When a patient comes in with a long list of symptoms; fatigue, joint pain, brain fog, unexplained skin issues, recurring infections, it’s often after months or even years of feeling unheard.

For many, the eventual diagnosis is an autoimmune condition. And for most, that diagnosis still doesn’t offer a roadmap for true healing. One of the first places I explore in these cases is the health of the gut.

What Is Autoimmunity?

Autoimmune disease occurs when the immune system mistakenly identifies the body’s own cells as foreign and begins to attack them. There are over 80 known autoimmune conditions, including Hashimoto’s thyroiditis, rheumatoid arthritis, celiac disease, lupus, multiple sclerosis, psoriasis, and inflammatory bowel disease (IBD). While each condition is unique in its impact on the body, they all share a common underlying feature: immune dysregulation.

Autoimmunity is not random. It is often the result of multiple contributing factors, including genetic predisposition, lifestyle choices, chronic inflammation, hormonal imbalances, nutrient deficiencies, infections, toxic exposures, and most notably, gut dysfunction.

Roughly 70 to 80 percent of the immune system is located in the gastrointestinal tract. This is where immune cells interact with dietary antigens, microbes, and metabolites on a daily basis. The gut lining functions as both a physical and immunological barrier, protecting the internal environment from potential threats while allowing beneficial nutrients to pass through.

When this barrier becomes compromised, a condition known as intestinal permeability or "leaky gut", it allows undigested food particles, bacterial fragments (such as lipopolysaccharides), and toxins to escape into the bloodstream.

These particles can trigger widespread immune activation and inflammation. Over time, this chronic stimulation may lead to immune confusion, in which the body begins attacking its own tissues.

How the Gut Fuels Autoimmune Progression

Scientific evidence has linked gut dysfunction with a growing number of autoimmune conditions. For example in celiac disease, gluten directly damages the intestinal lining, leading to an autoimmune response against the small intestine. In multiple sclerosis, researchers have found altered gut microbiota that correlate with disease progression.  In rheumatoid arthritis, specific gut bacteria have been identified that may trigger joint inflammation in genetically susceptible individuals.

Moreover, many autoimmune patients have imbalances in the gut microbiome. This is known as dysbiosis. Dysbiosis can reduce the production of short-chain fatty acids like butyrate, which are essential for regulating inflammation and maintaining the integrity of the gut barrier.

Once autoimmunity is in motion, it can further damage gut health. Inflammation can impair digestion, reduce nutrient absorption, alter the microbiome, and perpetuate a cycle of immune overactivity. It becomes a self-reinforcing loop. Fortunately, this cycle can be interrupted, often with the gut as the starting point.

An Integrative Approach to Autoimmune Support

Every patient presents a unique health history, and no two autoimmune journeys are the same. In functional medicine, we focus on identifying and addressing underlying contributors to immune dysfunction, particularly those rooted in gut health. While treatment is always tailored to the individual, several clinical goals guide the process:

Supporting Gut Barrier Integrity

When the intestinal lining becomes compromised, immune activation often follows. We work to strengthen the gut lining using well-researched nutrients such as L-glutamine, zinc carnosine, and collagen, along with soothing herbal formulas that may include slippery elm or marshmallow root. These interventions aim to reduce inflammation and help restore mucosal integrity.

Rebalancing the Gut Microbiome

Many autoimmune patients show signs of microbial imbalance, known as dysbiosis. Functional stool testing, when clinically appropriate, can help identify imbalances or overgrowths of bacteria, yeast, or parasites. We use dietary strategies, prebiotics, probiotics, and natural antimicrobials to support microbial diversity and reduce inflammatory triggers in the gut.

Calming Immune Overactivity

Nutrient deficiencies, especially vitamin D, omega-3 fatty acids, and magnesium, can contribute to immune dysregulation. Repletion, along with the use of stress-regulating botanicals (such as adaptogens), anti-inflammatory foods, and mindfulness-based practices, can help modulate immune response. In some cases, short-term elimination diets are used to identify food sensitivities that may be fueling chronic inflammation.

This approach does not replace conventional treatment but can complement it. The goal is to strengthen the foundation supporting the gut, regulating immune function, and improving quality of life through personalized, evidence-informed care.

It is important to clarify that integrative care does not mean ignoring or replacing conventional treatment. Many of my patients continue to work with their specialists and may be using immunosuppressive medications to manage symptoms. My role is to help balance and diversify the terrain of the gut, support the immune system, and calm the mind. This root cause approach will stop inflammation and autoimmune disease in its tracks.

A Connected Body, A Personalized Plan

Autoimmune symptoms can feel mysterious and overwhelming. But they are not random. They are signals of deeper imbalance, and for many patients, the gut is both the origin and the key to healing.

If you’ve been diagnosed with an autoimmune condition or are struggling with chronic symptoms that no one can quite explain, it may be time to take a closer look at your digestive health. Start with the foundations, your gut, your nutrition, your stress patterns, and allow healing to follow.

To learn more about how digestive health impacts your nervous system and hormones:

Watch: Leaky Gut is Not a Diagnosis

Read:  The Gut-Brain Connection

Ready to Take the First Step?

If you are living with an autoimmune diagnosis or suspect something deeper is going on, Dr. Gundle, DO. offers personalized, integrative care to help uncover root causes and restore balance, beginning with the gut.

→ Book a Gut-Immune Consultation
Let’s build a plan that treats you as a whole person, not just a condition.

About Dr. Avraham Gundle

Dr. Avraham Gundle DO, is a leading expert in gut health and functional medicine, dedicated to helping individuals uncover the root causes of digestive issues and restore balance through personalized, science-backed approaches.

With years of experience in integrative health, Dr. Gundle has guided countless patients toward lasting relief from conditions like bloating, IBS, food sensitivities, and microbiome imbalances. His practice focuses on empowering individuals to take control of their health through nutrition, stress management, and holistic wellness strategies.