When dealing with autoimmune disease, most people focus on diet, stress, and lifestyle changes—but what if an underlying infection is quietly driving your immune system into overdrive?
Many chronic infections, like Epstein-Barr virus (EBV), Lyme disease, and gut pathogens, have been linked to autoimmune conditions. These infections don’t always cause obvious symptoms, but they can trigger or worsen immune dysfunction, leading to increased inflammation and flare-ups.
How Hidden Infections Contribute to Autoimmune Disease
Your immune system is designed to fight off invaders like bacteria, viruses, and fungi. But some pathogens are tricky—they hide, persist, or even hijack immune function. When this happens, your immune system stays in a chronic state of activation, which can:
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Mimic your own tissues (molecular mimicry), leading to mistaken attacks on your body
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Increase inflammation, worsening autoimmune flares
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Disrupt gut health, which is key to immune balance
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Exhaust immune defenses, making it harder to regulate autoimmunity
Common Infections Linked to Autoimmune Conditions
- Epstein-Barr Virus (EBV) – Associated with Hashimoto’s, lupus, MS, and rheumatoid arthritis
- Lyme Disease & Co-Infections – Can contribute to chronic fatigue, joint pain, and immune dysregulation
- Gut Infections (H. pylori, Candida, SIBO, Parasites) – Disrupt gut health, leading to leaky gut and inflammation
- Cytomegalovirus (CMV) & Other Herpesviruses – Persistent viral infections can keep the immune system on high alert
Signs You May Have an Underlying Infection
- Chronic fatigue and brain fog
- Persistent joint or muscle pain
- Gut issues like bloating, IBS, or food sensitivities
- Frequent infections or slow recovery from illness
- Worsening autoimmune symptoms despite lifestyle changes
- Any chronic health issue
How to Address Infections Without Overwhelming Your Immune System
- Test, Don’t Guess – Work with a functional medicine practitioner to test for chronic infections using bloodwork, stool tests, or specialty panels.
- Using Broad Spectrum Antimicrobials is Essential – Herbs like oregano, berberine, and monolaurin can support pathogen balance but should be used strategically under guidance.
- Support Your Immune System – Along with killing the infections, and there are always multiple infections at the same time, focus on helping your immune system fight the infections with nutrients such as vitamin D, zinc, and NAC (converts to glutathione in your body and can be taken in oral form).
- Heal the Gut – Since 70% of your immune system is in the gut, supporting gut health with probiotics, anti-inflammatory foods, and gut-healing supplements such as the foundational triad of probiotics, vitamin D, and butyrate all together.
- Reduce Overall Stress on the Body – Address toxins, poor sleep, and chronic stress, which weaken immunity and make infections harder to manage.
Final Thoughts
If your autoimmune symptoms aren’t improving despite your best efforts, it might be time to look deeper into hidden infections. By addressing these stealthy triggers, you can help calm your immune system and reduce flares naturally.
