Interpreting the Unusual: Functional Insights from Atypical Breath Test Patterns

Dr. Bradley Bush, ND

Unlock hidden patterns in hydrogen and methane testing—learn how atypical breath test results reveal valuable functional insights for gut health and individualized treatment strategies.

Abstract

Breath testing is a cornerstone diagnostic tool for small intestinal bacterial overgrowth (SIBO) and carbohydrate malabsorption, yet atypical results often present interpretive challenges. This article examines six non-standard breath test patterns—including flat-methane, high baseline hydrogen, flat-negative, delayed motility spikes, multiple gas fluctuations, and atypical colon spikes—framing them as functional biomarkers rather than inconclusive noise. Clinical insights highlight how atypical profiles may reflect altered motility, compartmentalized dysbiosis, alternative hydrogen sinks, or upper gastrointestinal dysfunction. By integrating atypical results with patient history and symptoms, naturopathic physicians and functional medicine practitioners can apply more precise and individualized treatment strategies that extend beyond binary diagnostic criteria.

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Introduction

Breath testing remains one of the most widely used non-invasive methods for evaluating small intestinal bacterial overgrowth (SIBO) and carbohydrate malabsorption syndromes. Standardized protocols exist for administration and reporting, but interpretation continues to be debated—especially when results fall outside of classical positive or negative patterns. In these cases, clinicians often rely on experience and functional medicine insights to extract meaningful information for patient care.

Historically, limitations in breath test validation stemmed from assumptions that have since been challenged. For decades, small bowel aspirates were regarded as the diagnostic “gold standard,” shaping how sensitivity, specificity, and transit times for breath testing were defined. However, research has revealed significant drawbacks with aspirates, including a 19.6% contamination rate, which undermines their role as a definitive comparator.¹ Earlier studies that calibrated breath testing against aspirates may therefore have underestimated its diagnostic value.²

Consensus guidelines now acknowledge breath testing as a valid diagnostic tool when interpreted thoughtfully. The North American Consensus outlined criteria for hydrogen and methane interpretation while emphasizing that variability in patterns should not be dismissed as noise.⁴ More recently, atypical results such as flat-line hydrogen curves and high baseline hydrogen have been highlighted as potentially meaningful findings, not artifacts to be ignored.^4,5

Two of the most challenging atypical results are flat-line profiles and elevated baseline hydrogen.

• Flat-Line Pattern: Defined by very low hydrogen (≤3 ppm with no rise >1 ppm above baseline) and absent methane production, this profile often reflects hidden dynamics rather than a “negative” test. As noted by Rezaie (2020), flat-line patterns may indicate the presence of alternative hydrogen sinks, such as methanogens (converting H₂ to CH₄) or hydrogen sulfide–producing organisms. Clinically, these cases may represent suppressed gas activity rather than an absence of bacterial overgrowth. Integrating clinical symptoms, dietary triggers, or stool analysis can help differentiate true negatives from functional false negatives.
• High Baseline Hydrogen: Defined by an initial hydrogen level above 20 ppm in the absence of significant methane, this pattern may suggest proximal fermentation from small intestinal bacteria, delayed gastric emptying, or oral dysbiosis.^4,5 Persistently high hydrogen throughout testing can also signal gastroparesis or impaired motility, resulting in sustained fermentation prior to substrate administration. For clinicians, this pattern warrants consideration of upper GI dysmotility, prokinetic support, or further imaging studies.

Together, these atypical results underscore the need to move beyond binary interpretations. When considered alongside symptoms and patient history, flat-line and high baseline hydrogen patterns can reveal microbial imbalances and motility issues that inform more precise, individualized treatment strategies.

Background

Breath testing interpretation has traditionally focused on identifying a rise in hydrogen or the presence of methane, following established cutoffs. According to the North American Consensus, a ≥20 ppm rise in hydrogen within 90 minutes indicates bacterial overgrowth, while methane levels ≥10 ppm at any point define intestinal methanogen overgrowth.⁴ However, functional practice reveals that gas dynamics are more complex than binary thresholds.

