SIBO, ISO, IMO & More: 2026 Treatment Updates

The research around SIBO is evolving, and 2026 has brought more subtypes, testing and treatment options than ever before. Our guest this week, Dr. Allison Siebecker, is an expert in conventional and natural approaches to SIBO, helped to open one of the first integrative SIBO centers in the nation, and frequently teaches physicians about how to effectively treat even the toughest cases of SIBO, ISO, IMO and more.

Today, we explore how hydrogen, methane (IMO), and hydrogen sulfide–associated (ISO) pattern-typing can help us choose treatment options that help to decrease SIBO symptoms effectively. We discuss how impaired motility - particularly dysfunction of the migrating motor complex - can impact symptom persistence and relapse in addition to microbial type and load, and why we should address it in treatment plans. Dr. Siebecker also reviews the newest advances in SIBO testing, breath test interpretation, and how long to test depending on what you’re looking to discover.

If SIBO has felt like a guessing game in your practice, or if you’re just looking to stay on the leading edge, this episode offers a clearer, physiology-driven framework grounded in education that will help your clients get and stay well.

Timestamps

00:00 - Introduction to the episode and guest
03:45 - What SIBO is and how it’s currently defined (including ICD-10 update)
06:50 - Differentiating hydrogen, methane, and hydrogen sulfide subtypes
08:40 - Key symptoms: bloating, IBS symptoms, mood, fatigue
10:54 - Why gas types matter and how they affect motility
15:00 - Primary causes and risk factors: infections, meds, mold, structural changes
18:40 - Mold and mycotoxin impact on gut motility
21:59 - How to test: glucose vs. lactulose, two-hour vs. three-hour tests
24:14 - Choosing a testing method and interpreting flatlines
29:01 - Cost, access, and why testing saves time and money long term
31:03 - Choosing treatment based on gas type and severity
36:32 - Understanding treatment rounds and when to stop or switch protocols
38:59 - Why methane and hydrogen sulfide SIBO are more difficult to treat
43:26 - Nystatin, yeast overgrowth, and when to co-treat for CIFO
47:55 - Rifaximin as a eubiotic and why it’s well tolerated
49:46 - Preview of Part 2: Nutrition, prokinetics, supportive therapies

Clinician Questions & Evidence-Informed Takeaways

How is SIBO defined and what testing is recommended?
- SIBO is best understood as a clinical syndrome requiring both characteristic gastrointestinal symptoms and objective evidence of microbial overgrowth in the small intestine. Breath testing may support diagnostic clarity, subtype identification, and treatment planning, particularly in patients with IBS or recurrent digestive disorders (Pimentel, 2020).

What are the differences between hydrogen-, methane-, and hydrogen sulfide–associated SIBO patterns?
- Hydrogen-predominant SIBO typically reflects small intestinal fermentation, whereas methane-associated IMO and hydrogen sulfide patterns may involve both the small intestine and colon. Hydrogen predominant types are also usually caused by bacterial overgrowth, while methane and sulfide-predominant types can involve overgrowth of archaea. These distinctions influence motility, symptom expression, and selection of appropriate treatment options (Pimentel, 2020).

How does impaired gas handling contribute to SIBO and IBS symptoms?
- Symptom severity may be driven by reduced clearance of gas rather than gas volume alone. Dysfunction of the migrating motor complex and altered neuromuscular signaling can result in significant bloating, distension, and pain even with modest gas elevations. Helping patients restore normal gas-clearing abilities can help to alleviate symptoms, according to Dr. Siebecker (Serra, 2001).

How does methane slow intestinal transit and result in constipation-predominant presentations?
- Methane functions as a gasotransmitter that interacts with the enteric nervous system and may slow gut motility. This provides a physiologic explanation for constipation-predominant IBS patterns and the increased treatment complexity seen in methane-associated cases (Park, 2017).

Which breath test substrate provides the most clinically useful data for SIBO evaluation?
- There are multiple non-invasive tests available for the detection of SIBO that contain a carbohydrate drink and containers designed to collect breath samples at regular intervals (Losurdo 2020).
- Lactulose is preferred by Dr. Siebecker in clinical practice because it traverses the full length of the small intestine and into the colon, potentially reducing false-negative results associated with early glucose absorption that can occur in some patients. Dr. Siebecker recommends tests that are at least 3 hours in duration for most patients. (Pimentel, 2020)

How does breath test duration impact the detection of methane and hydrogen sulfide patterns?
- Shortened testing protocols may fail to capture later-rising methane or persistently low hydrogen and methane patterns. According to Dr. Siebecker, extended collection windows can improve detection of methane-associated IMO and suspected hydrogen sulfide physiology. It could also help to capture patients with SIBO who also have impaired motility and transit time (Tansel, 2023).

What is the clinical interpretation of a flatline hydrogen and methane breath test for SIBO?
- A flatline pattern (i.e. low and relatively stable hydrogen and methane values) could give clues to abnormal function in symptomatic patients. Dr. Siebecker suggests that in appropriate clinical contexts, abnormal patterns like flatline may suggest hydrogen sulfide overproduction or altered microbial metabolism of gases (Lakhoo, 2018).

