Why I Start With the Gut — And Why Your Doctor Probably Doesn't

Most chronic disease starts in your gut. Not some of it. Not the digestive stuff. Most of it.

Joint pain. Brain fog. Autoimmune flares. Anxiety that won't respond to medication. Skin problems. Weight that won't budge. Fatigue that no amount of sleep fixes. If you're looking for a gut health specialist near you who connects these dots, this is what I do every day in my Central Texas practice. These aren't separate problems that happen to occur in the same person. They're downstream effects of the same upstream dysfunction.

And that upstream dysfunction? It's usually in your gut.

Roughly 70% of your immune system lives in your gut. The majority of your serotonin — the neurotransmitter everyone associates with mood — gets produced there. Your gut decides what gets into your bloodstream and what doesn't. It's not just a digestive organ. It's a command center.

So when someone shows up with brain fog, joint pain, and fatigue — and their bloating is so constant they don't even mention it anymore because they think it's normal — I'm not thinking about three separate problems. I'm thinking about one broken system.

Why the Gut Is Always Tier One

In my clinic, I use a tiered framework. Tier one is the foundation — gut health, metabolic health, and your stress response. Tier two gets into hormones, toxins, infections. Tier three is the complex stuff — genetics, structural issues. Every patient runs through this sequence because it prevents the biggest mistake in medicine: chasing symptoms without understanding the system.

The gut sits at tier one for a reason. It's not just where you digest food. Roughly 70% of your immune system lives in your gut. The majority of your serotonin — the neurotransmitter everyone associates with mood and sleep — gets produced there. Your gut is essentially running your immune function, influencing your brain chemistry, and deciding what gets into your bloodstream and what doesn't.

So when someone walks in with brain fog, joint pain, fatigue, anxiety that won't respond to medication, skin problems, autoimmune flares, or weight that won't budge despite doing "everything right" — I'm thinking about the gut. Even when the patient isn't.

Does that make sense? The gut isn't just a digestive organ. It's a command center.

What's Actually Going Wrong

Most of the gut dysfunction I see falls into a few overlapping categories.

​Dysbiosis is the big one. Wrong balance of bacteria — too many inflammatory species, not enough protective ones. Sometimes it's from years of processed food. Sometimes it's antibiotics that wiped out the good bacteria along with the bad. Sometimes it's just chronic stress. Cortisol directly changes which bacteria thrive in your gut. Your stress is literally reshaping your microbiome.

Then there's intestinal permeability — what people call leaky gut. The lining of your intestine is supposed to be selective. It lets nutrients through and keeps everything else out. When that lining breaks down, you get undigested food particles, bacterial fragments, and toxins crossing into your bloodstream. Your immune system sees those as threats and starts firing. Chronically. That's how gut inflammation becomes whole-body inflammation — and whole-body inflammation is the common thread running through almost every chronic disease I treat.

And then the sneaky ones: SIBO — small intestinal bacterial overgrowth — candida, parasites. These are more common than most doctors realize because they don't always show up on standard testing. A patient can have SIBO for years and just be told they have IBS. Take this fiber supplement. See you in six months.

What you need to understand: these categories almost always overlap. Patients with dysbiosis usually have some degree of permeability. The permeability is driving inflammation. The inflammation is disrupting hormone metabolism. And now we're chasing hormone problems that are actually gut problems wearing a disguise.

The Connections Nobody's Making

A version of this walks into my office every week. Joint pain, brain fog, fatigue, two years of "normal" labs.

When we run comprehensive stool analysis — not the basic culture most doctors order, but testing that actually maps the full microbial ecosystem, inflammatory markers, and digestive function — we typically find significant dysbiosis and elevated markers for intestinal permeability. The gut is leaking, the immune system is chronically activated, and that inflammation is showing up as joint pain, cognitive dysfunction, and exhaustion.

