When your stomach feels bloated after a light meal, you’re gassy all day, and diarrhea or constipation won’t quit - it’s easy to blame it on stress or bad food. But for many people, the real culprit is something deeper: Small Intestinal Bacterial Overgrowth, or SIBO. It’s not just a buzzword. It’s a real, measurable condition where bacteria from the large intestine creep into the small intestine and start acting like unwelcome tenants - fermenting food, producing gas, and wrecking nutrient absorption. And while it’s often mistaken for IBS, the treatment is completely different.

What Exactly Is SIBO?

SIBO happens when bacteria that normally live in your colon - where they belong - start multiplying in your small intestine. That’s the part of your gut right after your stomach, where most nutrients get absorbed. Normally, your stomach acid, bile, and the natural movement of your intestines keep those bacteria in check. But when those systems slow down or break down, bacteria take over.

Doctors used to diagnose SIBO by sticking a tube down your throat to collect fluid from your small intestine. That’s invasive, expensive, and not widely available. Today, almost everyone starts with a breath test. Why? Because it’s simple, non-invasive, and works in most clinics. But here’s the catch: it’s not perfect.

How Breath Tests Work - And Why They’re Flawed

The two most common breath tests are the glucose breath test and the lactulose breath test. You fast for 12 hours, then drink a sugar solution. After that, you blow into a bag every 15 to 20 minutes for up to two hours. The machine measures hydrogen and methane gases in your breath. If those numbers spike too high, too fast, you’re flagged for SIBO.

Here’s the science behind it: bacteria in your small intestine feed on the sugar. As they digest it, they release hydrogen or methane gas. That gas gets absorbed into your blood, then exhaled through your lungs. That’s what the test picks up.

But here’s where it gets messy. Glucose is absorbed quickly in the upper part of the small intestine. If your sugar is gone before it reaches the lower areas where bacteria hang out, the test might miss the overgrowth - false negative. Lactulose travels further, so it’s better at catching bacteria deeper down, but it’s more likely to give false positives because it can trigger gas even if there’s no real overgrowth.

A 2019 meta-analysis found the glucose test is 83% specific - meaning if it says you have SIBO, you probably do. But it only catches about half the cases. Lactulose catches more cases, but only about 70% of the time. And that’s not counting the 15-20% of people who don’t produce hydrogen at all - they’re methane producers. If your test doesn’t measure methane, you’re getting half the picture.

And then there’s the preparation. You can’t take antibiotics for four weeks before the test. No laxatives. No probiotics. No proton pump inhibitors (like omeprazole) for at least two weeks. You have to eat a strict low-residue diet for 24-48 hours. Skip one rule, and your results are garbage. One study found that 25-30% of inconclusive tests happened because patients didn’t follow the prep.

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 doctors in the U.S. doing small bowel aspirates - the old-school method where a scope collects fluid directly from the small intestine. That’s the gold standard: if you have more than 100,000 bacteria per milliliter, you have SIBO. But it’s not practical for most clinics. It costs $2,000. It needs specialized equipment. It’s risky. And contamination rates are high.

Still, he argues that breath tests misdiagnose 40% of patients. That means people are getting antibiotics they don’t need - or missing SIBO entirely. And when you treat the wrong thing, symptoms don’t improve. That’s why some experts call breath tests a screening tool, not a diagnosis.

Dr. Mark Pimentel from Cedars-Sinai, who’s done more SIBO research than almost anyone, says breath tests are the best tool we have - even if they’re flawed. The key, he says, is matching the test result to your symptoms. A high methane level with chronic constipation? That’s likely SIBO. A high hydrogen level with bloating and diarrhea after eating carbs? That’s probably SIBO too. But if your symptoms don’t line up, the test might be wrong.

What Happens After a Positive Test?

If your breath test is positive, treatment usually starts with antibiotics. Rifaximin (Xifaxan) is the most common. It’s not absorbed into your bloodstream - it stays in your gut. You take 1,200 mg a day for 10 to 14 days. Studies show it works for 40-65% of people. But here’s the kicker: over 40% come back within nine months.

Why? Because antibiotics don’t fix the root cause. If your gut motility is slow, your stomach acid is low, or you’ve had surgery that changed your anatomy, the bacteria will come back. That’s why treatment has to be two-part: kill the bacteria, then fix the system that let them take over.

For methane-dominant SIBO, rifaximin alone doesn’t cut it. You need neomycin mixed in. That combo works better - but it’s harder on your kidneys and hearing. Some doctors now use herbal antimicrobials like oregano oil, berberine, or garlic extract. A 2020 study showed they work just as well as antibiotics for some patients, with fewer side effects.

And then there’s diet. The low-FODMAP diet helps reduce symptoms, but it doesn’t cure SIBO. The SIBO-specific diet - low in fermentable carbs, sugars, and fiber - is more targeted. You eat white rice, eggs, lean meats, low-FODMAP veggies like zucchini and spinach. No fruit, no dairy, no beans, no wheat. It’s strict. But for many, it’s the missing piece.

Who’s at Risk?

SIBO doesn’t happen out of nowhere. It’s usually a side effect of something else. About 30-50% of people with SIBO have had abdominal surgery - especially bowel resections or gastric bypass. Gastroparesis, where the stomach empties too slowly, shows up in 25-40% of cases. Elderly patients with low stomach acid (hypochlorhydria) are at higher risk. So are people on long-term proton pump inhibitors - those drugs cut stomach acid, and without it, bacteria survive and move up.

And then there’s IBS. Up to 85% of people diagnosed with IBS might actually have SIBO. That’s why many doctors now test IBS patients before prescribing antidepressants or antispasmodics. If SIBO is the real problem, those drugs won’t help. Antibiotics and diet will.

What’s Next for SIBO Testing?

Researchers are working on better tools. Mayo Clinic and Johns Hopkins are testing next-gen breath analyzers that can detect more gas types and use AI to interpret patterns. Cedars-Sinai just launched a phase 2 trial for a new device they say will be 85% accurate. There’s also work on stool DNA tests that could identify bacterial species without a breath test.

But for now, breath tests are all we’ve got. And they’re better than nothing. The key is knowing their limits. Don’t treat the test result alone. Treat the person. If your bloating improves with antibiotics and diet, you likely had SIBO - even if the test was borderline. If nothing helps, maybe it’s something else.

Bottom Line

SIBO is real. Breath tests are imperfect. Antibiotics help - but only if you fix the cause. If you’ve been told you have IBS and nothing works, ask for a breath test. Make sure it measures both hydrogen and methane. Follow the prep exactly. And don’t stop there. Work with a doctor who understands that SIBO isn’t just a bug - it’s a symptom of a broken system. Fix the system, and you might finally feel better.