Small Intestinal Bacterial Overgrowth: Breath Tests and Treatment Explained

If you’ve been struggling with bloating, gas, diarrhea, or constipation that won’t go away-even after cutting out gluten or dairy-you might be dealing with something deeper than just a food sensitivity. Small Intestinal Bacterial Overgrowth, or SIBO, is a hidden condition that affects millions but is often missed or misdiagnosed as irritable bowel syndrome (IBS). Unlike normal gut bacteria that live in the colon, SIBO happens when too many bacteria grow where they shouldn’t: in the small intestine. This disrupts digestion, damages the gut lining, and steals nutrients your body needs. The good news? There are clear ways to test for it-and treat it.

How SIBO Develops

Your small intestine isn’t meant to host large numbers of bacteria. That’s the colon’s job. But when the natural cleanup system fails-like the migrating motor complex (MMC) that sweeps bacteria downstream-bacteria start to multiply where they don’t belong. This isn’t random. It usually happens because something has slowed down your gut movement or changed the environment.

Common causes include past abdominal surgery, especially bowel resections or gastric bypass. About 30-50% of people who’ve had this kind of surgery develop SIBO. Long-term use of proton pump inhibitors (PPIs), like omeprazole, also raises your risk by 2-3 times. These drugs reduce stomach acid, which normally kills off harmful bacteria before they reach the small intestine.

Other triggers include diabetes, scleroderma, and cirrhosis. Even IBS has a strong link-up to 85% of people with IBS test positive for SIBO, depending on the test used. If your symptoms flare up after eating carbs, especially sugars or fiber, that’s a big red flag. Bacteria feed on these, producing gas that causes bloating, pain, and changes in bowel habits.

How Breath Tests Work

The most common way to check for SIBO is a breath test. It sounds simple: you drink a sugary solution and blow into a bag every 15-20 minutes for up to two hours. But the science behind it is precise.

The test looks for gases produced by bacteria: hydrogen and methane. When bacteria ferment sugar in the small intestine, they release these gases, which get absorbed into your blood and exhaled through your lungs. A rise of 20 parts per million (ppm) in hydrogen or 10 ppm in methane above your baseline level within 90-120 minutes usually means SIBO is present.

There are two main types of sugar used: glucose and lactulose. Glucose is absorbed quickly in the first part of the small intestine, so it’s better at detecting overgrowth near the top. Lactulose moves further down, so it can catch bacteria in the lower small intestine. But here’s the catch: glucose tests miss about half of SIBO cases because the sugar gets used up too soon. Lactulose catches more cases but gives more false positives-especially in people with fast gut movement.

According to a 2019 analysis of 17 studies, lactulose breath tests have a sensitivity of 62% and specificity of 71%. Glucose tests are more specific (83%) but only catch 46% of real cases. That means you could get a negative result even if you have SIBO.

Why Breath Tests Can Be Misleading

Breath tests are convenient and non-invasive, but they’re far from perfect. About 15-20% of people don’t produce hydrogen at all. These “non-hydrogen producers” might only make methane or even hydrogen sulfide-which current breath tests can’t detect. That’s why some people keep having symptoms even after a “negative” test.

Another problem? Rapid transit. If your food moves too quickly through your gut, the sugar reaches the colon before it should. That triggers a gas spike that looks like SIBO-but it’s just normal colonic fermentation. This happens in 10-15% of cases and leads to false positives.

And then there’s the issue of interpretation. One lab might call a 15 ppm rise in hydrogen positive. Another waits for 20 ppm. Some don’t even test for methane. That’s why two people with identical symptoms can get totally different results depending on where they test.

Dr. Eamonn Quigley, former president of the American College of Gastroenterology, calls breath tests a “screening tool,” not a diagnosis. That means if your test is positive, it’s a signal to dig deeper-not a final answer.

The Gold Standard: Fluid Culture

The only way to confirm SIBO with certainty is to take a fluid sample directly from the small intestine during an endoscopy. A doctor passes a tube through your mouth, past the stomach, and into the jejunum (the middle part of the small intestine). They collect 3-5 milliliters of fluid and send it to a lab to count bacteria. If there are more than 100,000 colony-forming units per milliliter (CFU/mL), it’s SIBO.