Nobody had looked. Not because their other doctors were bad — they were practicing the way they were trained. But the training doesn't include functional assessment of the gut microbiome. Your gastroenterologist is looking for pathology — Crohn's, ulcerative colitis, celiac, cancer. If the colonoscopy is clean and the basic blood work is in range, you get told you have IBS and handed a prescription that manages symptoms without touching the cause.

That gap between what we know about the gut and what most doctors were trained to do with it — that's where patients fall through the cracks. And it's a big crack.

Now, the serotonin piece is worth understanding too. About 90% of your body's serotonin is produced in the cells lining your intestines, not in your brain. So when someone comes to me on their second or third antidepressant and nothing's working, my first question isn't about their brain. It's about their gut.

I'm not oversimplifying mental health. I'm saying that if the organ producing 90% of your serotonin is inflamed and dysfunctional, maybe we should look at that before we add another medication targeting the 10% that's in your brain. It's not either-or. It's about finding the actual driver.

How I Actually Work This Up

When someone presents with symptoms that point toward gut dysfunction — and honestly, that's most of my patients — here's how we approach it.

We start with baseline labs. Metabolic markers, expanded thyroid panel — free T3, free T4, total T3, total T4, TSH. I want to know if the foundation is intact before I start digging into the gut specifically. We try not to hammer patients with a thousand dollars in labs on day one. Systematic. Start with what's most common and most likely to explain the symptoms.

If the metabolic picture doesn't fully explain what's going on — and with gut patients, it usually doesn't — then we go deeper. Comprehensive stool testing is the big one. I'm talking about advanced testing that maps the full microbial ecosystem, checks inflammatory markers, looks at digestive enzyme output, and screens for parasites and pathogenic bacteria. This is a completely different level than the basic stool culture your PCP might order.

Sometimes we add additional testing if we suspect bacterial overgrowth or fungal issues — these show up in ways that standard stool tests miss. And we're always looking at the blood work for signs of malabsorption, nutrient deficiencies, and immune activation that suggest the gut is driving problems elsewhere.

The point is we don't guess. We test, we find the specific dysfunction, and we target it.

Treatment — Layers, Not Silver Bullets

There's no one pill for gut health. Anyone who tells you otherwise is wrong. What works is a layered approach, and the layers depend entirely on what testing reveals.

We identify and remove what's causing the problem — inflammatory foods, infections, whatever's driving the dysfunction. If testing shows specific bacterial overgrowth, we treat it with targeted protocols. Candida, we address it. If gluten or dairy is driving inflammation based on your response, it has to go — at least temporarily, sometimes permanently. This isn't about trendy elimination diets. It's about removing specific triggers we've identified.

Then we support the digestive capacity that's been lost and rebuild the bacterial ecosystem with targeted interventions. We repair the gut lining itself using evidence-based protocols. We're sealing the leaks so the immune system can stand down.

Through all of this, we're working on the pillars — sleep, diet, stress management, movement. Because you can take every intervention in the world, and if you're sleeping four hours a night, eating processed garbage, and chronically stressed, your gut is going to stay broken. The medical interventions get you moving in the right direction. The lifestyle changes keep you there.

What This Looks Like in Practice

A version of this pattern is common: six weeks into treatment — targeted protocols for dysbiosis, gut lining support, dietary changes, and a focus on sleep and stress — brain fog typically starts clearing. By three months, joint pain is often down 80% or more. Energy comes back.

We don't touch the joints. We don't prescribe an antidepressant. We don't add a stimulant for the brain fog. We fix the gut, and the downstream problems start resolving on their own.

That's not magic. That's what happens when you address the actual cause instead of chasing individual symptoms. And it's why the gut is always tier one in my framework.

If This Sounds Familiar

If you're dealing with digestive issues that won't resolve, brain fog, autoimmune problems, mood issues that don't respond to treatment, unexplained fatigue, or stubborn weight — and nobody has done a thorough gut evaluation — that's probably the missing piece.

At Rooted Health, the gut is always where we start. Because in my experience, that's where the answers usually are.

Give us a call at 254-780-0023 or visit rootedhealthclinic.com to schedule a consultation.

Rooted Health Clinic — Salado, Texas