Alex Iturregui, functional medicine health coach


The primary goal of a healthy immune system is to protect us against foreign invaders that can cause illness, such as bacteria, viruses, parasites, mold, toxins, and even cancer cells. Our immune system comprises organs, white blood cells, antibodies, and chemicals. When this system works appropriately, it can identify which cells are our own and which are foreign to protect us from disease and infection through an immune response. It produces antibodies that help to destroy pathogens. In individuals with autoimmune diseases, the immune system can no longer differentiate between its cells and foreign invaders, causing it to attack healthy cells, tissues, and organs, weakening bodily function and even becoming life-threatening.

There are over 80 different types of autoimmune diseases, including rheumatoid arthritis, type 1 diabetes, lupus, Hashimoto’s thyroiditis, multiple sclerosis, and Crohn’s disease. Other diseases, such as type 2 diabetes, eczema, and dementia, are now being considered autoimmune diseases.


It is generally accepted that a common denominator in autoimmune disease is the genetic susceptibility of the host immune system to misinterpret a benign environmental antigen as a threat. The interaction between genes and the environment is fundamental to the immune response. However, research is increasingly validating a new paradigm in which genetic susceptibility coupled with increased intestinal permeability sets the stage for a specific environmental trigger. The trigger then causes a break in immunological tolerance and the onset of an autoimmune cascade.

Autoimmune diseases have three components in common:

• A genetic predisposition

• An environmental factor as a trigger or instigator: intolerances and food allergies, stress, chemicals, bacteria, viruses, fungi, parasites, heavy metals

• A breach in the intestinal barrier (leaky gut)

The intestinal epithelium is the largest mucosal surface in the body, providing an extensive interface with the external environment. Healthy, mature gut mucosa with intact tight junctions serve as the main barrier to the passage of macromolecules into the gut. Intestinal permeability is defined as how porous or leaky the small intestine lining is. When the integrity of the gut barrier is compromised, increasing intestinal permeability (also referred to as a “leaky gut”)—as is seen during prematurity or exposure to radiation, chemotherapy, and toxins—an immune response to environmental antigens that cross the gut mucosa may develop, leading to autoimmune diseases.

This complex interplay of genetics, environmental triggers, and intestinal permeability results in various autoimmune diseases that tend to look different depending on the antigens involved and may thus be viewed as separate entities. However, a broader perspective calls for innovative therapeutic strategies to reestablish the intestinal barrier function and further examine the specific environmental triggers that many of these conditions share.


There are many possible causes of increased intestinal permeability. Viral and bacterial infections, antibiotics and other medications, toxins, stress, inflammation, food intolerances, and imbalances in gut bacteria all have been suggested as causes.

Under healthy physiological circumstances, tight junction leakage is prevented by competent intercellular tight junctions. In susceptible individuals, the zonulin system is one of the main pathways that could be responsible for deregulating the tight junctions and perpetuating the autoimmune process. Zonulin, a protein that was discovered in 2000 by researcher and clinician Alessio Fasano, MD, and his team at the University of Maryland School of Medicine, is normally present in the intestines to increase the passage of fluids, macromolecules, and leukocytes but appears to be overexpressed in patients with autoimmune conditions, resulting in increased intestinal permeability. Studies show that gliadin in gluten is a major trigger that causes the release of zonulin secretion. Once gluten is removed from the diet, serum zonulin levels decrease, the intestine resumes its baseline barrier function, and the autoantibody titers are normalized. The autoimmune process shuts off, and the intestinal damage heals completely.

Besides celiac disease, several other autoimmune diseases, including type 1 diabetes, multiple sclerosis, and rheumatoid arthritis, are characterized by increased intestinal permeability. This increase allows the passage of antigens from the intestinal flora or other luminal contents, challenging the immune system to produce an immune response that can target any organ or tissue in genetically predisposed individuals.

There are various ways to address this, and your functional medicine provider may recommend dietary and other lifestyle changes and specific nutritional supplements to re-establish your intestinal barrier’s protective function.


There are hundreds of autoimmune disorders out there. Some common AD include:

Addison’s Disease

Alopecia Areata

Autoimmune Vasculitis

Celiac Disease

Crohn’s Disease

Graves’ Disease

Hashimoto’s Thyroiditis

Multiple Sclerosis

Myasthenia Gravis

Pernicious Anemia

Psoriasis and Psoriatic Arthritis

Rheumatoid Arthritis (RA)

Sjögren’s Syndrome

Systemic Lupus Erythematosus (Lupus, SLE)

Type 1 Diabetes

Ulcerative Colitis



Symptoms of an autoimmune disease can vastly differ depending on which autoimmune condition you are dealing with. However, early symptoms of many autoimmune conditions may be similar, and may include:

Brain Fog

Digestive Symptoms


Hair Loss


Low-Grade Fever

Muscle Aches

Numbness or Tingling in your Hands or Feet

Skin Rashes

Swelling and Redness

Swollen Glands

Trouble Concentrating

Various Pains

Weight Changes


I encourage you to find a Functional Medicine doctor near you. They will investigate the root cause/causes that are unique to you, which is critical for appropriate treatment and recovery. As new insights into the

mechanisms underlying autoimmune diseases and the therapeutic strategies used to treat them continue to emerge; Functional Medicine recognizes that genetics, environmental triggers, and intestinal permeability as being at the forefront of autoimmune disease research, and the Functional Medicine model is specifically designed to address these factors. With its focus on understanding each individual’s unique genetics and environment, their interactions, and the importance of the microbiome and intestinal permeability, Functional Medicine, as the Institute for Functional Medicine stated on its website, is perfectly positioned to help patients prevent and reverse autoimmune diseases.