Research shows that atypical results such as double peaks, suppressed gas curves, flat-line profiles, and high baseline hydrogen often reflect meaningful physiological differences rather than inconclusive outcomes. For example, lactulose breath tests that demonstrate two hydrogen peaks frequently correspond to small-bowel fermentation followed by colonic fermentation, as confirmed in scintigraphy–breath studies where hydrogen rises coincide with cecal filling.² Conversely, suppressed or flat hydrogen curves may indicate the presence of alternative hydrogen sinks such as methanogens or hydrogen sulfide–producing organisms.^4,5 Similarly, high baseline hydrogen may point to proximal bacterial overgrowth, gastroparesis, or oral dysbiosis, where fermentation occurs before substrate ingestion.

These atypical breath test presentations demonstrate how gas kinetics can be influenced by motility, microbial ecology, and compartmentalized dysbiosis. They also highlight the limitations of validation studies that benchmarked breath testing against contaminated aspirates or short antibiotic response windows.¹ In functional and naturopathic practice, where care strategies emphasize long-term outcomes, interpreting these atypical patterns provides critical insights into underlying physiology and individualized treatment planning.

By reframing so-called “gray zone” results as potential functional biomarkers, clinicians can uncover important aspects of gut dysfunction—including dysmotility, microbial distribution, or suppressed fermentation capacity—that are often overlooked in conventional frameworks.

Clinical Significance of Atypical Patterns

Hydrogen (H₂) and methane (CH₄) gases remain the core markers of breath testing. Produced by microbial fermentation of carbohydrates, their timing and distribution along the gastrointestinal tract can reveal underlying physiology beyond a simple positive or negative result. While many tests fit neatly within established diagnostic cutoffs, atypical patterns often provide deeper insight into motility, microbial compartmentalization, or hidden hydrogen sinks.

Below are six atypical profiles I frequently observed with a short clinical discussion:

1. Flat-Methane Pattern

Definition: Persistent methane elevation (≥10 ppm) across the 0–120 minute range.
Interpretation: Indicates methanogen overgrowth (often Methanobrevibacter smithii) distributed throughout the small intestine.
Clinical Implication: Commonly linked to chronic constipation. May warrant targeted therapies such as rifaximin-neomycin, rifaximin-allicin, or herbal antimicrobials with methane-reducing activity.

2. Baseline Elevated Hydrogen

Definition: Baseline hydrogen >20 ppm at time 0, in the absence of methane.
Interpretation: Suggests pre-existing fermentation before substrate ingestion, potentially due to proximal small bowel overgrowth, gastroparesis, or even oral dysbiosis. Sustained high hydrogen throughout the test may reflect impaired motility and reduced clearance rather than absolute bacterial density.^4,5
Clinical Implication: Consider prokinetic support, upper GI imaging, or evaluating oral health. Elevated results may overestimate true bacterial load if gas clearance is impaired. In patients with upper motility symptoms (e.g., GERD, nausea), rule out upper GI spasming secondary to high histamine activity with a trial of an H2 antihistamine with natural or prescriptive mast cell stabilizer (e.g., cromolyn sodium). 

3. Flat-Negative Pattern

Definition: Hydrogen ≤3 ppm throughout the test, with no methane production and no rise above baseline.
Interpretation: May reflect alternative hydrogen sinks (methanogens, hydrogen sulfide–producing bacteria) or suppression due to recent antibiotic use⁴ and also seen in patients using long-term herbal/ botanical SIBO treatments.
Clinical Implication: Context is critical when interpreting this pattern. A flat-negative result may reflect post-treatment microbial suppression, insufficient lactulose fermentation, or, in some cases, hydrogen sulfide–dominant SIBO. Patients with H₂S overgrowth typically present with sulfur-smelling gas and heightened sensitivity to high-sulfur foods and supplements (e.g., glutathione, allicin, garlic, MSM, alpha-lipoic acid). In such cases, sulfur-based antimicrobials should be avoided.

Stool analysis or repeat breath testing may help clarify ambiguous results. Importantly, diagnosing H₂S SIBO should be based on a consistent clinical picture rather than used as a default explanation for all flat-negative tests—an approach that risks overlooking more likely contributing factors.

