Small Intestinal Bacterial Overgrowth: Breath Tests and Treatment Explained

If you’ve had bloating, gas, diarrhea, or abdominal pain that won’t go away-even after trying diets, probiotics, or antacids-you might be dealing with Small Intestinal Bacterial Overgrowth (SIBO). It’s not just "bad digestion." It’s when bacteria that normally live in your colon start multiplying where they don’t belong: the small intestine. And it’s more common than you think. Studies suggest up to 80% of people diagnosed with IBS 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 supposed to be mostly clean. It’s where nutrients get absorbed, and it’s not meant to host large numbers of bacteria. That’s the colon’s job. But when something disrupts the natural balance-like slow movement, low stomach acid, or past surgery-bacteria from the large intestine creep up and start feeding on the food you eat before it’s properly digested. This causes fermentation, gas, bloating, and damage to the gut lining.

The classic definition of SIBO is more than 100,000 bacteria per milliliter in the jejunum (a part of the small intestine). That number comes from old-school fluid cultures taken during endoscopy. But today, most doctors skip the scope and go straight to breath tests because they’re easier, cheaper, and less invasive.

How Breath Tests Work (And Why They’re Controversial)

Breath tests measure gases produced when bacteria ferment sugars. You drink a solution of either glucose or lactulose, then blow into a bag every 15 to 20 minutes for up to two hours. The machine looks for spikes in hydrogen or methane gas.

- Glucose breath test: Glucose is absorbed quickly in the upper small intestine. If you have SIBO there, bacteria will ferment it fast and release gas early. This test is good at catching SIBO in the first part of the small intestine but can miss it further down. Its specificity is high (83%)-meaning if it’s positive, it’s likely real-but sensitivity is low (46%), so many cases get missed.

- Lactulose breath test: Lactulose isn’t absorbed until it reaches the lower small intestine or colon. It travels further, so it can detect overgrowth deeper in the gut. But because it’s not naturally digested by humans, it can cause false positives if your transit is too fast. Sensitivity is around 62%, specificity 71%. Not perfect, but more likely to catch SIBO than glucose.

Here’s the catch: 15-20% of people don’t produce hydrogen at all. They produce methane instead. That’s called Intestinal Methanogen Overgrowth (IMO). Methane slows down gut movement, often causing constipation. If your test doesn’t measure methane, you might be told you’re "negative"-even though you have SIBO.

And then there’s the prep. You have to fast for 12 hours. No antibiotics for 4 weeks. No laxatives or prokinetics for 7 days. No high-fiber foods or sugar for 24-48 hours before. Miss one rule, and your results are garbage. One study found that 25-30% of inconclusive tests were due to patients not following prep instructions.

Why Some Doctors Don’t Trust Breath Tests

Dr. Hisham Hussan at UC Davis Health says breath tests are only 60% accurate. He’s one of the few in Northern California who still uses the old method: pulling fluid from the small intestine during an endoscopy. That’s the gold standard. You get a direct count of bacteria, and you can test which antibiotics they’re sensitive to. But it’s expensive ($1,500-$2,500), invasive, and not widely available. Most clinics don’t have the equipment or the expertise.

Meanwhile, the American College of Gastroenterology says breath tests should be treated as a screening tool-not a diagnosis. Dr. Eamonn Quigley, former president of the ACG, put it bluntly: "We shouldn’t treat patients based on breath test results alone."

But here’s the reality: for most people, the endoscopy isn’t an option. So breath tests are what we’ve got. And if your symptoms match-bloating after meals, diarrhea or constipation, improvement with antibiotics-then a positive breath test, even with its flaws, can be a useful clue.

What Happens After a Positive Test?

If your breath test comes back positive, the next step is usually antibiotics. The most common is rifaximin (Xifaxan), taken at 1,200 mg per day for 10 to 14 days. It doesn’t get absorbed into your bloodstream-it stays in the gut. That’s why it’s so effective against gut bacteria without causing systemic side effects.

Studies show about 40-65% of people respond well to rifaximin. But here’s the kicker: over 40% of those who get better end up back where they started within 9 months. That’s because antibiotics kill bacteria but don’t fix the underlying cause.

If methane is high, doctors often add neomycin to the regimen. Methane producers respond better to the combo than to rifaximin alone.

Some patients try herbal antimicrobials-oregano oil, berberine, garlic extract. One 2014 study found herbal therapy worked just as well as rifaximin, with fewer side effects. But these aren’t regulated, and dosing varies wildly. Always talk to your doctor before trying them.

Fixing the Root Cause

Antibiotics give temporary relief. To keep SIBO from coming back, you need to fix what caused it in the first place.

Common triggers:

• Low stomach acid (common in older adults and people on long-term PPIs like omeprazole)
• Slow gut motility (from diabetes, hypothyroidism, or past surgery)
• Structural issues (adhesions, diverticula, or scar tissue from prior surgeries)
• Chronic use of proton pump inhibitors (PPIs)-they raise SIBO risk by 2 to 3 times
• IBS-up to 85% of IBS patients have SIBO

After antibiotics, many people benefit from prokinetics-medications that help your gut move. Low-dose naltrexone, prucalopride, or even ginger can help stimulate the migrating motor complex (MMC), the natural "cleaning wave" that sweeps bacteria out of the small intestine.

Dietary changes help too. The low-FODMAP diet reduces fermentable carbs that feed bacteria. But it’s not a long-term solution. You don’t want to starve your good gut bugs forever. Once SIBO clears, most people do well on a balanced diet with moderate fiber.

What’s Next for SIBO Testing?

New tech is coming. Researchers at Cedars-Sinai are testing a new breath analyzer they claim will be 85% accurate. Mayo Clinic and Johns Hopkins are working on ways to analyze gut gases directly from the small intestine using tiny sensors. Next-gen sequencing might one day tell us exactly which bacteria are overgrowing-and which antibiotics to use.

But right now, we’re stuck with what we’ve got: imperfect breath tests and the clinical judgment of the doctor interpreting them.

If you suspect SIBO, find a provider who understands it. Ask if they measure methane. Ask about prep protocols. Ask if they treat the root cause. Don’t just take a positive test and start antibiotics. That’s like putting a bandage on a broken leg.

When to Get Tested

Consider SIBO testing if you have:

• Chronic bloating, especially after eating carbs
• Diarrhea or constipation that doesn’t respond to usual treatments
• IBS diagnosis with no clear trigger
• History of abdominal surgery, PPI use, or diabetes
• Improvement of symptoms after taking antibiotics (even without a prescription)

Don’t self-diagnose. But don’t ignore persistent symptoms either. SIBO is treatable. But only if you know you have it-and know how to treat it right.