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The Influence of the Microbiome on our Immune System

Updated: Jan 17, 2021


Animals have evolved in the presence of both mutualistic and commensal bacteria for millennia. Today, mutualistic bacteria aid in digestion, produce neurotransmitters (e.g. dopamine), promote epithelial cell function, support nutrient absorption, and limit pathogen invasion, all from the safety of their host --- you.


A mutualistic bacterium is defined as being both helpful and gaining help from the host. In contrast, commensal bacteria are thought to benefit from living in their host while providing no benefit but also no harm. Both mutualistic and commensal bacteria are considered part of our normal gut flora, however we still don't have a complete grasp on the subtle differences between them.


In humans, most of the time we are unaffected by these microbes living in our gut. Occasionally, under specific conditions, commensals are able to evade the immune system’s patrol and exert pathologic effects, this is known as dysbiosis. Some disorders that have been associated with dysbiosis are inflammatory bowel disease (Crohn’s and ulcerative colitis), multiple sclerosis, and rheumatoid arthritis.


Surprisingly, new research has found that the above commensal-induced pathologies are not only influenced by genes but also the environment, infection history, age, and lifestyle. This is good news for people who want to take control of their health and have not been able to find answers elsewhere.


The immune system works in an orchestrated and complex way to protect us from both internal and external threats. It has evolved to have two branches known as the innate and the adaptive immune systems. These two branches work tirelessly to prevent viral and bacterial infections, worm and parasitic invasions, and autoimmune disease and cancer.


The innate immune system is a non-specific response and it is the initial response to any threat. The cells of the innate immune system stem from what is called the monocytic lineage, a type of white blood cell. These cells are the first responders to any sort of invasion that gets past our initial barriers, most commonly the skin and mouth. The innate monocytes divide at the scene and conquer the threat causing an acute reaction that can produce common signs of infection such as heat, pain, redness, and swelling.


The adaptive immune response is a bit more complex. These cells stem from the lymphocytic lineage of white blood cells and are commonly referred to as memory cells.


The memory the adaptive immune system retains is that of every threat and non-threat that has ever gotten passed the physical barriers of your body. This branch of the immune system even has a memory of every food you’ve ever eaten. It knows what is harmful and what is beneficial, what is self and what is not. It is the reason we are able to survive in harmony with commensal and mutualistic bacterium, and why we are able to come in contact with most things without being harmed. This response is something we continue to develop as we are exposed to more and more things throughout our lifetime. It is also the reason vaccines are so effective.


These two systems work together daily to keep us healthy. Unfortunately, it does not always work perfectly and is also responsible for autoimmune diseases, allergies, and several other abnormal physiologic reactions. While the immune system is associated with organs such as the lymph system, spleen, and bone marrow, the gastrointestinal (GI) system houses about 80% of our immune system's cells.


This is why dysbiosis and the immune system are so intimately connected. The bacteria that make up our GI system are policed by immune cells acting as barricades, deciding which bacteria can come in and which cannot. These immune cells keep populations of commensals down and regulate when those populations are getting to large.


When dysbiosis occurs, the immune system can begin to “favor” or express a certain immune response throwing the delicate balance off. When this happens specific pathways ramp up while others start to diminish. This can produce unnecessary amounts of certain hormones due to increased populations of commensals that may signal chronic inflammation, autoimmunity, and/or exacerbated allergic response. When this happens, it is often confusing and can be very difficult to untangle.


Luckily, immune responses and the hormone pathways associated with them have very specific manifestations that usually present themselves with physical symptoms. For example, if someone is experiencing hives and a rash when consuming peanuts we know this to be an allergic reaction. In immunology, this allergic reaction is known as a Th-2 response and researchers have figured out which immune cells are active during this response. By knowing what cells are active we can figure out what hormones are being produced, and how to shut that specific response down.


Allergies are the most dangerous response our immune system produces because the pathway is activated and carried out so rapidly. However, some of the more subtle responses may take years to manifest into physical symptoms and can be more challenging to treat. Luckily, researchers are starting to uncover ways to switch these immune responses and bring the immune system back into balance by influencing the microbiome through modifiable factors.


A philosophy used in functional medicine is known as the 5R protocol. Remove, replace, re-inoculate, repair, and rebalance the GI. Using modifiable lifestyle factors such as diet, stress reduction, exercise, and supplement intake, we can change the balance in our GI tract. When this balance is restored, the immune system quiets down and health can often return to "normal."


Oftentimes in conventional medicine immune system responses are seen as something that need to be managed. However, an immune response is a signal that a pathway or a system in the body is struggling and something has changed altering the homeostasis of the host and our microbiome. When these responses are managed and not investigated, they can start to manifest into chronic disease.


So what can we do to restore a healthy gut and keep our immune system functioning properly? We can exercise regularly and keep our stress under control. Exercise causes changes in our adaptive immune response causing white blood cells to circulate more rapidly detecting illness earlier. The rise in body temperature during exercise may also prevent bacteria overgrowth. Exercise also slows down the release of stress hormones, which is thought to protect against disease.


Certain foods have also been shown to have a vast impact on the immune system. Foods like blueberries, dark chocolate, and turmeric have anti-inflammatory properties that can quiet an overactive immune system.


Supplements such as probiotics and vitamin D have been shown to have an impact on what type of immune response pathway will be activated. However, everyone is unique and because we all have unique systems that have been evolving from our own personal experiences, it is important to figure out with your doctor which supplements and lifestyle modifications are most beneficial for you.


While the microbiome is a diverse and vast field of study that is mostly uncharted, we are beginning to understand the effects it can have on our health due to its influence on our immune system. By paying attention to our health, our physical immune response, and modifying behavior and diet accordingly, it may be possible to avoid some of these chronic disease processes that are becoming more and more prevalent in today’s society.

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