The Microbiome and Your Immune System

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Your immune system and microbiome are connected, and constantly shaping each other. Increasingly, more and more research is linking the microbiome to conditions such as allergies, inflammation and immune deficiencies. As the colder days begin to dominate, how can you protect yourself and keep your body’s defences fighting strong? Here, we delve deeper into what you can do to ensure you’re flu-free this Winter season. 

By Emilie Korsgaard Andreasen

The current epidemic of allergic diseases has long been linked to the microbial environment. Just how the gut bugs and the immune system influence each other, however, is still not completely understood. Luckily, researchers have recently revealed a tight connection between the two, with our environment and lifestyle being identified as some of the major players in the game1. However, it’s not only allergic diseases that matter when it comes to the wellbeing of the gut. New studies show that it’s also our diet and the vitamins we consume which can play a big role in maintaining a healthy immune response.

Clostridia – keeping the immune system from attacking the good guys

The gut microbiome regulates the host’s immune system, ensuring that our good gut bacteria are safe from being cleared out by the defence system. Notably, a new study underlines one particular class of bacteria as the hero of the interaction between our gut and immune system.

Researchers from Brown University showed that bacteria of the class Clostridia regulate the levels of a protein responsible for the conversion of dietary vitamin A to its active form in the gastrointestinal tract. Clostridia reduce the expression of the protein and promote increased vitamin A storage in the liver.

Establishing that bacteria can regulate how vitamin A is being metabolized in the intestine can help clarify the relationship between inflammatory diseases and the microbiome.

They showed that the expression of the protein, and thus the vitamin A in its active form, was lower in normal mice compared to germ-free mice. By suppressing the active form of vitamin A, the scientists found an enhanced resistance to colonization of Salmonella – and concluded that by reducing the synthesis of the active form of vitamin A, the commensal bacteria communities are protected from excessive immune activity while stabilizing the balance that prevents colonization by pathogens.

The scientists are optimistic about this finding helping in treatments for disorders like Crohn’s Disease, since vitamin A plays a role in inflammation in the bowel. They hope that establishing that bacteria can regulate how vitamin A is being metabolized in the intestine can help clarify the relationship between inflammatory diseases and the microbiome. The researchers state that both the diet and the bacteria in our gut are critically linked in regulating our immune cells and how they behave2.

The dangers of a Western diet

Boosting bacteria like Clostridia seems like the logical choice – after all, they appear to be able to shut out pathogens and stabilize the immune response for all the good gut bugs. So, just what kind of food should you eat to make sure you’re helping out your immune system?

A study found that the Western diet may not particularly be a good choice. Loaded in fats and sucrose, and low in fiber, this diet is one of the most prevalent in westernized countries – and is often associated with obesity. Western diets have also been known to influence microbial pathogenesis and chronic inflammation.

What’s more, the scientists reported that mice fed a Western diet had higher baseline inflammation and increased sepsis severity. Sepsis is a deleterious immune response to infection that leads to life-threatening organ dysfunction. They showed that the diet may be directly regulating the innate immune system though an unknown mechanism. Ultimately, it seems the Western diet is reprogramming the basal immune status and response to sepsis, leading to more severe disease and poorer outcomes3.

Boost your immune system by boosting your gut bugs

If you’re looking to help out your immune system, eating healthy is a good place to start. Here is a short overview of simple tips to keep your body’s defense system up and running.

  1. Calories and protein
    Don’t completely cut foods rich in calories and protein as these types of food is necessary for optimum immune function and an insufficiency decreases the immune system’s capacity to respond and impairs the construction and function of the thymus4.
  2. Salt
    Avoid too much salt as this has been observed to induce inflammation and worsen autoimmune disorders4.
  3. Saturated fatty acids
    Saturated fatty acids can act pro-inflammatory and can disturb the immune functions by changing the lipids of the membranes of the immune cells. Limit the intake of butter, cheese, pork and beef fat4.
  4. Omega-3 fatty acids
    Omega-3 fatty acids have been shown to have anti-inflammatory effects4. Get your dose through ground flaxseeds! 
  5. Vitamins
    Vitamins C and E supplementation are great to boost the general health as well as the immune system. Vitamin C is great to fight off colds by boosting white blood cells and vitamin E is good for maintaining a healthy immune system and reducing inflammation4,5. Eat more almonds and other nuts to provide your body with more vitamin E. Eat more fruits and vegetables to boost vitamin C.
  6. Zinc, selenium, iron
    Been sick lately? Try increasing your intake of zinc as disease progressions can lead to zinc deficiency, which can cause weakened immune function. Selenium and iron has been observed to boosts the bug killers of the body4.

Still don’t know where to start to boost your good gut bugs and your immune system? A good place could be to check out just what your microbiota says. Here at GUTXY we’re ready to guide you to better gut health!


  1. Mezouar, S. et al (2018) Microbiome and the immune system: From a healthy steady-state to allergy associated disruption. Human Microbiome Journal. 10;11-20.
  2. Grizotte-Lake et al. (2018) Commensals suppress intestinal epithelial cell retinoic acid synthesis to regulate interleukin-22 activity and prevent microbial dysbiosis. Immunity. 49;6. 1103-115.
  3. Napiera, B. et al. (2019) Western diet regulates immune status and the response to LPS-driven sepsis independent of diet-associated microbiome. PNAS. 116;9. 3688-3694.
  4. Kafeshani, M. (2015) Diet and immune system. Immunopathol Persa. 1;1. 04.
  5. Lewis et al. (2018) Regulatory role of vitamin E in the immune system and inflammation. IUBMB Life. 71;4.


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