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  • Liz Hoobchaak

Autoimmune Disease and Leaky Gut: The Hidden Link

Updated: Nov 12, 2023

There are over 100 different known autoimmune diseases. Each one is unique in that it affects a different body tissue, such as nerves, muscles, skin, joints, digestive system, etc. However, they all stem from a dysfunction in how the immune system is operating. 70-80% of our immune system resides in our body's biggest organs: the skin and gastrointestinal tract, or “gut.”


When things enter our body through our gut or skin, our immune system has certain cells that inspect these particles and decide whether they are foreign and dangerous, or if they are benign and harmless. An autoimmune disease arises when our immune system starts to recognize benign healthy cells, or our bodies' own cells, as dangerous and begins to send out the signals for more specialized immune cells to mount an attack.


Most individuals who are diagnosed with any one autoimmune syndrome are three times more likely than others to develop additional autoimmune diseases down the road. That is why it is critical to understand the mechanism of how they may occur and what we can do to minimize our chances by optimizing our health through proper diet and lifestyle. This article will go into more detail about the anatomy of the gastrointestinal tract and how it can become compromised, which may lead to disease progression and additional autoimmune diagnosis.


Anatomy and Physiology of the Gut

Let’s do a quick basic review of the anatomy and physiology of our gastrointestinal system. Understanding how things should work will help us understand how things can go wrong and what we can do about it. The main component of the gut includes all the specialized tissues that form the gastrointestinal tract that begins at the mouth and ends with the anus. Along the way, food passes through the esophagus, stomach, small intestines, large intestines and finally exits the body as stool. All of these segments have different levels of digestions and absorption of key nutrients from the ingested food.


When ingested food has entered the stomach, formal digestion begins with hydrochloric acid. This acid helps to break down certain proteins as well as increase acidity in the stomach. The small intestine is where the majority of the digestion and absorption of all the key macronutrients (carbohydrates, proteins and fats) as well as micronutrients (vitamins and minerals) occurs. There are accessory organs in the small intestine that help to facilitate this digestion and absorption. These include the liver, gallbladder and pancreas, which all produce secretions and digestive enzymes to aid in this process.


By the time food has reached the beginning of the large intestine, all essential digestion and absorption has already taken place. The colon, which is towards the end of the large intestines, is responsible for reabsorbing the extra secretions created throughout the whole digestive process to help maintain an overall water balance in the body. Whatever material is left over becomes stool. The formation of stool, as well as constancy and frequency, is reliant on the types of foods consumed, amount and type of liquid, the time it has spent traveling through your gastrointestinal system and the composition of your gut microbiome.


Gut Microbiome

The topic of the gut microbiome is too large to fully explain in one small article. It is an area of immense research that scientists are only starting to scratch the surface of understanding. In a nutshell, the gut microbiome is a complex ecosystem of trillions of microscopic living organisms (microbes) including bacteria, fungi and viruses, that live in relationship with us throughout the entire gastrointestinal tract.


The majority of these microbes are found in the cecum, a small structure that is part of the large intestine. There are up to 1,000 different species of bacteria that form their own colonies. While some of these bacteria are associated with disease, others are actually extremely important for our overall health including our immune system. There are roughly 40 trillion bacteria cells in our body which is more cells than actual human cells. This means we are more bacteria than we are human!


Altogether, these microbes may weigh as much as 2-5 pounds which is roughly the weight of your brain. They essentially function as an extra organ in your body that influences your overall health. Disturbances to this gut microbiome often lead to dysfunction in the gastrointestinal system and immune system which in turn may lead to disease.


Leaky Gut

The gastrointestinal tract is lined with a mucous barrier. This mucous lining functions as a barrier to protect the gut tissue from various pathogenic substances from the environment that may enter the body and cause harm. Housed within the lining of the gut wall are specialized cells that act as the main communicators between the entering microorganisms and the gut based immune system. Therefore, our gut is one of the first locations where this interface between our immune system and entering particles from our environment occurs.

Damage to the integrity of this mucous lining may lead to a dysfunction of the specific cells within our intestinal wall that affect our immune system. Damage to the mucous barrier can also lead to increase in permeability of the intestinal wall. “Leaky Gut” is a common catch-phrase term that describes this increased permeability of the lining of the small intestines where there is selective absorption of specific key nutrients. When this happens, there is unregulated passage of bacteria and other environmental toxins across the mucosal barrier, through the intestinal wall and possibly into the bloodstream. The body then mounts an attack against these foreign invaders in the form of an immune response. In individuals with a genetic predisposition, a leaky gut may allow certain environmental factors to enter the body, which could then trigger the initiation and development of an autoimmune disease.


How Does the Gut Become Compromised?

Growing evidence shows that the gut microbiome is very important in supporting the integrity of the gut wall and plays a key role in regulating environmental pathogens that may enter the body. Our gut microbiome is influenced by many factors beginning from before birth when we are still in the womb. Anything entering the body through the gastrointestinal tract will impact the trillions of microbes in our gut microbiome. There is always a constant fluctuation of the “good” bacteria and the “bad” bacteria based on what our body comes into contact with.


There are several ways this mucous barrier may become damaged and “leaky gut” may occur. Dysbiosis is when an imbalance occurs in the helpful bacteria and the harmful bacteria. When more harmful bacteria are present, inflammation will slowly start to degrade the integrity of the gut wall.


The main contributing factors include:


Ingesting “anti food or man-made ingredients'' - Including sugar and other artificial sweetners, genetically modified foods (GMOs), wheat based products, grains that contain gluten, processed meats and other foods, and the many additives and preservatives that are added to our foods to make them more shelf stable.


Environmental Toxin Overload - On a daily basis, we come across over 80,000 chemicals and other toxic substances through the food we ingest, the water we drink, the air we breathe and the many household items we use. The main toxins we come in contact with are pesticides and fertilizers that are found in our crops and through contaminated tap water that contains run-off from industrial power plants.


Prolonged Exposure to Stress - Stress can weaken your immune system which inhibits your body's ability to eliminate harmful bacteria and viruses, which results in inflammation and leaky gut.


Certain Medications- Long term use of non steroidal anti-inflammatory drugs (NSAIDs), such as aspirin and ibuprofen, may increase intestinal permeability. Antibiotics are also a culprit in creation of leaky gut.


What to do about this?

For those with autoimmune disease, focusing on improving gut health through diet and lifestyle changes is often overlooked in favor of more risky and expensive medical treatments. Modulating the gut microbiome can serve as a potential method for improving intestinal permeability and can help prevent or alter the course of autoimmune disease in susceptible individuals.


The focus should begin with removing “anti-food” and introducing nutrient-dense foods to support a more optimal microbiome. We want to address the numerous environmental stressors and exposure to toxins that negatively impact our nervous system and hence our digestive function and gut integrity. Start by making small changes toward a healthier diet and lifestyle, and you can make a huge impact on your overall health, functioning and wellbeing.


Article written by:

Liz Hoobchaak, PT, DPT, CNPT, CAHNS



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