The Hidden Truth About Autoimmune Diseases Your Doctor Isn't Telling You

If you're living with an autoimmune disease, you've probably heard the same frustrating advice: "It's genetic. It's chronic. You'll need to manage it forever."

But here's what traditional medicine isn't telling you: autoimmune diseases don't just happen randomly, and they're not simply bad genetics.

As Co-Founder of MSW Nutrition, I've spent years researching the mechanisms behind autoimmune development. What I've discovered—and what the scientific literature consistently confirms—is that the immune system responds to deeper stress signals in the body. When those signals aren't addressed, symptoms continue even when you feel like you're doing everything right.

Today, I'm breaking down the five real root causes of autoimmune diseases that rarely get discussed in rheumatology offices. Understanding these triggers is the first step toward taking back control of your health.

Here's something that should shock you: vitamin D deficiency is the cause of most autoimmune diseases.

Not a contributing factor. Not a risk factor. The actual foundation.

Research demonstrates an inverse association between vitamin D levels and the development of multiple autoimmune diseases including lupus (SLE), Hashimoto's thyroiditis, type 1 diabetes, multiple sclerosis, Crohn's disease, ulcerative colitis, psoriasis, and rheumatoid arthritis.

Here's why this matters: Your immune system IS your vitamin D.

Vitamin D activates your white blood cells. When you have inflammation—caused by stress, poor diet, infections, or environmental toxins—your body converts whatever vitamin D you have into an anti-inflammatory hormone. This hormone is your body's natural defense mechanism against the chronic inflammation that develops 10 to 20 years before you ever receive an autoimmune diagnosis.

But here's the problem: most people are severely deficient.

I'm not talking about being slightly low. I'm seeing lab values of 19, 20, 29 ng/mL when the reference range starts at 30. And even 30 isn't enough. If you want to prevent or manage autoimmune diseases, you need to be at 50-60 ng/mL minimum, ideally 70-90 ng/mL.

The deeper issue: When your body constantly converts vitamin D into anti-inflammatory hormones year after year (fighting hidden inflammation you don't even know exists), you can develop something called vitamin D resistance. Your body becomes less responsive to vitamin D even when you supplement, which is why some people with autoimmune diseases require high-dose vitamin D therapy.

After vitamin D deficiency lays the groundwork, gut damage accelerates autoimmune development.

Here's what's happening inside your body:

Your digestive tract is supposed to be a highly selective barrier—a force field that allows nutrients in while keeping toxins, bacteria, and undigested food particles out. When this barrier breaks down (what we call "leaky gut"), everything changes.

The statistics are alarming:

• 1 in 4 people worldwide have fatty liver disease
• 1 million Americans have their gallbladder removed every year
• An estimated 1 in 3 to 1 in 4 people have leaky gut

When your gut lining develops microscopic holes, it allows things into your bloodstream that don't belong there: bacteria, heavy metals, food dyes, microplastics, toxic waste from your environment, and partially digested food particles.

Your immune system sees these as invaders and mounts an attack. Over time, this constant immune activation leads to autoimmune diseases.

What causes gut damage?

Research clearly shows these common triggers:

• Processed foods and additives that promote GI tract inflammation
• Non-steroidal medications like aspirin, ibuprofen, and Motrin that damage the intestinal brush border
• Alcohol consumption and high-fructose beverages
• Chronic stress that inhibits the immune system's healing capacity
• Pathogenic microbes including Candida species, Salmonella, Giardia, Yersinia, H. pylori, Blastocystis hominis, and Shigella

Your gut also houses your microbiome—trillions of bacteria, viruses, and fungi, both beneficial and harmful. When this delicate balance is disrupted (from antibiotics, poor diet, or medications), pathogenic organisms overgrow and further damage your intestinal lining.

This creates a vicious cycle: gut damage leads to immune dysfunction, which leads to more inflammation, which causes more gut damage.

Here's a fact that changes everything about how we understand autoimmune diseases:

Almost all autoimmune diseases have been associated with at least one infection.

Just one infection can trigger autoimmune development.

Think about your health history for a moment:

• How many bacterial infections required antibiotics when you were younger? (Strep throat is extremely common)
• What viral infections did you contract? (Flu, herpes, chickenpox, mononucleosis, Epstein-Barr)

Here's what medical school doesn't emphasize enough: these infections never truly leave your body.

Viral infections remain dormant inside you forever. Think about cold sores (herpes simplex)—they flare up during times of stress because the virus is always there, waiting. The same principle applies to other viral infections you've had throughout your life.

Research confirms that bacterial infections like Staphylococcus aureus and Streptococcus are related to several autoimmune diseases and chronic inflammation. Repeated strep infections, for example, can lead to PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections), which causes neurological issues.

The accumulation effect:

Every bacterial, viral, parasitic, and fungal infection you've encountered adds to your body's total pathogenic load. When combined with vitamin D deficiency and gut damage (which allows these pathogens to circulate more freely), you create the perfect storm for autoimmune development.

These dormant infections constantly trigger low-grade inflammation. Your immune system remains activated, trying to keep these infections in check. Over years and decades, this chronic activation can cause your immune system to become confused and start attacking your own tissues.

