A Practical Approach to Treating SIBO: Dr. Kim's Approach Integrative Medicine Functional Medicine Perspective
- John Kim
- 4 days ago
- 6 min read
By Yoon Hang Kim, MD
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.
Professional: www.yoonhangkim.com | Clinical: www.directintegrativecare.com
A Practical Approach to Treating SIBO: Dr. Kim's Approach Integrative Medicine Functional Medicine Perspective
DISCLAIMER: This article is for educational purposes only and does not constitute medical advice. Always consult with a qualified healthcare provider before making changes to your treatment plan.
Introduction
Small intestinal bacterial overgrowth (SIBO) affects a significant portion of patients with functional GI symptoms—some estimates suggest it underlies 60-70% of irritable bowel syndrome cases.¹ Yet treatment outcomes remain frustratingly inconsistent, with relapse rates as high as 44% within nine months.²
After more than two decades in integrative medicine, I've developed a systematic approach that achieves sustained remission in over 90% of my patients. The key? Applying Occam's Razor: start with the simplest intervention and build complexity only when necessary.
Why Occam's Razor?
Occam's Razor tells us to favor the simplest sufficient explanation. In SIBO treatment, this means addressing the fundamental driver—substrate availability—before reaching for antimicrobials. Rather than throwing multiple treatments at the problem simultaneously, we remove the fuel source first. This stepwise approach consistently yields better outcomes with fewer complications.
The Stepwise Protocol
Remove the Fuel. This is foundational. Bacteria in the small intestine ferment poorly-absorbed carbohydrates, producing hydrogen, methane, or hydrogen sulfide gases that drive symptoms.³ By reducing fermentable substrates, we starve the overgrowth of its food supply. Simple concept, powerful results.
Consider Elemental Diet First. The evidence here is compelling. Pimentel's landmark study showed a 14-day elemental diet normalized breath tests in 80% of SIBO patients.⁴ A 2024 comprehensive review confirms that while antibiotics achieve roughly 50% efficacy, elemental diet consistently outperforms them.⁵ A 2025 trial reported 83% symptom improvement with excellent tolerability.⁶
The practical limitations are real—the chalky taste, nutritional inadequacy for long-term use, potential weight loss. But as a short-term reset? It's hard to beat.
Try Alternative Diets if Needed. Not everyone can tolerate elemental diet, and that's okay. The Low Fermentation Diet from Drs. Pimentel and Rezaie at Cedars-Sinai reduces fermentable substrates while preserving the migrating motor complex through 4-5 hour meal spacing.⁷ Dr. Norm Robillard's Fast Tract Diet uses a Fermentation Potential scoring system to quantify which foods are most likely to feed bacterial overgrowth.⁸ Both are more sustainable long-term options.
Test After 21+ Days of Relief. Once symptoms have been stable for three weeks or more, that's the window for comprehensive GI testing. I typically start with GI-MAP for its quantitative PCR methodology, reserving CDSA for culture-based confirmation when needed. Testing during active overgrowth just muddies the picture.
Target Treatment Based on Findings. Now we can see what we're actually dealing with: infections requiring antimicrobials, pancreatic insufficiency needing enzymes, dysbiosis patterns that respond to specific probiotics, or parasites requiring targeted treatment. This precision approach replaces shotgun therapy with mechanism-based interventions.
Individualize. Medicine remains as much art as science. Some patients—those with severe symptoms, significant comorbidities, or multiple treatment failures—may need concurrent rather than sequential interventions. The protocol is a framework, not a straitjacket. Shared decision-making matters.
Expect Better Outcomes. With this approach, I achieve sustained remission in over 90% of patients—compared to the roughly 50% response rates reported for antibiotics alone.⁵ The difference comes from addressing root causes rather than just suppressing bacterial populations that will inevitably return.
Stay Diagnostically Flexible. SIBO isn't one thing. Hydrogen sulfide-dominant cases behave differently and may need low-sulfur protocols.⁹ Alpha-gal syndrome—now recognized by the AGA as a differential for unexplained GI symptoms—can masquerade as SIBO or IBS.¹⁰ Three-quarters of alpha-gal patients with GI symptoms improve simply by eliminating mammalian products.¹¹ When treatment isn't working, question the diagnosis.
