Every year, more Michigan patients walk into my office exhausted, frustrated, and confused. They’ve been treated for Lyme disease—sometimes more than once—yet their symptoms linger or evolve into something that no longer resembles the original infection. They bounce between specialists, accumulate new diagnoses, and begin to wonder if they’re missing something far more complex beneath the surface.

The challenge is that our conventional medical model was built around acute infections, not long-term immune dysregulation. Standard Lyme disease treatment is designed for early detection, early antibiotics, and rapid resolution. But many patients don’t fit this clean, linear model. They continue to experience neurological, immunologic, and inflammatory symptoms long after the initial infection should have cleared.

This is where functional medicine changes the conversation.

Functional medicine doesn’t view “chronic Lyme disease” as simply a lingering infection. Instead, it recognizes that Borrelia and its co-infections can disrupt the immune system, overwhelm detoxification pathways, and activate the fight-or-flight response in a way that creates ongoing physiologic strain. The illness becomes multifactorial—driven by microbes, toxins, and a dysregulated stress response.

What Chronic Lyme Disease Really Is 

Acute vs. Persistent Lyme

In early Lyme disease, the immune system recognizes the infection quickly. Patients often receive timely treatment, and most recover fully. But persistent Lyme is different. Here, the organism has already begun to evade immune detection, hide in tissues, and trigger inflammation that doesn’t simply shut off when antibiotics stop.

Some people recover quickly because their immune systems remain balanced, resilient, and uncompromised. Others do not—usually because additional layers of stressors, toxins, or co-infections are present long before the tick bite ever happened.

The Role of Immune Dysregulation

Borrelia is uniquely skilled at confusing and exhausting the immune system:

• It changes shape and hides within tissues.
• It disrupts cytokine balance, pushing the immune system into chronic inflammation.
• It interferes with detox pathways, allowing toxins to accumulate.
• It alters nervous system signaling, contributing to anxiety, sensory overload, and autonomic symptoms.

Why “Chronic Lyme” Is Often a Misnomer

Many patients who believe they have chronic Lyme actually have Lyme plus a constellation of other issues. Mold exposure, biotoxins, stealth pathogens, and chronic stress physiology create overlapping symptom clusters that mimic Lyme and worsen its impact.

From a functional medicine standpoint:

• It’s not just the microbe—
• It’s the inflammation,
• The immune imbalance,
• The toxin burden, and
• The nervous system overload

that drive symptoms over time.

Understanding Lyme Through the Root Cause Triad

In functional medicine, healing requires understanding everything that is influencing the body’s perception of threat. The Root Cause Triad outlines the three core categories that drive persistent symptoms.

Microbes

Borrelia as the Primary Driver

Borrelia burgdorferi—when not dealt with early—sets the stage for chronic immune confusion.

Co-Infections

Tick bites rarely carry just one organism. Many Michigan patients also test positive or show clinical patterns of:

• Bartonella
• Babesia
• Mycoplasma
• Anaplasma
• Ehrlichia

Viral Reactivation

EBV, HHV-6, and CMV often reactivate when the body is overwhelmed, further draining energy and creating neurologic stress.

Secondary Infections

Once the immune system is strained, opportunistic bacteria, fungi, or yeast can take hold, worsening inflammation.

Toxins

Biotoxins from Mold Exposure

Patients exposed to mold often experience symptoms nearly identical to persistent Lyme. Mold toxins suppress immune function and destabilize the nervous system, making microbial treatment less effective.

Environmental Toxicants

Heavy metals, pesticides, cleaning chemicals, and fragrances can intensify neurological symptoms and energy depletion.

Internal Toxin Buildup

When detox pathways are impaired, the body struggles to clear microbial byproducts. This increases inflammation and prolongs symptoms.

Stress Response

Chronic Fight-or-Flight Activation

Many patients are stuck in survival mode due to infection, toxins, or emotional strain. This amplifies pain, anxiety, fatigue, and sensory disruption.

Medical Trauma

After months or years of feeling dismissed or misunderstood, the limbic system becomes hypersensitive and reactive.

HPA-Axis Disruption

Long-term stress creates hormonal imbalances, sleep problems, mitochondrial dysfunction, and worsening fatigue.

Functional Medicine Testing for Chronic Lyme Disease

Identifying chronic Lyme patterns requires far more than a standard Lyme test. Because these patients are dealing with layers of immune dysregulation—not just a single infection—we use a comprehensive testing strategy that reveals the full story behind each person’s symptoms.

Comprehensive Tick-borne Panel

A deeper look at microbial drivers is essential. Chronic Lyme rarely occurs in isolation, so we evaluate for:

• Borrelia
• Bartonella
• Babesia
• Anaplasma
• Ehrlichia
• Rickettsia

These organisms interact with one another, and the immune system responds differently depending on the combination. Many patients diagnosed with “chronic Lyme” actually have unrecognized co-infections that must be addressed to see real improvement.