Let's talk about stress and autoimmune diseases in a way you've probably never heard before.

When you're under stress, your brain sends signals to your adrenal glands (two small glands sitting above your kidneys) to produce cortisol and cortisone—your body's natural steroids that reduce inflammation.

Sound familiar? It should. Cortisone is the same medication prescribed by doctors for autoimmune diseases.

Your body already makes it naturally. The problem is what happens over time.

Think about your life from your teenage years through your 20s, 30s, and 40s:

• Bacterial and viral infections (creating stress signals)
• Poor diet and alcohol consumption (metabolic stress)
• Long work hours and inadequate sleep (physical stress)
• Emotional trauma and daily pressures (psychological stress)
• Living with undiagnosed inflammation for years (systemic stress)

All of this sends constant signals from your brain to your adrenal glands: "Make more cortisol! Make more cortisone! We're under attack!"

The inevitable outcome: After years of this relentless demand, your adrenal glands become exhausted. You develop what's called adrenal burnout or adrenal fatigue.

Research confirms the interconnection between the immune and neuroendocrine systems: inflammatory cytokines (IL-6, IL-1β, and TNF-α) stimulate the hypothalamic-pituitary-adrenal (HPA) axis, promoting steroid hormone secretion. When you have chronic inflammation from autoimmune diseases, this system is constantly activated.

The testing gap:

Traditional doctors rarely check these critical inflammatory and adrenal markers:

• Interleukin-6 (IL-6) — acute inflammatory marker, often elevated in autoimmune diseases
• HSCRP (high-sensitivity C-reactive protein) — chronic inflammatory marker
• DHEA-S — adrenal hormone that supports immune function

When these markers are elevated and DHEA-S is low, it indicates your body is inflamed and your adrenals are depleted—yet you're still being given synthetic cortisone, creating dependency rather than addressing the root problem.

Now that you understand the five root causes of autoimmune diseases, here's your action framework:

1. Optimize Vitamin D levels (target 50-90 ng/mL)

• Get tested with a 25-hydroxy vitamin D blood test
• Supplement with vitamin D3 (consider our product The D)
• Retest every 3-6 months

2. Heal your gut barrier

• Remove inflammatory triggers (consider a no grains, no sugar approach)
• Support regular elimination with Good Poops Protocol
• Consider comprehensive gut testing (GI-MAP test)
• Add gut-healing nutrients

3. Address infection burden

• Work with a functional practitioner to test for chronic infections
• Support immune function with adequate vitamin D
• Consider antimicrobial protocols when appropriate

4. Support liver detoxification

• Reduce alcohol and sugar consumption
• Support glutathione production with targeted nutrients (Liver Boost)
• Address fatty liver through diet and lifestyle
• Consider MTHFR genetic testing

5. Rebuild adrenal reserves

• Prioritize sleep and stress management
• Support adrenal function with adaptogenic nutrients (Zen)
• Test inflammatory markers (IL-6, HSCRP) and DHEA-S
• Reduce reliance on synthetic steroids when possible (under medical supervision)

1. Prevalence of Autoimmune Diseases – Over 100 recognized autoimmune diseases with rising prevalence
   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691096/
2. Vitamin D and Autoimmune Disease Association – Inverse association between vitamin D and development of multiple autoimmune diseases
   https://www.sciencedirect.com/science/article/abs/pii/S1568997219301508?via%3Dihub
3. Vitamin D's Role in Immune System Function – How vitamin D receptor and activating enzymes work in immune cells
   https://pmc.ncbi.nlm.nih.gov/articles/PMC9010814/
4. Vitamin D Resistance in Autoimmune Diseases – High-dose vitamin D3 therapy and acquired resistance mechanisms
   https://pmc.ncbi.nlm.nih.gov/articles/PMC8058406/
5. Additional Vitamin D Research – Comprehensive vitamin D immune system mechanisms
   https://pmc.ncbi.nlm.nih.gov/articles/PMC3440067/
6. Leaky Gut and Autoimmune Pathogenesis – How intestinal permeability triggers autoimmune responses
   https://pmc.ncbi.nlm.nih.gov/articles/PMC7767453/
7. Autoimmune Diseases Overview – Environmental triggers and infection roles
   https://www.ncbi.nlm.nih.gov/books/NBK459437/
8. Bacterial Infections and Autoimmune Diseases – Staphylococcus aureus and chronic inflammation
   https://pubmed.ncbi.nlm.nih.gov/28919485/
9. Glutathione and Immune Function – Antioxidant defense systems in inflammatory conditions
   https://pubmed.ncbi.nlm.nih.gov/19393193/
10. Glutathione Levels in Immune Response – Cysteine supplementation and immunological functions
    https://pubmed.ncbi.nlm.nih.gov/11115795/
11. Glutathione Concentration in Hepatocytes – Liver's role in antioxidant production
    https://pmc.ncbi.nlm.nih.gov/articles/PMC2696075/
12. Adrenal Steroids and Immune Function – HPA axis and autoimmune disease connection
    https://pmc.ncbi.nlm.nih.gov/articles/PMC9207529/`