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Why I Switched to Three-Gas Breath Testing for SIBO

Yoon Hang 'John' Kim, MD, MPH

Tree-Gas Breath Testing for SIBO



About Dr. Kim


Dr. Yoon Hang "John" Kim is a board-certified integrative medicine physician with over 20 years of clinical experience. He completed his integrative medicine fellowship at the University of Arizona under Dr. Andrew Weil and holds certifications in preventive medicine, medical acupuncture, and integrative/holistic medicine. Through his telemedicine practice, Dr. Kim specializes in utilizing LDN or Low Dose Naltrexone for treating autoimmune conditions, chronic pain, integrative oncology, and complex conditions including fibromyalgia, chronic fatigue, MCAS, and mold toxicity. He is the author of three books and more than 20 articles, and has helped establish integrative medicine programs at institutions nationwide.

Three-Gas Breath Testing for SIBO

I've been treating SIBO for over two decades now, and for most of that time, the standard two-gas breath test served us reasonably well. We'd measure hydrogen and methane, apply the consensus thresholds, and treat accordingly. But something always nagged at me: there were patients who had all the classic symptoms—the bloating, the unpredictable bowels, the fatigue—yet their breath tests came back essentially flat. Normal. Nothing to see here.

Except there clearly was something to see. These weren't anxious patients imagining symptoms. They were suffering, and we were missing something.

The addition of hydrogen sulfide measurement to breath testing has, for me, filled in that diagnostic gap. It's not revolutionary—it's more like finding the missing piece of a puzzle you've been working on for years.

The Cross-Feeding Problem

Here's what's actually happening in the gut that explains those 'flatline' results. When bacteria ferment carbohydrates, they produce hydrogen. That's straightforward. But hydrogen doesn't just sit there—it's currency in the microbial economy. Other organisms consume it.

Methanogens like Methanobrevibacter smithii grab hydrogen to make methane. Sulfate-reducing bacteria—Desulfovibrio being the main culprit—use it to produce hydrogen sulfide. So if you've got a gut dominated by sulfate-reducers, they're essentially vacuuming up all the hydrogen before it can be detected in your breath. The test looks negative, but there's plenty of bacterial overgrowth happening. We just couldn't see it.

Once I understood this, those frustrating false-negative cases started making sense.

What the Numbers Mean

The 2017 North American Consensus gave us standardized cutoffs, which was helpful. Before that, everyone was using slightly different criteria and it made comparing results a headache.

For hydrogen, we're looking for a rise of 20 ppm or more above baseline within the first 90 minutes. That timing matters—it tells us the fermentation is happening in the small intestine, not the colon. For methane, it's simpler: 10 ppm at any point suggests methanogen overgrowth. And for hydrogen sulfide, the threshold that's emerged from validation studies is 3 ppm.

I should note—these are guidelines, not gospel. A patient with levels just under threshold but classic symptoms still warrants clinical attention. The numbers inform the decision; they don't make it for you.

Different Gases, Different Presentations

What I find clinically useful about three-gas testing is how well the gas patterns correlate with symptom clusters. It's not perfect, but it's consistent enough to guide treatment.

Hydrogen-Dominant

These are your classic SIBO patients—bloating that gets worse as the day goes on, diarrhea or loose stools, cramping after meals. They tend to respond well to dietary carbohydrate restriction. I usually start with a modified low-FODMAP approach rather than the strict elimination version. Pulling out onions, garlic, wheat, and the high-fructose fruits often provides meaningful relief. Most people don't need to live on rice and chicken forever.

Methane-Dominant

Constipation is the hallmark here. Methane actually slows gut motility—it's not just a marker of overgrowth, it's directly contributing to the problem. These patients need the dietary piece, but they also need prokinetic support. I emphasize meal spacing—four to five hours between meals—to let the migrating motor complex do its job. That 'housekeeping wave' can't run properly if you're grazing all day.

Hydrogen Sulfide-Dominant

This is the group we were missing with two-gas testing. The telltale sign is really foul-smelling gas—sulfurous, rotten-egg quality. They often have diarrhea, but what strikes me is how many have systemic symptoms: fatigue, brain fog, sometimes even joint pain. The dietary approach here is different—we're restricting sulfur-containing foods rather than just fermentable carbs. That means cutting back on eggs, red meat, and the cruciferous vegetables that are otherwise so healthy. It's counterintuitive for patients who've been told to eat more broccoli.

Treatment Implications

Knowing the gas pattern changes how I prescribe. The ACG guidelines support rifaximin for hydrogen-dominant SIBO, and it works well for most. But methane is stubborn—those archaea are tough organisms. I usually need to combine rifaximin with either neomycin or metronidazole to make a dent.

For hydrogen sulfide overgrowth, the emerging approach is rifaximin plus bismuth. The bismuth does double duty—it binds hydrogen sulfide directly and helps break up biofilms. I've been pleased with the results, though I'll admit the evidence base is still developing.

Medications alone rarely provide lasting resolution. The bigger question is always: why did the overgrowth happen in the first place? Was there a motility issue? Inadequate stomach acid? Structural problem? Addressing root causes is what separates temporary improvement from durable results.

The Bottom Line

Three-gas testing isn't a revolution—it's a refinement. But for patients who've been told their tests are normal despite ongoing symptoms, that refinement can be the difference between continued suffering and finally getting answers. If you've had inconclusive breath testing in the past, it may be worth retesting with a platform that measures all three gases.

As Dr. Weil taught me years ago: marry yourself to results, not methods. When new tools improve our diagnostic accuracy, we should use them.


Three-Gas Breath Testing for SIBO


At www.directinegrativecare.com Dr. Kim is dedicated to guiding you on your path to wellness through a deeply personalized and supportive approach. We focus on integrative medicine, looking beyond symptoms to uncover the root causes of chronic conditions and develop a treatment plan tailored specifically to your unique health journey. By combining compassionate care with innovative therapies, our goal is to empower you with the knowledge and tools needed to achieve lasting health. We invite you to explore our website to learn more about how our patient-centered practice can help you find balance and vitality. 


Yoon Hang Kim MD

Integrative & Functional Medicine Physician

Virtual Practice Serving IA, IL, MO, FL, GA, and TX


References

Pimentel, M., Saad, R. J., Long, M. D., & Rao, S. S. C. (2020). ACG clinical guideline: Small intestinal bacterial overgrowth. American Journal of Gastroenterology, 115(2), 165–178. https://doi.org/10.14309/ajg.0000000000000501

Rezaie, A., Buresi, M., Lembo, A., Lin, H., McCallum, R., Rao, S., Schmulson, M., Valdovinos, M., Zakko, S., & Pimentel, M. (2017). Hydrogen and methane-based breath testing in gastrointestinal disorders: The North American Consensus. American Journal of Gastroenterology, 112(5), 775–784. https://doi.org/10.1038/ajg.2017.46

Takakura, W., & Pimentel, M. (2020). Small intestinal bacterial overgrowth and irritable bowel syndrome—An update. Frontiers in Psychiatry, 11, 664. https://doi.org/10.3389/fpsyt.2020.00664

 
 
 

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