Marry the Result, Not the Process. This is something my mentor Dr. Andrew Weil taught me that has shaped my entire practice philosophy. Low-dose naltrexone (LDN) is a perfect example—an unexpected tool that can restore balance to immune and nervous system function in the gut.¹²
A Word on LDN
I've found LDN particularly valuable in SIBO patients, and it's worth explaining why. At standard doses, naltrexone is an opioid antagonist used for addiction. But at low doses (typically 1.5-4.5mg), something interesting happens: the brief receptor blockade triggers a rebound increase in endorphin production and receptor sensitivity.
The downstream effects include immune modulation, reduced neuroinflammation through microglial regulation, and—importantly for SIBO—potential improvements in gut motility.¹⁵ The GI tract is one of the body's most critical immune-nervous system interfaces. When we restore balance there, motility often follows.
LDN is generally well-tolerated. Some patients experience vivid dreams or mild sleep disruption initially, but these typically resolve within a week or two. It's obtained through compounding pharmacies since standard commercial doses are much higher. And it shouldn't be used with opioid medications for obvious reasons.
Is LDN a magic bullet? No. But it exemplifies the kind of flexible, outcome-oriented thinking that serves patients better than rigid adherence to any single methodology.
The Bottom Line
SIBO treatment doesn't have to be complicated or frustrating. Start simple—remove the fuel. Add complexity only as needed. Test when symptoms are controlled, then target your interventions based on what you find. Stay flexible, question your assumptions when things aren't working, and remember that the goal is lasting relief, not just temporary suppression.
A Practical Approach to Treating SIBO: Dr. Kim's Approach Integrative Medicine Functional Medicine Perspective
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
1. Pimentel M, Chow EJ, Lin HC. Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. Am J Gastroenterol. 2000;95(12):3503-3506.
2. Lauritano EC, et al. Small intestinal bacterial overgrowth recurrence after antibiotic therapy. Am J Gastroenterol. 2008;103(8):2031-2035.
3. Rezaie A, Buresi M, Lembo A, et al. Hydrogen and methane-based breath testing in gastrointestinal disorders: The North American Consensus. Am J Gastroenterol. 2017;112(5):775-784.
4. Pimentel M, Constantino T, Kong Y, et al. A 14-day elemental diet is highly effective in normalizing the lactulose breath test. Dig Dis Sci. 2004;49(1):73-77.
5. Nasser J, Mehravar S, Pimentel M, et al. Elemental diet as a therapeutic modality: A comprehensive review. Dig Dis Sci. 2024. doi:10.1007/s10620-024-08543-1.
6. Rezaie A, Chang BW, de Freitas Germano J, et al. Effect, tolerability, and safety of exclusive palatable elemental diet in patients with intestinal microbial overgrowth. Clin Gastroenterol Hepatol. 2025. doi:10.1016/j.cgh.2025.03.002.
7. Pimentel M, Rezaie A. The Low Fermentation Diet. Cedars-Sinai Medical Center / Good LFE. Available at: goodlfe.com.
8. Robillard N. Fast Tract Digestion IBS. Digestive Health Institute, 2013. Presented at Digestive Disease Week 2013.
9. Birg A, Hu S, Lin HC. Reevaluating our understanding of lactulose breath tests by incorporating hydrogen sulfide measurements. JGH Open. 2019;3(3):228-233.
10. McGill SK, et al. AGA Clinical Practice Update on Alpha-Gal Syndrome for the GI Clinician: Commentary. Clin Gastroenterol Hepatol. 2023;21(5):1178-1184.
11. Commins SP. Diagnosis & management of alpha-gal syndrome: lessons from 2,500 patients. Expert Rev Clin Immunol. 2020;16(7):667-677.
12. Younger J, Parkitny L, McLain D. The use of low-dose naltrexone (LDN) as a novel anti-inflammatory treatment for chronic pain. Clin Rheumatol. 2014;33(4):451-459.
13. Chedid V, Dhalla S, Clarke JO, et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med. 2014;3(3):16-24.
14. Shah SC, Day LW, Somsouk M, Sewell JL. Meta-analysis: antibiotic therapy for small intestinal bacterial overgrowth. Aliment Pharmacol Ther. 2013;38(8):925-934.
15. Weinstock LB, et al. Low dose naltrexone: Side effects and efficacy in gastrointestinal disorders. Dig Dis Sci. 2013;58(suppl):S192.
© Yoon Hang Kim, MD • www.directintegrativecare.com
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