Why Your Gut Symptoms Keep Coming Back and Why the Real Problem Might Be Your Brain

by Heidi Toy, Functional Medicine

If you’ve dealt with chronic gas, bloating, constipation, diarrhea, or abdominal pain, you’ve probably walked the typical functional medicine path: see a practitioner, run a GIMAP or Gut Zoomer, and start an expensive protocol filled with antimicrobials, probiotics, binders, and gut healing supplements.

And what usually happens? You feel better… until the symptoms return.

Most people assume their practitioner didn’t know how to help, but that’s rarely the case. The issue is that many well-meaning clinicians are trained to look for root causes in the gut but not the mechanisms driving gut dysfunction. And the mechanism that is almost always overlooked is the brain–gut connection.

The Missing Piece in Most Gut Workups - A typical GI intake covers medications, infections, alcohol use, testing, and maybe a quick check for hypermobility. All these are important, but functional gastroenterologists, like Dr. Steven Sandberg-Lewis, emphasize that the true driver of chronic gut issues is often never mentioned: a past traumatic brain injury (TBI).

Here’s the surprising part: You don’t need to hit your head to injure your brain. Whiplash, falls, concussions, sports injuries, broken noses, broken tailbones, and blast exposure can all “shake” the brain enough to affect gut function—even decades later.

If nobody screens for these events, the real mechanism behind your gut issues goes undetected.

How a Brain Issue Turns Into Gut Symptoms - Your entire digestive system depends on brain and nerve communication. When the brain is inflamed or injured, several things happen:

• Gut motility slows or becomes irregular

• Blood flow to the gut decreases

• Digestion becomes impaired

• The gut lining weakens (leaky gut)

• Microbiome balance shifts

• Inflammation rises

Leaky gut allows bacteria and toxins to slip into the bloodstream. This triggers a systemic immune response that can travel back to the brain creating a vicious cycle where brain and gut inflammation continually worsen each other.

This is why your symptoms may improve temporarily with supplements yet return over and over again. You’re treating the consequences, not the cause.

“I Practiced the Same Way… Until I Learned Better”

For years, I also relied heavily on stool testing and gut protocols. Clients improved, but many relapsed. Eventually I realized what many advanced practitioners now understand: If you don’t evaluate the brain–gut axis, you’re doing an incomplete workup.

Once you include the brain, cases that seem “mysterious” suddenly make sense. And protocols finally stick.

“Has your brain ever been shaken?”

This includes:

• Whiplash

• Falls

• Contact sports

• Broken tailbone

• Broken nose

• Blast exposure

• Any injury that jolted the body

These events can be the real driver of chronic digestive symptoms that won’t resolve.

The Bottom Line - Gut symptoms are rarely just gut problems. If your issues keep returning despite all the testing, supplements, and protocols, you likely need a deeper evaluation—one that includes the brain.

When the brain–gut axis is disrupted, no stool test in the world can fix the problem.