How should breath test severity inform SIBO treatment sequencing and prognosis?
- In Dr. Siebecker’s experience, higher gas levels may justify consideration of strategies with greater average reduction potential, such as elemental diet, while lower or moderate elevations may be approached with pharmaceutical or herbal treatment options. Severity-based planning can improve timelines and patient expectations.

If patients relapse after SIBO treatment, what does that mean?
- Symptom recurrence shortly after treatment more often reflects incomplete microbial reduction or the existence of undertreated root causes rather than true relapse. This distinction supports staged treatment approaches with reassessment rather than premature abandonment of therapy. Patients with incomplete resolution can also be evaluated for other disorders like pancreatic exocrine insufficiency, bile acid malabsorption, lactose intolerance, etc. (Rao, 2019).

Under what circumstances should coexisting fungal overgrowth be considered in SIBO patients?
- Dr. Siebecker explains that small intestinal fungal overgrowth (SIFO) testing could be considered in patients with prior candidiasis, repeated antibiotic exposure, or persistent symptoms despite improving SIBO markers. Evaluation is typically individualized rather than routine (Soliman, 2025).

What is the role of prokinetics in long-term SIBO management?
- Prokinetics support the migrating motor complex and may help maintain treatment gains following antimicrobial therapy. Addressing motility is central to relapse prevention and sustained gut health (Kim, 2023).

What factors should be reassessed in patients with recurrent or refractory SIBO?
- Persistent or relapsing SIBO warrants reassessment of medications (particularly opioids), structural contributors, metabolic and neurologic conditions, immune dysfunction, environmental exposures, and lifestyle factors influencing gut physiology (Rao, 2019 and Pimentel, 2020).

Guest

Dr. Alison Siebecker, ND is a naturopathic physician, internationally recognized SIBO expert, and educator whose work has shaped how clinicians understand small intestine overgrowth, breath testing, and integrative treatment options. She is known for her clear clinical algorithms, deep expertise in SIBO subtypes, and commitment to practitioner education. Her ongoing collaboration and dialogue with leading researchers—including Dr. Mark Pimentel’s research group—continues to advance the field. You can learn more about her at https://www.siboinfo.com/

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Disclaimer

The views expressed on this podcast are those of the hosts and guests and don’t necessarily reflect those of Fullscript or any affiliated organizations. This podcast is for informational and educational purposes only and is not intended to be medical advice. For your safety, always check with your doctor or healthcare provider before making changes to your health routine.

Citations

Pimentel M, Saad RJ, Long MD, Rao SSC. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. Am J Gastroenterol. 2020;115(2):165-178.
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.
Serra J, Azpiroz F, Malagelada JR. Impaired transit and tolerance of intestinal gas in the irritable bowel syndrome. Gut. 2001;48(1):14-19.
Park H, Lee K, Park S, et al. The effects and mechanism of action of methane on ileal motor function. Neurogastroenterol Motil. 2017;29(9):e13067.
Losurdo G, Leandro G, Ierardi E, Perri F, Barone M, Di Leo A. Breath Tests for the Non-invasive Diagnosis of Small Intestinal Bacterial Overgrowth: A Systematic Review With Meta-analysis. J Neurogastroenterol Motil. 2020;26(1):16-28.
Tansel A, Levinthal DJ. Understanding Our Tests: Hydrogen-Methane Breath Testing to Diagnose Small Intestinal Bacterial Overgrowth. Clin Transl Gastroenterol. 2023;14(4):e00567. Published 2023 Apr 1. doi:10.14309/ctg.0000000000000567
Birg A, Hu S, Lin HC, et al. Reevaluating our understanding of lactulose breath tests by incorporating hydrogen sulfide measurements. JGH Open. 2019;3(2):228-233.
Lakhoo, Krutika MD1; Liu, Xiaochen MSc1; Lentz, Greg2; Lin, Eugenia BS1; Chang, Bianca W. MD3; Pimentel, Mark MD1; Pichetshote, Nipaporn MD1; Rezaie, Ali MD, MSc1. Phenotype and Antibiotic Response in Patients With Flat Line Breath Test Results: A Large Scale Database Analysis: 448. American Journal of Gastroenterology 113():p S261, October 2018.
Soliman N, Kruithoff C, San Valentin EM, Gamal A, McCormick TS, Ghannoum M. Small Intestinal Bacterial and Fungal Overgrowth: Health Implications and Management Perspectives. Nutrients. 2025;17(8):1365. Published 2025 Apr 17. doi:10.3390/nu17081365
Rao, Satish & Bhagatwala, Jigar. (2019). Small Intestinal Bacterial Overgrowth: Clinical Features and Therapeutic Management. Clinical and Translational Gastroenterology. 10. e00078. 10.14309/ctg.0000000000000078.
Kim YJ, Jo IH, Paik CN, Lee JM. Efficacies of prokinetics and rifaximin on the positivity of a glucose breath test in patients with functional dyspepsia: a randomized trial. Rev Esp Enferm Dig. 2023 Mar;115(3):121-127. doi: 10.17235/reed.2022.8735/2022. PMID: 35748472.