Microbiome Update: The Latest Science On The Gut-Immune Connection

Today’s blog article covers some of the fascinating recent research that looks at different ways the microbiome directly influences, and even works together with the body’s immune system.

It’s well known that the health of the microbiome and digestive system affects our overall health, but now we are discovering more and more how and why this happens.

This information may lead to more specific treatments for disease, new testing methods and ultimately more personal empowerment when it comes to our health and disease prevention. 

In this article, you will learn more about:

  • The microbiome itself
  • The connections between the microbiome and immune system
  • New research on the gut-lung axis
  • New research on short chain fatty acids
  • New research on how the microbiome protects us from viruses
  • New research on autoimmunity
  • Dr. Shippy’s top 4 action steps for supporting your microbiome, starting today

Let’s dive in!

Microbiome Recap

The microbiome is made up of more than 100 trillion individual microorganisms and thousands of species bacteria, yeast and viruses. The microbiome is dynamic and adjusts very quickly to changes in your diet, stress levels, exercise routines, toxin exposures and many other factors.

The health of the microbiome is linked to just about every system in the body and we are understanding these intricate connections more every day and how they influence your health.

It’s impossible to talk about the microbiome without discussing links with the immune system. The gut provides a first line of defense between the body and pathogens that enter the GI tract through eating, drinking and normal daily activities.

In addition, 60 to 70 percent of the body’s immune system lives in the gut! This includes GALT, or gut-associated lymphoid tissues, where you’ll find immune cells ready for action. 

It’s no wonder that the health of the microbiome, and how we care for it on a daily basis, greatly influences our immune resilience, the ability to fight off infection and to prevent chronic disease. 

Let’s take a look at some of the most recent research connecting the microbiome and the immune system. 

The Gut-Lung Axis

In the time of COVID-19, many are paying close attention to the science of the lungs. Like the gut, the lungs also contain a thin layer of mucosal cells that provide a barrier to the inside of the body. The lungs contain immune cells as well, to fight pathogens and toxins that enter the body through the air. 

We now know that there is a gut-lung axis and that the microbiome in the gut influences the microbiome in the lungs, and therefore how the immune system functions in the delicate tissue of the lungs. 

Over 16 million Americans have COPD, or chronic obstructive pulmonary disease, which includes emphysema, chronic bronchitis and other conditions that impair the ability to breathe. COPD is one of the pre-existing conditions that makes it hard for the body to fight COVID-19.

Risk of COPD increases with smoking and is also influenced by air pollution, mold and outdoor air pollution including smoke from forest fires. There is even a surprising link between air pollution and autoimmune disease

In a recent study, researchers compared the gut microbiome of those with COPD with healthy people. What they found is astounding and also not surprising: the microbiome in those with COPD is distinct from those with healthy lung function. They were able to identify bacterial species, including Streptococcus sp00187445, Streptococcus vestibularis and bacteria in the Lachnospiraceae family that directly correlate with reduced lung function. This suggests that in the future, we may be able to anticipate lung function via a stool test. 

Short Chain Fatty Acids 

When it comes to the microbiome, balance is key. In a healthy microbiome, the beneficial bacteria (or probiotics) help to keep any pathogens in check.

This is why taking probiotics, prebiotics and eating fermented foods is so beneficial for increasing and maintaining the populations of these helpful organisms. 

A new study sheds some light into how the beneficial bacteria displace more undesirable species and it has to do with short chain fatty acids, or SCFA. 

SCFAs is a group of small-chain fats, that include primarily acetate, propionate and butyrate. These small fats are produced by bacteria, mainly from the Firmicutes and Bacteroidetes phyla, as byproducts from fiber digestion. And, SCFA protect against infections from E. coli, salmonella and other pathogens. 

The mechanism behind this protection was discovered in recent research in mice. Researchers discovered the SCFA produced in the colon bind to a protein on immune cells called apoptosis-associated speck-like protein, or ASC.

This protein is part of the inflammasome, which is an immune protein structure that you may have heard about in the context of COVID-19. When activated, the inflammasome produces inflammatory signals. This is how your immune system kills pathogens including bacteria and even viruses when detected in the gut.  

