The thyroid gets a lot of attention for being the body's 'thermostat,' but for patients with chronic illness, it's more like a tightly regulated command center that’s easily disrupted by stress, toxins, and infection. What many don’t realize is that symptoms of low thyroid function—fatigue, brain fog, cold intolerance—can show up long before a TSH level goes out of range.
For patients dealing with conditions like CIRS (Chronic Inflammatory Response Syndrome) or chronic vector-borne infections, thyroid dysfunction often isn’t about the gland itself. It’s about how illness rewires the entire hormone signaling cascade—and how your body starts redirecting energy, sometimes in all the wrong ways.
🌌 The Thyroid Cascade: TSH, Free T4, Free T3, and Reverse T3
To understand thyroid function, we need to look at four key markers:
- TSH (Thyroid Stimulating Hormone): Released by the pituitary, it tells the thyroid to produce hormone.
- Free T4: The primary hormone released by the thyroid—inactive, but a storage form.
- Free T3: The active form of thyroid hormone that enters cells and drives metabolism, energy, and mitochondrial function.
- Reverse T3 (rT3): An inactive form made from T4. It blocks T3 receptors and slows down cellular activity. Think of it as the “hibernation hormone.”
In times of stress, illness, trauma, or inflammation, the body starts converting more T4 into reverse T3 instead of active T3. This is a protective mechanism—a way of slowing down metabolism to conserve resources. But in chronic illness, this pattern can get stuck.
Let’s bring this to life with a few real-world examples.
🔹 Case 1: The “Normal Labs” Patient with Crushing Fatigue
Lisa, a 43-year-old teacher, came in exhausted, foggy, and gaining weight despite clean eating. Her primary doctor had told her, “Your thyroid is normal.” But deeper testing revealed:
- Normal TSH
- Low-normal Free T3
- Elevated Reverse T3
Lisa had been battling mold exposure and long-standing Lyme disease. Her body, locked in chronic stress and inflammation, was converting her T4 into reverse T3, essentially slamming the brakes on her metabolism. We started her on a low dose of natural desiccated thyroid (NDT), focused on detox and limbic support, and watched as her rT3 dropped and her energy returned.
🌌 Case 2: When Thyroid Hormone Does Nothing—or Too Much
Emily, a 39-year-old graphic designer with CIRS and mold toxicity, came to the clinic after being placed on T4 medication by her previous provider. Despite achieving textbook 'optimal' thyroid levels, she felt no different—still exhausted, foggy, and flat. The issue? Receptor resistance. Her cells couldn’t use the hormone properly because they were still inflamed. The numbers had improved, but the symptoms hadn’t budged.
Then there was Joel, a 45-year-old with high reverse T3 and a biotoxin burden from a water-damaged building. When we trialed a low dose of NDT, he felt wired, anxious, and overstimulated. Labs were improving, but he was miserable. In his case, ramping up metabolism only accelerated detox beyond what his body could handle. We scaled back, let the system stabilize, and focused on drainage and nervous system regulation first.
For both of them, the takeaway was clear: the goal isn’t to normalize labs at all costs. It’s to find the right metabolic pace for healing—and to adjust support as the terrain improves.
⚖️ Case 3: When Antibodies Hijack the Thyroid
Derek, age 36, had erratic mood swings, brain fog, and alternating bouts of palpitations and fatigue. His labs showed both TPO and Tg antibodies, along with fluctuating TSH levels. Over time, his thyroid output had become unstable—sometimes overactive, sometimes underactive—as his immune system launched a slow attack against his own thyroid tissue.
Eventually, his gland was too damaged to keep up. What’s more, we identified chronic Bartonella as a likely root cause—one that’s been linked in research to autoimmune thyroid disease, particularly Hashimoto’s.
Autoimmune thyroid disease is common in patients with immune dysregulation. The main thyroid autoantibodies include:
- TPO antibodies: Interfere with hormone synthesis; hallmark of Hashimoto’s.
- Thyroglobulin antibodies: Disrupt hormone storage.
- TSI: Mimic TSH, causing hyperthyroid symptoms (seen in Graves’).
- TRAb: Can stimulate or block the TSH receptor—causing wild swings between hyper- and hypothyroidism.
Understanding these antibodies helps clarify not only what’s wrong—but why.
🖊️ Case 4: From NDT to T4-Only as the Body Heals
Jasmine, 52, had been on NDT for years and felt decent—but couldn’t taper down without crashing. After starting treatment for mold illness and Babesia, her labs started shifting. Reverse T3 dropped, and she began converting her own T4 into active T3 more effectively. Over time, we switched her to a custom T4/T3 blend, then eventually to T4-only. Not because her thyroid magically healed—but because her immune system stopped jamming the conversion pathway.
This is the trajectory we often see:
- Start with NDT when conversion is poor.
- Transition to adjustable T4 + T3 as inflammation improves.
- Eventually stabilize on T4 alone as the body regains balance.
⚡️ The Takeaway: Your Thyroid is Listening to Your Immune System
If there’s one thing these cases show, it’s that thyroid function can’t be divorced from the rest of the body—especially not in patients with CIRS, mold exposure, or vector-borne infections. You can have perfectly “optimized” labs and still feel awful. That’s not in your head—it’s in your physiology.
Inflammation can block thyroid hormone receptors. Biotoxins can disrupt conversion and overwhelm detox pathways. And sometimes, giving more hormone just turns up the dial on a system that’s already overloaded.
What matters most isn’t chasing perfect lab numbers. It’s pacing treatment to match what your body can actually use, tolerate, and benefit from in that moment.
As the root causes are addressed—whether through detox, antimicrobial treatment, or nervous system retraining—thyroid physiology often begins to normalize on its own. Hormone resistance fades. Conversion improves. And many patients gradually need less medication, not more.
In other words: healing the system helps the thyroid do its job. And that’s what root cause medicine is all about.
Follow along for more stories, science, and support as we unravel the complexities of chronic illness and hormone health.