Small Intestinal Bacterial Overgrowth: Breath Tests and Treatment Explained

What Is Small Intestinal Bacterial Overgrowth (SIBO)?

Small Intestinal Bacterial Overgrowth, or SIBO, happens when too many bacteria settle in the small intestine-where they don’t belong. Normally, most gut bacteria live in the colon. But in SIBO, bacteria from the large intestine creep upward or multiply out of control in the small bowel. This disrupts digestion, damages the gut lining, and causes symptoms like bloating, gas, diarrhea, constipation, and nutrient deficiencies. The traditional diagnostic cutoff is more than 100,000 bacteria per milliliter in a fluid sample from the jejunum, but that’s hard to get. So doctors rely on breath tests instead.

How Breath Tests Work for SIBO

There are two main breath tests used to detect SIBO: the glucose breath test and the lactulose breath test. Both work the same way-you drink a sugar solution, and the bacteria in your small intestine ferment it, producing gases like hydrogen or methane. You breathe into a bag every 15 to 20 minutes for about two hours. The machine measures how much gas is in your breath.

For a positive result, hydrogen levels must rise by at least 20 parts per million (ppm) above baseline, or methane by 10 ppm, within the first 90 to 120 minutes. The glucose test is absorbed quickly in the upper small intestine, so it’s better at catching overgrowth near the top. The lactulose test travels farther, so it can detect bacteria lower down-but it’s more likely to give false positives because lactulose can be fermented by colon bacteria if transit is too fast.

Why Breath Tests Are Controversial

Even though breath tests are used in 85% of SIBO diagnoses in the U.S., they’re not perfect. A 2019 meta-analysis of 1,843 patients found the lactulose test has only a 62% sensitivity and 71% specificity. The glucose test is more specific (83%) but misses nearly half of true cases. That means some people are told they have SIBO when they don’t-and others with real SIBO are told they’re fine.

Another problem? Not everyone produces hydrogen. About 15-20% of people are methane-dominant or non-producer types. If you only test for hydrogen, you’ll miss them. That’s why labs now measure methane too. Methane is linked to constipation, and it responds better to different antibiotics like neomycin.

Also, if you don’t follow prep rules-fasting 12 hours, avoiding antibiotics for 4 weeks, stopping laxatives and prokinetics for 7 days-you’ll get a messed-up result. One study found 25-30% of inconclusive tests were due to patients not following prep instructions.

The Gold Standard: Endoscopic Fluid Culture

The real gold standard for diagnosing SIBO is taking a fluid sample from the small intestine during an endoscopy. A doctor inserts a tube past the stomach, past the duodenum, and into the jejunum, collects 3-5 mL of fluid, and sends it to a lab to count bacteria. If it’s over 10^5 CFU/mL, you have SIBO.

But this test isn’t perfect either. It’s invasive, expensive ($1,500-$2,500), and only available in major hospitals. Contamination rates are high-up to 35% of samples get polluted by mouth or stomach bacteria. That’s why most doctors don’t use it routinely.

Still, some experts argue it’s necessary. Dr. Hisham Hussan at UC Davis Health, who started routine aspirate testing in August 2024, says breath tests are only 60% accurate. He’s seen patients misdiagnosed and mistreated because of false breath test results. The big advantage of fluid culture? It tells you exactly which bacteria are there-and which antibiotics they’re sensitive to. Breath tests can’t do that.

Who Gets SIBO? Common Causes and Risk Factors

SIBO doesn’t just happen randomly. It’s usually the result of something breaking down in your gut’s natural defenses. These include:

• Low stomach acid: Especially common in older adults. Stomach acid kills bacteria before they enter the small intestine. Long-term use of proton pump inhibitors (PPIs) like omeprazole increases SIBO risk by 2-3 times.
• Motility problems: If your gut doesn’t move food and bacteria along properly, they pile up. This happens in gastroparesis, diabetes, scleroderma, and even chronic IBS.
• Surgery or structural changes: Scar tissue, blind loops, or bypasses from gastric surgery create pockets where bacteria can hide and multiply. Up to half of post-surgical patients develop SIBO.
• Cirrhosis: Liver disease messes with bile flow and gut immunity, increasing SIBO risk by 15-25%.
• IBS overlap: Between 30% and 85% of people diagnosed with IBS test positive for SIBO, depending on the test used. Many IBS symptoms-bloating, cramping, altered bowel habits-look exactly like SIBO.

How SIBO Is Treated

Once diagnosed, treatment usually starts with antibiotics. The most common is rifaximin (Xifaxan), taken at 1,200 mg per day for 10 to 14 days. Studies show 40-65% of people improve, but the problem is recurrence. Up to 40% of patients have symptoms return within 9 months.

If methane is high (linked to constipation), doctors often add neomycin to rifaximin. This combo works better than rifaximin alone. Some doctors also use herbal antimicrobials like oregano oil, berberine, or garlic extract-though evidence is weaker than for antibiotics.

Antibiotics don’t fix the root cause. That’s why many people need a second step: improving gut motility. Prokinetics like low-dose naltrexone or prucalopride help the gut move again. Dietary changes help too. The low FODMAP diet, elemental diet, or SIBO-specific diet (low sugar, low fermentable carbs) can reduce symptoms while you’re treating the infection.

What Happens After Treatment?

Recovery isn’t just about killing bacteria. You need to prevent them from coming back. That means:

• Addressing the root cause-like stopping PPIs if possible, managing diabetes, or treating motility issues.
• Rebuilding gut health with probiotics and prebiotics (but carefully-some strains can worsen SIBO).
• Monitoring symptoms and retesting if they return.

Some people need repeated antibiotic courses. Others benefit from long-term dietary management. A 2022 study in the Journal of Clinical Gastroenterology found that patients who stuck to a low-fermentable diet after treatment had lower recurrence rates than those who didn’t.

The Future of SIBO Testing

Right now, breath testing is the only widely available option. But it’s not enough. Researchers are working on better tools. Mayo Clinic and Johns Hopkins are testing intraluminal gas sensors that measure gases directly inside the gut. Cedars-Sinai is running a phase 2 trial for a new breath analyzer they claim will be 85% accurate.

Another big shift is moving away from just counting bacteria to identifying species using DNA sequencing. This could tell us not just if SIBO is present, but which bugs are causing problems-and which drugs will work best.

For now, though, breath tests are what we have. And they’re improving. Labs now routinely test for methane, and guidelines are slowly becoming more standardized. But the bottom line hasn’t changed: a positive breath test means nothing without clinical context.

When to Question a SIBO Diagnosis

If you’ve been told you have SIBO but your symptoms don’t match-like if you have severe pain, weight loss, or blood in stool-you should dig deeper. SIBO is often overdiagnosed. Many people get breath tests after being told they have IBS, and if the test is positive, they’re labeled with SIBO-even if the test was done poorly or their symptoms don’t fit.

Always ask: Did I follow the prep rules? Was methane measured? Is my doctor considering my full history-not just the test result? A good gastroenterologist will treat the person, not the number on the graph.