SIBO.
Bacteria living in the wrong section of the intestine. Bloating, gas, food reactions — the picture clears once the location is corrected.
Right bugs. Wrong place.
SIBO is small intestinal bacterial overgrowth — bacteria that belong in the large intestine migrating up into the small intestine, where bacterial populations should normally be sparse. These displaced bacteria ferment carbohydrates prematurely, producing excess hydrogen, methane, or hydrogen sulfide gas that inflames the small intestinal lining.
That fermentation gas is the direct cause of the bloating, cramping, and unpredictable bowel changes that define the condition. The hallmark is bloating that gets worse through the day, especially after meals — often within 60 to 90 minutes of eating.
Research published in the American Journal of Gastroenterology found SIBO in up to 78% of patients carrying an IBS diagnosis, which suggests a large share of people labeled with IBS actually have an underlying, treatable bacterial overgrowth. Most SIBO patients have been told they have IBS for years before breath testing reveals the real driver.
Our functional medicine team in Jacksonville and Orange Park uses breath testing to identify the specific SIBO pattern — hydrogen-dominant, methane-dominant, or hydrogen sulfide — then applies a targeted antimicrobial and dietary protocol followed by prokinetic support to restore normal gut motility and prevent relapse.
Does this sound familiar?
Confirm. Clear. Reseed.
Why bacteria overgrow in the first place
Your small intestine has built-in defenses that keep bacterial populations in check — stomach acid, digestive enzymes, and the migrating motor complex, the wave-like contractions that sweep bacteria downstream between meals. SIBO develops when those defenses fail.
The usual mechanical drivers: impaired gut motility (a slow migrating motor complex), structural abnormalities like adhesions or strictures, low stomach acid — frequently from chronic proton pump inhibitor use — post-surgical changes to GI anatomy, and systemic conditions like diabetes or hypothyroidism that affect the gut's nerve function. Immune dysfunction can contribute as well.
Why it's so often mislabeled as IBS
Standard gastroenterology workups rarely include breath testing, so the fermentation gases that define SIBO go unmeasured. Patients get an IBS label — which describes the symptoms without identifying the cause — and cycle through diets and medications that manage rather than resolve the problem.
That matters because SIBO is treatable in a way that a vague IBS diagnosis is not. Identifying the specific gas pattern points to the right antimicrobial and the right dietary strategy, which is the difference between chasing symptoms and actually clearing the overgrowth.
Preventing relapse after treatment
Clearing the overgrowth is only half the job. Because the underlying motility problem is usually what allowed bacteria to accumulate in the first place, SIBO has a real tendency to return if that root cause is ignored.
This is why prokinetic support to restore the migrating motor complex, plus attention to stomach acid and diet, is built into the plan from the start. A gut-healing phase then rebuilds the lining and microbiome so the improvement holds rather than fading within a few months.
What a SIBO evaluation looks like
A SIBO evaluation starts with a validated lactulose or glucose breath test, which measures the hydrogen and methane your gut bacteria produce after you consume a sugar substrate. The gas curve tells us not only whether overgrowth is present but which pattern is driving it — and that distinction shapes the entire protocol.
Alongside testing, we take a detailed history: prior abdominal surgery, PPI use, thyroid function, and the timing of your bloating all help explain why the overgrowth took hold. Comprehensive lab panels round out the picture where nutrient deficiencies or thyroid involvement are suspected.
From diagnosis through resolution, our team guides each phase — confirm the pattern, clear the overgrowth, restore motility, then reseed and repair — so you're never left guessing what the next step is or why it matters.
Questions, answered.
Test, don't guess.
A 30-minute consult to determine if SIBO testing is appropriate and the steps to confirm or rule it out.
Book a SIBO consult