Autoimmune Conditions & Hidden Root Causes

A Functional Medicine Approach to Healing Chronic Inflammation

Autoimmune diseases are often treated with medications that suppress the immune system — but what if the immune system isn’t broken? What if it’s responding to something deeper?

At our clinic, we take a root-cause approach to autoimmune conditions — investigating the underlying triggers that keep the immune system on high alert. One of the most overlooked contributors? Chronic viral and bacterial infections, along with toxic exposures, chronic stress, and inflammatory diets.

We believe autoimmune disease is not simply a mistake of the immune system — it's a message from the body asking for deeper support and healing.

Understanding Autoimmunity

Autoimmune diseases occur when the immune system begins attacking the body’s own tissues. Common autoimmune conditions include:

  • Hashimoto’s thyroiditis

  • Rheumatoid arthritis

  • Lupus (SLE)

  • Multiple sclerosis

  • Psoriasis

  • Sjögren’s syndrome

  • Celiac disease

  • Crohn’s disease and ulcerative colitis

  • Type 1 diabetes

Many patients suffer for years before receiving a diagnosis — and even then, the standard care often doesn’t explain why it started or how to address the cause.

Root Causes of Autoimmune Conditions

Through the lens of functional medicine and informed by the work of thought leaders like Medical Medium, we recognize that autoimmune conditions are rarely random. They’re often the result of multiple interacting factors, including:

1. Chronic Viral & Bacterial Infections

Viruses and bacteria can hide in the body for years, reactivating during times of stress, toxin exposure, or immune dysfunction. These include:

  • Epstein-Barr Virus (EBV)

  • Herpes viruses (HSV-1, HSV-2, HHV-6, CMV)

  • Varicella-zoster (shingles)

  • Streptococcus bacteria

  • Lyme and coinfections

  • H. pylori and gut pathogens

These pathogens can inflame tissues (thyroid, nerves, joints, skin, etc.) and drive the immune system to attack where they live — not because the body is confused, but because it’s defending itself.

2. Environmental Toxins

Toxins from the environment can weaken the immune system and feed pathogens. These include:

  • Heavy metals (mercury, aluminum, lead)

  • Pesticides and herbicides (like glyphosate)

  • Mold exposure (mycotoxins)

  • Synthetic fragrances, plastics, and industrial chemicals

Toxins often burden the liver and lymphatic system, creating a cycle of inflammation and immune dysfunction.

3. Inflammatory Diets

Certain foods can contribute to gut permeability (“leaky gut”), feed viral or bacterial pathogens, and promote systemic inflammation. Common triggers include:

  • Gluten

  • Dairy

  • Eggs

  • Corn and soy

  • Refined sugar and processed foods

  • Industrial seed oils (canola, soybean, corn oil)

4. Chronic Stress and Nervous System Imbalance

Chronic emotional stress can impair digestion, weaken detox pathways, and suppress immunity — allowing dormant viruses and bacteria to reactivate. Long-term stress also triggers the adrenal glands and alters hormone levels, further affecting immune balance.

How We Help: Testing & Treatment Options

We take a whole-person, functional medicine approach to autoimmune conditions, starting with thorough evaluation and root-cause testing.

Functional Testing May Include:

  • Comprehensive blood panels (including thyroid antibodies, ANA, CRP, homocysteine)

  • Viral panels (e.g., EBV early antigen, CMV, HSV, HHV-6)

  • Stool testing to assess gut infections, inflammation, and microbiome balance

  • Heavy metal testing (urine or hair analysis)

  • Mycotoxin testing for mold exposure

  • Food sensitivity or allergy testing

  • Hormone and adrenal function testing (DUTCH, cortisol panels)

  • Micronutrient testing to uncover deficiencies affecting immune resilience

Treatment & Healing Protocols

Rather than suppressing the immune system, our approach supports the body in removing what’s triggering it. Treatment plans are personalized but often include:

1. Antiviral & Antibacterial Support

We use natural and evidence-informed therapies to reduce pathogen load:

  • L-lysine, zinc, vitamin C, monolaurin, lemon balm, cat’s claw, licorice root

  • Functional medicine-grade botanicals with antimicrobial activity

2. Liver and Detoxification Support

  • Nutrients like NAC, glutathione, and milk thistle

  • Celery juice and leafy greens for liver support

  • Detox binders (charcoal, bentonite clay) if needed

  • Infrared sauna, dry brushing, and lymphatic support

3. Gut Healing Protocols

  • Elimination of reactive foods (gluten, dairy, eggs, etc.)

  • Probiotics, prebiotics, and digestive enzymes

  • Support for SIBO, leaky gut, and microbiome imbalances

4. Targeted Nutrient Repletion

  • Methylated B vitamins (especially for those with MTHFR/SNPs)

  • Magnesium, selenium, vitamin D, omega-3s

  • Adaptogenic herbs to support adrenal function and stress response

5. Nervous System Regulation

  • Mind-body practices like meditation, EFT tapping, vagus nerve exercises

  • Support for emotional healing and trauma (when appropriate)

  • Sleep optimization and circadian rhythm support

Autoimmune Recovery Is Possible

You don’t have to settle for symptom management alone. Our functional medicine approach helps you uncover and treat the real causes of your autoimmune condition — not just mask the symptoms.

By reducing pathogen load, lowering inflammation, restoring gut and liver health, and supporting the immune system, many patients see major improvements in energy, mood, digestion, joint health, and more.

Start Your Healing Journey

If you’re living with an autoimmune diagnosis or unexplained symptoms, let us help you get to the root of it all. Schedule a consultation today and discover a more personalized path to long-term wellness and immune balance.