How Chronic Toxic Microbes Disrupt Your Immune System
If you’ve been diagnosed with multiple conditions—fatigue,brain fog, joint pain, autoimmune issues—but nothing seems to truly explainyour symptoms, you’re not alone. Many of the patients I see have been down thelong road of specialists, prescriptions, and diagnoses that never quite get tothe bottom of what’s really going on. They’re often told “everything looksnormal,” or worse, they’re handed a label like fibromyalgia or chronic fatiguesyndrome with no clear path forward. But deep down, they know something isn’tright.
One of the most overlooked drivers of this kind of chronicillness is what I call toxic microbes—stealth pathogens like Borrelia(Lyme), Bartonella, Babesia, Candida, and certain molds that not only infectthe body but also disrupt and dysregulate the immune system itself.These microbes are sneaky. They don't always cause fever or classic infectionsymptoms. Instead, they quietly hijack the immune system, produce toxicbyproducts (biotoxins), and trigger a cascade of inflammation that can show upanywhere in the body—from your joints to your brain to your hormones.
At the Restorative Medicine Center, we use what I’vedeveloped as the Root Cause Triad to assess and treat these deeperissues. The Triad looks at three primary categories of immune disruption: Microbes,Toxins, and the Stress Response. Chronic microbial infections often show upin all three areas: not only do they act as the initial biological trigger, butthey also produce toxins (biotoxins), and they keep your nervous system stuckin a perpetual state of fight-or-flight. This combination is the perfect stormfor immune imbalance and inflammation.
The problem is, conventional medicine typically doesn’tgo looking for these infections unless you have a very specific symptom profile—andeven then, standard testing often fails to detect them. That’s why patients cansuffer for years without real answers. In functional and integrative medicine,we dig deeper. We don’t stop at the surface symptoms. We ask: Why is yourimmune system overreacting? Why is it attacking your own tissues? What iskeeping it stuck in dysfunction?
Defining theProblem: What Are Toxic Microbes?
When we talk about toxic microbes, we’re referring toa specific category of infectious organisms that don’t just invade the body—theyfundamentally disrupt how the immune system functions. These are not themicrobes that cause a straightforward sore throat or a quick stomach bug. Theseare stealth pathogens—invisible troublemakers that hide deep in tissues,evade the immune system, and slowly create a toxic internal environment thatleads to chronic illness.
In our Root Cause Triad framework, we divide these microbesinto two categories: Primary and Secondary.
Primary Microbes: The Biotoxin Producers
Primary microbes are the heavy hitters. These organisms,such as Borrelia (Lyme disease), Bartonella, Babesia, Candida,and Aspergillus, don’t just cause infection—they generate biotoxins.These biotoxins are poisonous byproducts that interfere with immune signaling,block detoxification pathways, and trigger widespread inflammation. Over time,they can lead to what we call Chronic Inflammatory Response Syndrome (CIRS)—astate where your immune system is stuck in overdrive, reacting to everythingand healing nothing.
Because these microbes produce toxins that directly confuseand dysregulate your immune response, they are a foundational part of manyautoimmune and inflammatory conditions. And yet, they’re rarely tested for—oreven considered—in traditional medical workups.
Secondary Microbes: The Opportunists
Once the immune system is overwhelmed and inflamed, itcreates the perfect breeding ground for secondary microbes—organismsthat might normally be harmless or controlled by a healthy immune system. These include various strains of gut bacteria, viruses, and yeasts. They don’t usually trigger illness on their own, but in the context of immune dysfunction,they compound the problem, contributing to symptoms like fatigue,bloating, rashes, and mood instability.
Think of it this way: if primary microbes are the arsonistsstarting the fire, secondary microbes are the smoke that suffocates everythingafterward.
Why Stealth Pathogens Are So Often Missed
What makes this even more frustrating for patients is thatmany toxic microbes don’t show up in standard labs. They often don’t causefevers. They may not spike your white blood cell count. They don’t follow the “rules”of typical infections. Instead, they settle in for the long haul—disrupting mitochondrial function, triggering chronic inflammation, and pushing your immune system to the brink.
So when your labs come back “normal,” but you still feel terrible—you’re not imagining things. You may be living with a chronic,toxic infection that’s flying under the radar.
How Toxic Microbes Disrupt the Immune System
Once toxic microbes gain a foothold in the body, the realdamage begins—not just from the infection itself, but from the long-termconfusion they create within the immune system. These pathogens are not justinvaders; they are master manipulators of your biology.