CIRS and Biotoxin Biomarkers

Many persistent Lyme symptoms overlap with Chronic Inflammatory Response Syndrome (CIRS), especially when mold or biotoxin exposure is also present.

We evaluate biomarkers such as:

• C4a
• TGF-β1
• MMP-9
• VEGF
• ECP

These markers help us identify specific inflammatory pathways and patterns of immune imbalance that conventional labs do not routinely measure. When these biomarkers are elevated or dysregulated, it signals that the immune system is still reacting to something—whether microbes, toxins, or both.

Mold/Mycotoxin Testing

Because mold illness and Lyme disease so frequently coexist, we evaluate:

• Environmental mold exposure
• Urine mycotoxin testing

Many Michigan patients discover that their Lyme symptoms worsen dramatically in moldy environments. Mold toxins inflame the nervous system, impair detoxification, and suppress immunity, making microbial treatments less effective and recovery more difficult.

Immune System Assessment

Chronic infections and biotoxin exposures place a heavy burden on immune function. We assess:

• Immunoglobulin levels (IgG, IgA, IgM) to evaluate immune strength and resilience
• ANA and autoantibody screening to identify autoimmune patterns
• hsCRP for systemic inflammation

Understanding these patterns allows us to see whether symptoms are driven by immune exhaustion, hyperactivation, or autoimmune tendencies.

Hormone and Adrenal Evaluation

The stress of chronic infection affects hormonal systems profoundly. We assess:

• Cortisol patterns to understand adrenal strain and HPA-axis disruption
• Full thyroid panel, including reverse T3, to evaluate how infection and inflammation affect metabolism and energy regulation

Nutrient and Mitochondrial Markers

Microbes and toxins both deplete key nutrients. We evaluate:

• Magnesium levels
• B-vitamin status
• Glutathione levels

We may also use organic acid testing to evaluate mitochondrial energy production, oxidative stress, and detoxification capacity. Mitochondria are often one of the hardest-hit systems in chronic Lyme, so targeted support is essential for recovery.

Functional Medicine Treatment Strategy for Chronic Lyme

Healing chronic Lyme requires a clear, structured roadmap that respects the body’s limits. Treatment is paced intentionally—always individualized, always guided by tolerance.

Stabilize the System (“Stay Calm”)

Before we aggressively treat microbes or detox pathways, we help the nervous system find its footing.

This includes:

• Practices that regulate the autonomic nervous system
• Sleep optimization and circadian rhythm repair
• Foundational diet and hydration strategies
• Gentle movement, stretching, and pacing to avoid energy crashes

Treat Microbial Drivers

Once stability is established, we gently begin addressing the infections.

This may include:

• Herbal antimicrobials
• Antibiotics when appropriate
• Targeted Bartonella and Babesia strategies
• Supporting immune resilience to improve microbial clearance
• Careful management of die-off reactions to prevent overwhelming inflammation

Remove Toxins and Reduce Inflammatory Load

Microbial treatment cannot be successful if toxins remain in the system. We address:

Environmental toxins

• Mold remediation and avoidance
• Home air quality improvements

Detoxification pathways

Supporting:

• Glucuronidation
• Methylation
• Mitochondrial function

Therapies that enhance detoxification

• Far-infrared sauna
• Red and near-infrared light therapy
• Binders when appropriate

Balance the Stress Response

The stress response system is often exhausted by the time patients reach us. Rebalancing it is essential for long-term recovery.

We incorporate:

• Limbic retraining strategies (including Primal Trust–aligned approaches)
• Reducing EMF exposure
• Breathwork, grounding, and gratitude practices
• Gentle nervous system therapies that restore resilience

Restore Long-Term Immune Resilience

Finally, we work to rebuild the strength and adaptability of the entire system.

This includes:

• Rebalancing the microbiome
• Correcting nutrient deficiencies
• Gradual progression of physical activity
• Ongoing tracking of biomarkers
• Regular evaluation of symptom patterns and treatment tolerance

Start Addressing the Real Root Causes of Chronic Lyme

Chronic Lyme symptoms rarely persist because of Borrelia alone. More often, they reflect deeper immune strain driven by microbes, toxins, and a nervous system that has been running in overdrive for far too long. Functional medicine offers a structured, evidence-informed way to understand what your body has been trying to tell you—and finally address the root causes of your symptoms.

If you’re ready to move beyond temporary fixes and begin targeted, individualized care, our team is here to guide you every step of the way.

Restorative Medicine Center Dr. Teresa Birkmeier-Fredal, MD
705 Barclay Circle, Suite 115
Rochester Hills, Michigan 48307

Phone: 248-289-6349
Website: https://www.restorativemedcenter.com

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