4. Delayed Gut Motility Pattern

Definition: Hydrogen spike occurring after 120 minutes, often with a secondary peak.
Interpretation: Indicates delayed orocecal transit or slow motility.
Clinical Implication: Suggests underlying motility disorder. Management may include prokinetics, vagal tone support, and/or thyroid assessment. Never underestimate the impact that reduced T3 hormone has on gut motility, especially when a delayed gut motility pattern is present. Thyroid antibody testing is required to effectively rule out thyroid disease. 

5. Multiple Peaks and Valleys

Definition: Fluctuating rises and dips in hydrogen and/or methane.
Interpretation: May represent patchy bacterial overgrowth, compartmentalized dysbiosis, sometimes seen in mast cell activation or disordered motility.
Clinical Implication: This pattern often responds better to phased or broad-spectrum protocols rather than single-agent therapy. In some cases, irregular motility may be influenced by histamine activity. A trial of an H₂ antihistamine combined with a natural or prescription mast cell stabilizer (e.g., cromolyn sodium) can help determine whether histamine is contributing to symptoms.

Clinical Pearl:
I frequently work with a compounding pharmacy to prepare a cromolyn sodium solution (100 mg/mL in olive oil). Dosing typically begins at ¼ mL once to four times daily, with gradual titration up to 1 mL four times daily as needed. While conventional dosing is 100–200 mg four times daily, most patients rarely require doses that high. Compounded formulations allow for slower introduction, improved tolerance, and lower out-of-pocket costs, particularly when used alongside H₂ antihistamines and natural stabilizers such as quercetin.

6. Atypical Colon Spike

Definition: A large hydrogen or methane spike at 140–180 minutes.
Interpretation: Suggests colonic fermentation, possibly due to dysbiosis or ileocecal valve dysfunction.
Clinical Implication: This pattern is not diagnostic for SIBO but often correlates with IBS- or IBD-like symptoms. Patients may benefit from colon-directed therapies, including probiotics, fiber modulation, or parasite treatment. When inflammatory bowel disease or other colonic inflammation is suspected, additional anti-inflammatory support may be necessary.

In my clinical experience, this presentation occurs most frequently in patients with recurrent SIBO. For such cases, modifying the treatment plan to incorporate agents like mimosa pudica, higher-dose dihydroberberine, or short therapeutic trials of nitazoxanide and/or ivermectin can help both in symptom resolution and in clarifying potential root causes.

Conclusion

While atypical breath test results may initially seem inconclusive or confusing, they often reveal hidden layers of dysfunction when interpreted in the context of patient history and symptoms. Patterns such as flat-methane, delayed hydrogen spikes, or multiple fluctuations can inform targeted, individualized treatment approaches that improve outcomes in cases where standard diagnostic frameworks fall short.

For naturopathic physicians and functional GI specialists, learning to decode these patterns expands the diagnostic and therapeutic power of breath testing, moving beyond a binary SIBO diagnosis into a more nuanced understanding of the gut’s complex microbial terrain.

References

1. Cangemi DJ, Lacy BE, Wise J. Diagnosing Small Intestinal Bacterial Overgrowth: A Comparison of Lactulose Breath Tests to Small Bowel Aspirates. Dig Dis Sci. 2021;66(6):2042–2050.
2. Riordan SM, McIver CJ, Walker BM, Duncombe VM, Bolin TD, Thomas MC. The lactulose breath hydrogen test and small intestinal bacterial overgrowth. Am J Gastroenterol. 1996;91(9):1795–1803.
3. Rezaie A, Buresi M, Lembo A, Lin H, McCallum R, Rao S, Schmulson M, Valdovinos M, Zakko S, Pimentel M. Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. Am J Gastroenterol. 2017;112(5):775–784.
4. Rezaie A. Shedding Light on Elevated Baseline Hydrogen and Flat-Line Patterns During Breath Testing. Am J Gastroenterol. 2020;115(6):956–957.
5. Lim J, Rezaie A. Pros and Cons of Breath Testing for Small Intestinal Bacterial Overgrowth and Intestinal Methanogen Overgrowth. Gastroenterol Hepatol (N Y). 2023 Mar;19(3):140-146.