Small Intestinal Bacterial Overgrowth: Breath Tests and Treatment Explained

When your gut feels bloated, gassy, or crampy-even after eating something simple like salad or yogurt-you might assume it’s just indigestion. But if these symptoms stick around, don’t respond to usual remedies, and come with diarrhea, constipation, or even nutrient deficiencies, it could be something deeper: Small Intestinal Bacterial Overgrowth, or SIBO. It’s not rare. In fact, up to 80% of people diagnosed with irritable bowel syndrome (IBS) may actually have SIBO. The problem? Most doctors don’t test for it. And even when they do, the tests aren’t perfect.

What Exactly Is SIBO?

Your small intestine is meant to be mostly clean. Unlike your colon, which is packed with trillions of bacteria helping break down fiber, your small intestine should have very few. When bacteria from the colon creep up and multiply-more than 100,000 per milliliter-it’s called SIBO. These bacteria ferment food too early, producing gases like hydrogen and methane that cause bloating, pain, and changes in bowel habits.

It doesn’t just happen out of nowhere. SIBO often follows something that slowed down your gut movement: past surgery, long-term use of acid-reducing pills like omeprazole, diabetes, scleroderma, or even just aging. People with low stomach acid, which happens more often after 60, are at higher risk because acid normally kills off unwanted bacteria before they reach the small intestine.

How Do You Test for SIBO?

The go-to test isn’t a blood draw or a colonoscopy. It’s a breath test. And it’s surprisingly simple-you drink a sugary solution, then breathe into a bag every 15 to 20 minutes for about two hours.

There are two main types:

• Glucose breath test: Uses 10 grams of glucose dissolved in water. Glucose gets absorbed quickly in the upper small intestine, so if bacteria there are overgrown, they’ll start fermenting it right away and release hydrogen or methane gas. This test is good at catching SIBO in the first part of the small intestine, with about 83% accuracy when it comes to ruling out false positives.
• Lactulose breath test: Uses 10 grams of lactulose, a sugar your body can’t digest. It travels further down the small intestine before being fermented, so it can detect bacteria deeper along the tract. But it’s less precise-only about 62% sensitive-and more likely to give false positives if your gut moves too fast.

Both tests require strict prep. You have to fast for 12 hours. No antibiotics for four weeks. No laxatives, probiotics, or prokinetics for at least seven days. Even eating high-fiber foods the day before can throw off results. One study found that nearly 30% of failed tests were due to patients not following the prep correctly.

Positive results mean a spike of 20 ppm (parts per million) in hydrogen or 10 ppm in methane above your baseline within two hours. Methane is especially important-it’s linked to constipation-predominant symptoms and is now called Intestinal Methanogen Overgrowth (IMO). Treating methane-producing SIBO often needs a different combo of antibiotics than hydrogen-dominant cases.

Why Breath Tests Are Controversial

Here’s the catch: breath tests aren’t the gold standard. The real gold standard is a fluid sample taken directly from the small intestine during an endoscopy. Doctors insert a tube, go past the stomach, and collect fluid near the start of the small intestine. If there are more than 100,000 bacteria per milliliter, that’s SIBO.

But that procedure is expensive-up to $2,500-and not widely available. Only a handful of hospitals, like UC Davis Health, do it routinely. And even then, contamination during collection can mess up results.

Breath tests are cheaper, non-invasive, and accessible. About 85% of SIBO tests in the U.S. are breath tests. But their accuracy? It’s messy. One expert says they’re only 60% accurate. Another says they’re the best tool we’ve got. The truth? They’re a screening tool, not a confirmation.

That’s why some doctors won’t treat SIBO based on breath tests alone. They want symptoms to match. If you have bloating, gas, and diarrhea, and your breath test is positive, that’s strong evidence. But if you’re asymptomatic and your test is positive? It might just be noise.

What Happens After a Positive Test?

If you’re diagnosed with SIBO, the first-line treatment is usually antibiotics. Rifaximin (Xifaxan) is the most common-it’s not absorbed into your bloodstream, so it works right in your gut. The standard dose is 1,200 mg a day for 10 to 14 days. About half of people see improvement.

But here’s the problem: it often comes back. Studies show over 40% of patients relapse within nine months. That’s because antibiotics don’t fix the root cause. If your gut motility is slow, your stomach acid is low, or you’ve had surgery, the bacteria will come back.

For methane-dominant SIBO, rifaximin alone doesn’t cut it. You need to add neomycin or another antibiotic like metronidazole. Some clinics now use herbal antimicrobials-oregano oil, berberine, garlic extract-as alternatives, especially for people who can’t tolerate antibiotics. One 2020 study found herbal treatments worked just as well as antibiotics in 46% of cases, with fewer side effects.

How to Prevent SIBO From Coming Back

Antibiotics fix the overgrowth. But they don’t fix the reason it happened. That’s why long-term management is key.

• Improve gut motility: Medications like low-dose naltrexone or erythromycin can help move things along. Natural options include ginger tea, regular walking after meals, and avoiding lying down for two hours after eating.
• Fix low stomach acid: If you’ve been on proton pump inhibitors (PPIs) for years, talk to your doctor about tapering off. Some people benefit from apple cider vinegar or betaine HCl supplements under supervision.
• Adjust your diet: A low-FODMAP diet helps reduce the fuel bacteria feed on. But it’s not meant to be permanent. Once symptoms improve, you slowly reintroduce foods to find your tolerance.
• Use probiotics wisely: Not all probiotics help. Strains like Saccharomyces boulardii may reduce bloating without feeding bacteria. Avoid Lactobacillus and Bifidobacterium if you have hydrogen-dominant SIBO-they can make it worse.

Some people find success with elemental diets-liquid nutrition formulas that are pre-digested. These starve the bacteria for 14 to 21 days, giving your gut a reset. It’s tough to stick to, but studies show up to 80% of patients clear SIBO after one cycle.

What’s Next for SIBO Testing?

The field is changing. Researchers at Cedars-Sinai and Mayo Clinic are testing new breath analyzers that can detect multiple gases at once, including hydrogen sulfide-a gas that’s harder to measure but linked to diarrhea and inflammation. Early versions are hitting 85% accuracy in trials.

There’s also talk about stool DNA tests that could identify bacterial strains without invasive procedures. And some labs are exploring real-time gas sensors you wear at home, so you can track changes over days instead of one two-hour test.

But for now, the best approach is simple: if you’ve had unexplained gut issues for months, ask for a breath test. Make sure the clinic follows strict prep guidelines. Don’t accept a diagnosis without matching symptoms. And always pair treatment with lifestyle changes to prevent relapse.

SIBO isn’t a death sentence. It’s not even rare. But it’s easily missed. The key is knowing what to ask for-and what to do after you get the results.