Digestive Health / SIBO

SIBO Treatment in San Diego, CA — Small Intestinal Bacterial Overgrowth

SIBO treatment in San Diego — comprehensive breath testing and personalized protocols for small intestinal bacterial overgrowth. By Dr. Joseph Dubroff, N.D.

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SIBO treatment small intestinal bacterial overgrowth San Diego
The IBS That Isn't IBS

SIBO Is Probably the Most Misdiagnosed GI Condition in Modern Medicine.

Small Intestinal Bacterial Overgrowth — SIBO — is what happens when bacteria that should live in your colon end up colonizing your small intestine instead. The small intestine is supposed to be relatively low in bacteria; the colon is where most of your microbiome lives. When that geography breaks down, you get fermentation of carbohydrates happening in the wrong place, producing excessive hydrogen or methane gas in a part of the GI tract that wasn't designed to handle it.

The result is a remarkably consistent symptom picture: bloating that gets worse through the day, distention after meals (you look pregnant by dinner even if you're not), gas, abdominal pain, irregular bowel patterns. Most patients with this presentation get diagnosed with IBS — Irritable Bowel Syndrome — which is essentially a diagnosis of "we don't know what's wrong with your gut, but something is." A substantial portion of those IBS diagnoses are actually undetected SIBO.

The reason it goes undetected is that diagnosing SIBO requires a specific test — a hydrogen-methane breath test — that most primary care doctors and even many GI specialists don't routinely order. Without that test, you can't identify the condition. And without identification, you can't treat it correctly. Patients spend years cycling through dietary trials, probiotics, and IBS medications that don't address what's actually happening.

Three Types — Different Treatments

Hydrogen, Methane, or Hydrogen Sulfide.

Not all SIBO is the same. The breath test identifies which type of overgrowth is happening — and the type determines the treatment. Treating methane-dominant SIBO with a hydrogen protocol fails. Identification matters.

— Type 01
H₂

Hydrogen SIBO

Bacteria fermenting carbohydrates and producing excess hydrogen gas. Classically presents with diarrhea-pattern symptoms, urgent bowel movements, post-meal bloating, and abdominal pain. Generally the most responsive type to treatment. Targeted antimicrobial protocols (botanical or pharmaceutical) typically resolve it.

— Type 02
CH₄

Methane SIBO (IMO)

Methanogens (archaea, not bacteria) producing methane gas in the small intestine — sometimes also the large intestine. Classically presents with constipation, severe bloating, and stubborn weight gain. Methane slows gut motility, which makes it harder to resolve. Requires a different antimicrobial approach than hydrogen-dominant SIBO.

— Type 03
H₂S

Hydrogen Sulfide SIBO

The most recently identified type — sulfate-reducing bacteria producing hydrogen sulfide gas. Often associated with diarrhea, sulfur-smelling gas, and sensitivity to high-sulfur foods (eggs, garlic, broccoli). Requires specialized testing to identify and a distinct treatment approach focused on sulfate-reducing bacteria.

Common Questions

SIBO FAQs

How is SIBO diagnosed?+
Through a hydrogen-methane breath test. You drink a solution containing lactulose (or sometimes glucose), then breathe into collection tubes at timed intervals over 2-3 hours. The test measures hydrogen and methane in your breath — both gases are produced by gut bacteria fermenting the test solution. The pattern of gas rise tells us whether SIBO is present, what type, and roughly where in the small intestine the overgrowth is concentrated.
What causes SIBO?+
Multiple potential causes. The most common are reduced gut motility (often from a prior food poisoning episode that damaged the migrating motor complex), proton pump inhibitor use that lowers stomach acid (your stomach acid normally sterilizes incoming bacteria), structural issues like adhesions or ileocecal valve dysfunction, or chronic stress affecting GI function. Identifying the underlying driver is part of the workup, because without addressing it, SIBO tends to recur after treatment.
How is SIBO treated?+
A targeted antimicrobial protocol — either botanical (oil of oregano, berberine, neem, allicin) or pharmaceutical (rifaximin, sometimes paired with neomycin or metronidazole for methane). Treatment typically runs 4-8 weeks. Often followed by a "prokinetic" phase to restore the gut's natural sweeping motility that prevents recurrence. The specific protocol depends on the type identified on breath testing.
Will I have to follow a strict diet?+
During active treatment, often yes — typically a low-FODMAP, low-fermentable-carbohydrate approach to reduce the bacterial fuel supply. The diet isn't permanent. Once the overgrowth is resolved, the goal is gradually reintroducing foods and restoring a normal varied diet. Long-term strict elimination diets actually weaken the gut microbiome over time, so getting through the treatment phase and rebuilding is the priority.
Does SIBO come back?+
It can — particularly if the underlying driver isn't addressed. That's why a thorough workup matters. Identifying why SIBO developed (slow motility, low stomach acid, structural issues, food poisoning history) and addressing it through prokinetic therapy, dietary support, and lifestyle changes substantially reduces recurrence. Some patients require periodic re-treatment; others stay clear for years.
My GI doctor said my colonoscopy was clear. Could I still have SIBO?+
Yes — and very likely if you have classic SIBO symptoms. A colonoscopy doesn't and can't detect SIBO. The bacterial overgrowth happens in the small intestine, which a colonoscopy doesn't reach (an endoscopy reaches only the upper small intestine). The only reliable diagnostic for SIBO is the breath test, which is rarely ordered in conventional GI workups.
Get Started

Get the Test You Were Never Offered.

Book a free consultation. Dr. Dubroff will tell you whether breath testing makes sense for your symptoms — and what a targeted SIBO protocol could look like.

Book Free Consultation Call 949-444-0583