This method is accurate-but rarely used. Why? It’s expensive ($1,500-$2,500), invasive, and not widely available. Only a handful of centers, like UC Davis Health, do it routinely. Dr. Hisham Hussan, who leads their endoscopy program, says breath tests are only about 60% accurate. That means 4 in 10 people are misdiagnosed.

The real advantage of fluid culture? It can tell you exactly which bacteria are overgrowing-and which antibiotics they’re sensitive to. Breath tests can’t do that. If you’ve had SIBO before and it came back after treatment, a culture might show you why.

What Happens After a Positive Test?

If your breath test is positive and your symptoms match, treatment usually starts with antibiotics. The most common is rifaximin (Xifaxan), taken at 1,200 mg per day for 10-14 days. It’s not absorbed into your bloodstream-it stays in your gut and kills bacteria where they are.

Studies show 40-65% of people improve after one course. But here’s the problem: more than 40% relapse within nine months. Why? Because antibiotics don’t fix the root cause. If your gut motility is still slow, or your stomach acid is still low, bacteria will grow back.

For methane-dominant SIBO (often linked to constipation), doctors often combine rifaximin with neomycin. This combo works better than rifaximin alone. Some clinics also use herbal antimicrobials like oregano oil, berberine, or garlic extract-especially for people who can’t tolerate antibiotics or want to avoid them.

After antibiotics, diet plays a big role. Low-FODMAP, Specific Carbohydrate Diet (SCD), or GAPS diets are often recommended to starve the bacteria. But these aren’t long-term fixes. They help during treatment, but once you reintroduce foods, symptoms can return if the underlying issue isn’t resolved.

Preventing SIBO From Coming Back

To keep SIBO away, you need to fix what caused it in the first place. That might mean:

• Stopping or reducing PPIs if you’re on them long-term
• Taking prokinetic medications like low-dose erythromycin or prucalopride to boost gut motility
• Addressing low stomach acid with betaine HCl (under medical supervision)
• Managing underlying conditions like diabetes or thyroid disorders
• Using digestive enzymes or bile acid binders if needed

Some people benefit from intermittent fasting or eating three meals a day with no snacks. This gives your gut time to activate the migrating motor complex, which naturally cleans out bacteria between meals.

Re-testing after treatment is important. Many clinics recommend a follow-up breath test 2-4 weeks after finishing antibiotics to see if the overgrowth cleared. But remember: a negative test doesn’t always mean you’re cured. If your symptoms are gone, that’s often more important than the number on the report.

The Future of SIBO Testing

New technology is on the horizon. Researchers at Cedars-Sinai and Mayo Clinic are developing breath analyzers that can detect hydrogen sulfide, a gas many current tests miss. Others are working on wireless capsules that measure gas levels directly inside the gut-no breath samples needed.

In June 2024, Dr. Mark Pimentel’s team announced a phase 2 trial of a new breath analyzer predicted to be 85% accurate. If successful, it could become the new standard.

For now, though, breath testing remains the most practical option. It’s accessible, affordable, and widely available. But it’s not a magic bullet. It’s a tool-and like any tool, it works best when used wisely, with the right preparation and interpretation.

How to Prepare for a Breath Test

Getting an accurate result depends almost entirely on how well you prepare. Here’s what you need to do:

• Fast for 12 hours before the test-only water allowed
• Avoid antibiotics for at least 4 weeks
• Stop laxatives and prokinetics (like domperidone or prucalopride) for 7 days
• Follow a low-residue diet for 24-48 hours before: no beans, broccoli, dairy, fruit, or whole grains
• Don’t smoke, exercise, or sleep during the test
• Stay seated and calm during the 2-hour testing window

Many people fail their test not because they have SIBO, but because they didn’t follow the rules. One study found that 25-30% of inconclusive results were due to poor preparation.

If you’re constipated, you may need extra prep time. Some clinics recommend a 3-day diet and even a bowel cleanse before testing.

When to Ask for a Second Opinion

If you’ve been told you have SIBO but don’t respond to treatment, or if your symptoms are getting worse, it’s time to dig deeper. Ask your doctor:

• Was methane tested? (If not, demand it)
• What was the exact gas rise used to define a positive result?
• Have you considered a small bowel aspirate?
• Could my symptoms be from something else-like bile acid malabsorption or celiac disease?

SIBO is real. But it’s not the only reason for chronic digestive issues. Don’t let a single test define your health journey.