Biotoxins and Immune Confusion
Primary microbes such as Borrelia (Lyme), Bartonella,Babesia, Candida, and certain molds release biotoxins—poisonous compounds that scramble normal immune signaling. Instead of mounting a clear and effective immune response, your body gets stuck in a pattern of either chronic overactivation (which leads to inflammation and autoimmunity) or immune suppression (which opens the door to more infections and poor healing).
Even more concerning, some of these biotoxins mimic human molecules. This molecular mimicry tricks the immune system into attacking your own tissues—a major contributor to autoimmune disease. It’s like friendlyfire: the immune system sees your own cells as a threat and launches anassault. This is one of the primary ways toxic microbes contribute to complex conditions like Hashimoto’s, rheumatoid arthritis, lupus, and evenneuropsychiatric syndromes like PANS and PANDAS.
Chronic Inflammation and CIRS
When your body is constantly exposed to microbial biotoxins,it can develop a condition known as Chronic Inflammatory Response Syndrome(CIRS). CIRS is a state of persistent, unrelenting inflammation triggeredby the body’s inability to clear these toxins effectively.
Originally defined by Dr. Ritchie Shoemaker, CIRS is nowrecognized as a hallmark of patients who have been exposed to mold,Lyme-related organisms, or other toxic microbes, and whose immune systemsare “stuck” in a dysfunctional loop. It’s like the body’s fire alarm won’t shutoff—even when the smoke has cleared.
At the Restorative Medicine Center, we look at specificimmune biomarkers to determine if CIRS is present. These include:
● VEGF (Vascular Endothelial Growth Factor)– often low, indicating poor tissue oxygenation
● MMP-9 (Matrix Metalloproteinase-9) –elevated with inflammation and vascular instability
● TGF-B1 (Transforming Growth Factor Beta 1)– a sign of immune overdrive and tissue remodeling
● C4a – a complement protein elevated inresponse to biotoxin exposure
● Plus cortisol levels, Vitamin D ratios,immunoglobulin levels, ANA/autoantibodies, and hsCRP
Together, these labs give us insight into how your immunesystem is functioning and whether biotoxins are playing a role in your illness.
The Downstream Mess
When toxic microbes and their byproducts keep your immunesystem in chaos, the downstream effects can touch nearly every system in thebody. This is why patients with CIRS or chronic infections often end up with along list of diagnoses and symptoms:
● Autoimmune Diseases: Triggered bymolecular mimicry and immune confusion (Hashimoto’s, lupus, multiplesclerosis).
● Hormone Disruption: Chronic inflammationaffects hormone receptors and adrenal/thyroid function—so even if your hormonelevels are “normal,” they may not be working properly.
● Allergies and Sensitivities: Foodsensitivities, chemical intolerances, and mast cell activation are all signs ofimmune hyper-reactivity.
● Neuropsychiatric Symptoms: Especiallycommon in stealth infections like Bartonella and Lyme—these include anxiety,OCD, rage episodes, memory loss, and attention issues. In children, this oftenpresents as PANS or PANDAS, where infections lead to sudden behavioraland emotional changes.
This is why addressing the infection itself is only part ofthe solution. We must also calm the immune system, support detox pathways, andrebalance the body’s communication networks.
Real HealingStarts at the Root
You’re not “just anxious.” You’re not imagining yourfatigue, your joint pain, your brain fog, or your child’s sudden behavioralchanges. When symptoms don’t fit neatly into a conventional diagnosis—or whentreatments never seem to get you all the way better—it’s easy to start doubtingyourself. But the truth is: you may be dealing with chronic toxic microbesthat traditional testing often misses.
These stealth infections are experts at hiding from routinelabs, masking themselves as other illnesses, and keeping your immune systemlocked in dysfunction. But they are not invisible to a trained eye—and they arenot untreatable.
Chronic illness isn’t a life sentence. When we takethe time to understand the microbial, toxic, and stress-related roots ofdisease—what we call the Root Cause Triad—the body has an incredible capacity to heal. Our job is to help it do just that, with clarity, strategy,and compassion.
If this sounds like your story—or your child’s story—we’rehere to help.
At Restorative Medicine Center, we specialize in next-level functional and integrative care. Our mission is to dig deeper,uncover the microbial and toxic burdens that are disrupting your immune system,and guide you through a personalized plan to true, lasting healing.
No gimmicks. No bandaids. Just real answers and a plangrounded in science and compassion.
📍 Visit or Contact Us:
Dr. Teresa Birkmeier-Fredal, MD Restorative Medicine Center
705 Barclay Cir #115, Rochester Hills,MI 48307
📞 Phone: 248.289.6349
📠 Fax: 248.289.6923
🕘 Office Hours: Mon -Thurs: 9am - 5pm; Fri: Closed
🌐 www.restorativemedcenter.com