolic disorders, and cancer. 

The study from Nature found that certain species of gut bacteria produce short-chain fatty acids (SCFAs) – which may help to regulate inflammation.

They produce short-chain what-what?

Short-chain fatty acids are nutrients that support the health of the intestines and the balance of the gut microbiome. Bacteria living in the colon produce them. One type of short-chain fatty acid called butyrate is especially relevant.

The cells in your colon (the end of the large intestine) prefer butyrate as a fuel source. These cells tend to operate best when using butyrate for energy. Athletes tend to have high levels of butyrate in their guts.

People with high levels of butyrate in their guts have:

  • A regulated gut immune system 
    • improved tolerance to food
    • → lowered levels of inflammation
  • Better cellular health than those with low levels of butyrate
  • Improved healing
  • Less intestinal permeability than those with low levels of butyrate (10)

Low levels of butyrate are associated with:

    • Obesity
    • Dysbiosis
    • Intestinal permeability
    • IBD
    • Poor appetite regulation
    • Food intolerances
    • High inflammation levels

Check out our blog on short-chain fatty acids to learn more about how to increase your SCFA production!

What Happens to the Immune System If You Have Dysbiosis?

Scientists have discovered that when the gut microbiome is disrupted, the harmful bacteria that proliferate can lead to chronic inflammation and other types of immune-related diseases, including autoimmune diseases such as rheumatoid arthritis and multiple sclerosis. 

Dysbiosis has also been linked to an increased susceptibility to infections, including viral infections such as influenza and COVID-19.

To keep your immune system strong, keep your gut microbiome strong! Check out our blog titled “How to Get Rid of Harmful Gut Microbes” to learn how to keep your gut microbiome healthy. 


  1. Belkaid, Yasmine, and Timothy W. Hand. “Role of the Microbiota in Immunity and Inflammation.” Cell, vol. 157, no. 1, 2014, pp. 121-141. DOI: 10.1016/j.cell.2014.03.011.
  2. Arpaia, Nicholas, et al. “Metabolites Produced by Commensal Bacteria Promote Peripheral Regulatory T-cell Generation.” Nature, vol. 504, no. 7480, 2013, pp. 451-455. DOI: 10.1038/nature12726.
  3. Kamada, Nobuhiko, et al. “Regulation of Immune Responses by the Microbiota.” Nature Reviews Immunology, vol. 13, no. 10, 2013, pp. 790-801. DOI: 10.1038/nri3535.
  4. Li, Jing, et al. “Gut Microbiota Dysbiosis Contributes to Rheumatoid Arthritis Development via Activating Autoreactive T Cells in a GM-CSF-Dependent Manner.” Cell Reports, vol. 20, no. 11,