When mice were fed fiber, or fed SCFA directly, they had greater survival when exposed to Salmonella. This is likely true in humans too, as we’ve known for a long time that a fiber-rich diet leads to better health. 

Anti-Viral Activity Of The Microbiome

The microbiome plays an important role in the body’s resilience when faced with a virus. In another recent study in mice, researchers showed that bacteria in the gut play an important role in protecting the host from viral infections. 

In this study, Bacteriodes fragilis, a specific bacteria strain that is common in humans as well, was shown to have a molecule on the surface of their cell that activates a receptor (called TLR-4 TRIF) on immune cells in the gut.

This leads to the release of Interferon-beta, or IFN-ß, from the immune cell. Interferons are cytokines, signaling molecules that help to regulate the immune system and fight viral infections, including influenza in this study. 

In the study, mice were treated with antibiotics, which wipes out both pathogens and beneficial bacteria, when they were exposed to the virus they were more likely to become infected with the virus and have worse outcomes. In addition, when mice were given the surface molecule from Bacteriodes fragilis, their immunity improved. 

So now, not only do we know that a healthy microbiome is anti-viral, but we understand more about why. And it’s likely that this isn’t specific to this bacteria; many other beneficial bacteria likely trigger a similar immune response. 

Microbiome And Autoimmunity 

In Functional Medicine, it’s been known for a long time that changes in the microbiome may be an important root cause in the development of autoimmunity. It makes sense given that so much of the immune system is in the gut and autoimmunity occurs when the immune system becomes unbalanced and confused. 

Multiple sclerosis, or MS, is the most common autoimmune disease of the central nervous system and affects 2.3 million people. This autoimmune disease really highlights the connection between the gut and brain, or the gut-brain axis, and the composition of the microbiome plays an important role in MS. 

In recent research, it was shown that immune cells from the gut are able to travel through the body and into the brain during an MS flare with the purpose of calming down brain inflammation. Immune cells called B cells that produce IgA antibodies may help to bring MS back into remission, by reducing these flares. Those with MS have more of the bacteria that interact with these B cells. 

Take Action 

While much of this article zoomed in to the small, yet profound, discoveries of connections between the microbiome and immune health, we can also zoom out to take in the big picture.

How we support the microbiome in our daily lives largely determines our immune systems resilience and ability to return to homeostasis when we are exposed to a pathogen. Here are some action steps to consider in your daily life:


1. Eat fiber. Dietary fiber, found in many staples of the Paleo diet, including nuts, seeds, vegetables, starchy tubers, berries and other fruit, provides the fuel to your microbiome to produce the SCFA that help to regulate the immune response and protect the body from infection. 


2. Get tested. Whether you have digestive symptoms or not, periodic stool testing provides incredibly helpful data on the health of your microbiome, and therefore immunity and overall health. The GI MAP test, is a simple at-home kit that looks at many of the beneficial bacteria discussed here, along with pathogens and markers for digestive organ function. It also looks at specific bacteria that are linked to autoimmune disease. 


3. Balance your microbiome. Through a personalized 5R gut healing protocol, you can reorganize and balance your microbiome. This includes: removing what is damaging to the gut, replacing what you need more of, repairing the gut lining through specific nutrients and herbs, re-inoculating with beneficial bacteria and rebalancing your lifestyle to support a healthy microbiome over the long-term. 


4. Use digestive support supplements. Since we know that digestive health is the foundation of overall health, some extra support in this area is particularly helpful when recovering from an illness, with increased age and through periods of stress. Several gentle options are available here

Hopefully, now you can see some of the important links between the microbiome and the immune system. Although we tend to think of ourselves as living alone in our body, we actually share the space with trillions of microscopic organisms in a symbiotic relationship. While we give them a cozy place to live, they provide us with so many wonderful benefits and are absolutely essential to both our immune health and long-term wellness. 


  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7676259/ 
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7524008/ 
  3. https://www.cell.com/cell/fulltext/S0092-8674(20)31454-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867420314549%3Fshowall%3Dtrue 
  4. https://immunology.sciencemag.org/content/5/53/eabc7191