Have you ever felt like your gut was in chaos—like nothing you eat sits right, no doctor can find a clear cause, and your symptoms don’t seem to make sense? You’re not alone. I’ve had many patients tell me they’ve tried everything—probiotics, elimination diets, GI scopes—only to come back with normal labs and no answers. That’s when I start looking deeper. For many of my patients, the root cause for some gut problems lies in an unexpected place: Lyme disease.

We know Lyme disease can affect joints, the brain, and the heart. But what many people—and even some physicians—don’t realize is that it can hijack your nervous system, especially the autonomic nervous system (ANS). This is the control center for all the things your body does automatically: regulating heart rate, blood pressure, body temperature—and yes, digestion.

What Happens When Lyme Hits the Nervous System?

The Lyme bacterium, Borrelia burgdorferi, doesn’t just stay in the bloodstream. It can cross into tissues and nerves, and when it reaches the autonomic nervous system, the signals that keep everything running smoothly can go haywire.

When this happens, Lyme disease patients may experience something called dysautonomia—a dysfunction of the autonomic nervous system. One common manifestation? Gut problems that seem out of proportion to what’s found on testing.

Here’s what I’ve seen in my practice:

• Gastroparesis: Food sits in the stomach too long, causing bloating and nausea.

• IBS-like symptoms: Diarrhea alternating with constipation, often unexplained.

• Low stomach acid: Leading to indigestion, malabsorption, and poor appetite.

• Nutrient deficiencies: Even with a good diet, patients may become deficient in key vitamins and minerals.

• Weight loss or gain: As a result of poor absorption or sluggish metabolism.

Lyme disease and the Gut: A Patient’s Story

I had one patient—a young woman—who came to me after seeing three different gastroenterologists. She was tired all the time, bloated after every meal, and described her gut as “frozen.” She had tried everything, from high-FODMAP diets to multiple supplements. But nothing worked.

What stood out to me was that her gut symptoms weren’t her only complaints. She also mentioned brain fog, dizziness when standing, and a history of hiking in the Hudson Valley. Her Lyme disease test had been “borderline” and dismissed. But when we dug deeper, her history and symptoms pointed clearly to Lyme disease and autonomic involvement.

We started treatment for Lyme—and slowly, her digestion started to improve. Her motility returned. Her bloating eased. She started absorbing nutrients again and finally felt well enough to enjoy a meal without discomfort.

Why This Matters

Too often, these cases get misdiagnosed as “just anxiety,” or “stress-related IBS.” But Lyme disease can mimic or trigger all of these conditions by interfering with the nerves that regulate gut function.

If your patient is having gut problems but everything else checks out—don’t forget to consider Lyme disease. Ask about:

• Tick bites (even if they don’t remember one)

• A past rash that looked like a bull’s-eye

• Unexplained fatigue, joint pain, or brain fog

• Dizziness or trouble regulating body temperature

• Mood changes that came out of nowhere

Lyme disease is often a clinical diagnosis, meaning we rely on patient’s history and symptoms—not just lab tests—to guide treatment.

Hope for Recovery

Recovery takes time, especially when Lyme affects the nervous system. But healing is absolutely possible. When we address the underlying infection and support the nervous system, patients often see remarkable improvements—not just in their gut, but in their energy, focus, and overall quality of life.

If you’re someone who’s been struggling with unexplained gut symptoms and nothing seems to make sense, don’t give up. You may be dealing with something real—and treatable.

The gut and Lyme connection is real. And it’s time we start talking about it.