Clinical Background
This case highlights a 42 year old female with long-standing, treatment-refractory hydrogen and intestinal methanogen overgrowth (IMO) SIBO, ultimately driven by post-infectious motility dysfunction. Her case illustrates a common and often overlooked pattern, repeated antimicrobial success without durable resolution, followed by relapse when therapy stops.
The key clinical inflection point was identifying impaired migrating motor complex (MMC) function secondary to post-infectious IBS, and addressing motility before re-treating bacterial overgrowth.
Initial Presentation
The patient presented with an eight-year history of gastrointestinal symptoms including:
- Chronic constipation (bowel movements every 3 to 4 days without laxatives)
- Significant postprandial bloating and abdominal distension
- Frequent burping and upper GI pressure
- Broad food sensitivities, particularly fermentable carbohydrates and nightshades
- Symptom flares shortly after completing prior SIBO treatments
Her symptom onset correlated clearly with a history of foodborne illness. She reported two separate episodes of severe food poisoning while traveling internationally approximately eight years prior. Symptoms began shortly thereafter and progressively worsened over time.
Prior Treatment History
Before presentation, the patient had undergone multiple standard and integrative SIBO treatments, including:
- Botanical antimicrobial protocols (multiple rounds)
- Elemental diet (2-week course)
- Rifaximin & Neomycin based therapy for mixed type SIBO
Each intervention led to partial improvement in symptoms and improvement in breath test values, but symptoms reliably returned within weeks to months after treatment cessation.
This pattern raised early concern for an unresolved underlying mechanism rather than inadequate antimicrobial selection.
Objective Testing: Baseline
Lactulose Breath Test (Baseline)
- Hydrogen: peak 78 ppm by 90 minutes
- Methane: peak 18 ppm
- Interpretation: Mixed hydrogen and IMO SIBO, moderate to severe burden
Repeat Breath Test After Prior Treatment (Historical)
Following rifaximin and botanical therapy:
- Hydrogen: reduced to 42 ppm
- Methane: reduced to 10 ppm
Despite improvement in labs and 80% improvement in symptoms during treatment and immediately after, the patient’s constipation, bloating, and food reactions returned within 4 to 6 weeks of treatment, the longest duration of improvement was 8 weeks.
Identifying the Missing Piece: Post-Infectious IBS
Given the history of food poisoning, symptom chronicity, and repeated relapse, IBS-SMART testing was pursued to evaluate for post-infectious autoimmunity affecting gut motility.
IBS-SMART Results
- Anti-vinculin antibody: 2.15 (positive, reference < 1.68)
- Anti-CdtB antibody: 2.84 (positive)
These findings supported post-infectious IBS with autoimmune-mediated damage to the enteric nervous system, impairing MMC function and predisposing the patient to recurrent SIBO.
Phase 1: Initial Motility Support
Given the positive IBS-SMART findings, treatment focus shifted away from repeated eradication and toward restoring motility.
The initial approach included:
- Iberogast, dosed nightly to support upper GI and small bowel motility
- Additional herbal motility support targeting the MMC
After approximately two months, the patient reported:
- Mild improvement in bloating
- Slight increase in bowel frequency
- Reduced postprandial discomfort
However, constipation and food sensitivity persisted, and symptom improvement plateaued.
Phase 2: Escalation to Prescription Prokinetic Therapy
At this point, a shared decision-making discussion was held reviewing pharmaceutical prokinetic options appropriate for post-infectious IBS and SIBO relapse prevention.
Prokinetic Classes Reviewed
- Dopamine antagonists (e.g., metoclopramide)
- Motilin receptor agonists (low-dose erythromycin)
- 5-HT4 receptor agonists (prucalopride)
- Opioid receptor antagonists (low-dose naltrexone)
- Herbal prokinetics (ginger, Iberogast, combination products)
Based on safety profile, selectivity, and efficacy for MMC stimulation, low-dose prucalopride (Motegrity) was chosen, consistent with current functional and gastroenterology guidance.
Intervention
- Prucalopride initiated at low dose (MMC-supportive dosing at night)
Clinical Response to Motility Restoration
After three months on low-dose prucalopride:
- Bowel movements increased to daily or every other day without laxatives
- Bloating reduced substantially
- Food tolerance improved
- Burping and upper GI pressure largely resolved
Importantly, these improvements occurred without concurrent antimicrobial therapy, supporting motility as a primary driver of symptoms.
Phase 3: Re-Treatment of SIBO After Motility Optimization
With improved motility established, the patient underwent another targeted SIBO treatment.
Repeat Lactulose Breath Test (Pre-Retreatment)
- Hydrogen: 55 ppm @ 90 minutes
- Methane: 14 ppm at max
This confirmed persistent but improved overgrowth.
Post-Treatment Breath Test (After Motility + Antimicrobials)
- Hydrogen: 12 ppm @ 90 minutes
- Methane: 3 ppm at max
- Interpretation: Resolution of SIBO
This pattern, successful eradication only after MMC support, is consistent with data showing higher success rates when motility is addressed in recalcitrant cases.
Maintenance and Transition Phase
The patient remained on low-dose prucalopride for an additional eight months to allow for ongoing MMC support and neural recovery.
She was then transitioned to a non-prescription motility formula, alongside:
- Food introductions with attention to meal spacing
- Nervous system regulation strategies
- Stress reduction and vagal tone support
- Continued avoidance of grazing and late-night eating
At follow-up, she remained symptom-free with stable bowel habits and sustained food tolerance.
Key Takeaways for Recalcitrant SIBO
1. Recurrent SIBO Is Often a Motility Disorder
Repeated antimicrobial “failure” frequently reflects unaddressed MMC dysfunction rather than resistance or inadequate dosing.
2. Post-Infectious IBS Is Common and Testable
A history of food poisoning plus positive anti-vinculin or anti-CdtB antibodies strongly predicts relapse risk and should prompt early motility support.
3. Treat Motility Before Re-Treatment
Establishing effective prokinetic therapy before repeating antimicrobials significantly improves long-term outcomes.
4. Prokinetics Are Not Laxatives
Their goal is coordinated, fasting-state small bowel clearance, not stool softening or colonic stimulation.
5. Duration Matters
Many patients require months, not weeks, of MMC support before transitioning off prescription therapy.
Conclusion
This case illustrates a foundational principle in functional medicine, chronic gastrointestinal conditions rarely exist in isolation, and durable healing requires identification and correction of upstream dysfunction rather than repeated symptom suppression. In patients with recalcitrant SIBO, particularly those with a clear post-infectious timeline, persistent relapse is often not a treatment failure but an indication that the underlying terrain has not yet been adequately addressed.
From a functional medicine perspective, impaired motility represents a systems-level disruption involving the enteric nervous system, immune activation, autonomic balance, and gut-brain signaling. The presence of anti-vinculin and anti-CdtB antibodies reframed this case away from an eradication-only approach and toward restoring physiologic function, specifically the migrating motor complex and small bowel clearance mechanisms.
By prioritizing motility support before repeating antimicrobial therapy, this patient was able to move from transient improvements to sustained resolution. This reflects a core functional medicine strategy, sequence matters. Supporting nervous system signaling, immune regulation, and mechanical function of the gut created the conditions necessary for antimicrobial therapies to be effective and for results to persist over time.
This is the level of clinical reasoning we teach inside the Adapt Practitioner Training and Certification Program. Our curriculum trains clinicians to recognize patterns like post-infectious IBS, interpret advanced testing in context, and design treatment sequences that address root cause physiology rather than chasing symptoms. If you want to confidently manage complex, recalcitrant cases like this in your own practice, Adapt provides the clinical framework, tools, and mentorship to do so.
