Don’t Miss Your Gut: Functional stool and SIBO testing: what to expect

1. What Is SIBO and Why Testing Matters

Small intestinal bacterial overgrowth (SIBO) is the abnormal proliferation of bacteria in the proximal small intestine, a region that normally contains very few microbes. The excess bacteria ferment carbohydrates, producing gases that trigger bloating, abdominal pain, diarrhoea, and, over time, malabsorption of nutrients such as iron and fat‑soluble vitamins [1].

Because the symptoms overlap with irritable bowel syndrome (IBS) and other functional gut disorders, many patients remain undiagnosed. A confirmed diagnosis allows targeted therapy—often antibiotics and dietary changes—that can dramatically improve quality of life. In Australia, the Australian Association of Clinical Microbiology (AACM) recommends testing for SIBO in patients with persistent gut symptoms after standard investigations have ruled out structural disease [2].

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2. Types of SIBO Tests

2.1 Breath Tests – The Gold Standard

The most widely used diagnostic tool is the hydrogen/methane breath test. Two substrates are common:

Substrate	Test Window	Typical Cut‑off
Glucose	2–3 h	Rise >20 ppm above baseline
Lactulose	4–5 h	Rise >12 ppm above baseline

Glucose is absorbed quickly, so a positive result indicates overgrowth in the proximal small intestine. Lactulose travels further; a delayed rise suggests distal overgrowth or rapid transit [1,2].

The test is non‑invasive, inexpensive, and can be performed in a private clinic or at home with a kit. However, it requires strict preparation: fasting, avoiding antibiotics and PPIs for at least 4–6 weeks, and a low‑FODMAP diet for 2–3 days before the test to minimise false positives [1].

2.2 Stool Culture Panels

Stool testing for bacterial overgrowth is less common but useful when breath tests are inconclusive or when the clinician suspects a specific bacterial profile. Panels can identify Enterococcus, Streptococcus, and Clostridium species that may be overrepresented in the small intestine. The main limitation is that stool reflects the distal gut; it may not capture proximal overgrowth accurately [3].

2.3 Hydrogen‑Sulfide Testing

A subset of patients harbour sulphate‑reducing bacteria that produce hydrogen sulfide (H₂S), a gas linked to mucosal damage and pain. The hydrogen‑sulfide breath test measures H₂S spikes after lactulose ingestion. Although not yet standardised in Australia, emerging evidence suggests that H₂S testing can guide targeted antibiotic therapy for refractory SIBO [4].

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3. Preparing for a Test

Preparation is critical to avoid false positives or negatives:

1. Dietary Restrictions
   * 48 h before the test: low‑FODMAP diet (avoid onions, garlic, beans, wheat).
   * 24 h before: avoid dairy, alcohol, and high‑fiber foods.

2. Medication Interruption
   * Discontinue proton‑pump inhibitors (omeprazole, esomeprazole) and H₂ blockers for at least 4 weeks.
   * Stop antibiotics, bismuth subsalicylate, and metronidazole 4–6 weeks prior.

3. Fasting
   * Fast for 12 h (overnight) before the test.

4. Hydration
   * Drink 500 ml of water 30 min before the first breath sample to ensure adequate saliva flow.

5. Avoid Physical Activity
   * Refrain from strenuous exercise 24 h before the test, as it can alter gut motility.

Adhering to these steps improves test reliability and reduces the risk of misdiagnosis [1,2].

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4. Interpreting Results

A breath test result is typically presented as a graph of hydrogen/methane concentration over time. Clinicians look for:

Parameter	Interpretation
Baseline	<10 ppm (normal)
Peak rise	>20 ppm (glucose) or >12 ppm (lactulose) indicates SIBO
Methane	>10 ppm suggests Methanobrevibacter smithii overgrowth, often linked to constipation‑dominant IBS

If the test shows a high methane level, the clinician may consider a methane‑specific treatment (e.g., rifaximin plus neomycin). A negative test does not entirely rule out SIBO; in such cases, stool culture or repeat testing after a dietary change may be warranted [3].

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5. Treatment Pathways

5.1 Antibiotic Regimens

The cornerstone of SIBO treatment is antibiotics that target small‑intestine bacteria:

Antibiotic	Typical Dose	Duration
Rifaximin	550 mg 3×/day	14 days
Neomycin	500 mg 4×/day	10 days
Combination	Rifaximin + Neomycin	10–14 days

Rifaximin is preferred due to its poor systemic absorption and low side‑effect profile. For patients with high methane levels, a combination of rifaximin and neomycin is often used [3,5].

5.2 Dietary Modifications

A low‑FODMAP diet reduces fermentable carbohydrates, limiting substrate for bacterial overgrowth. Once symptoms improve, a personalised re‑introduction plan restores gut diversity.

Probiotics are controversial; some strains (e.g., Lactobacillus rhamnosus) may compete with overgrown bacteria, but evidence is mixed. Clinicians often recommend a short course of a multi‑strain probiotic after antibiotic therapy [5].

5.3 Gut‑Healing Protocols

Functional medicine and naturopathic approaches emphasise gut barrier integrity. Common interventions include:

• Digestive enzymes (pancreatin, lipase) to aid nutrient absorption.
• L‑glutamine to support enterocyte repair.
• Omega‑3 fatty acids for anti‑inflammatory effects.
• Herbal antimicrobials (e.g., oregano oil, berberine) as adjuncts to antibiotics in some cases [6,7].

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6. Functional Medicine Approach

Functional medicine integrates conventional diagnostics with personalised nutrition and lifestyle changes. A typical protocol involves:

1. Comprehensive Testing – Breath test, stool panel, and markers of gut permeability (lactulose/mannitol ratio).
2. Root‑Cause Analysis – Identifying factors such as stress, food sensitivities, and prior antibiotic use.
3. Targeted Treatment – Combining antibiotics with gut‑healing supplements and a customised low‑FODMAP diet.
4. Monitoring and Re‑testing – Repeat breath test after 4–6 weeks to assess remission.

Functional medicine practitioners often collaborate with naturopaths, leveraging complementary expertise. For example, a naturopath might focus on herbal antimicrobials and nutritional counselling, while the functional medicine doctor manages antibiotic therapy and metabolic testing. This overlap can provide a holistic, patient‑centred care pathway [6,7].

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7. Choosing a Provider

Selecting a clinician experienced in gut diagnostics is crucial. In Australia, both naturopaths and functional medicine doctors are increasingly credentialed in SIBO testing. When evaluating a provider:

Criterion	Why It Matters
Certification	Look for accreditation from recognised bodies such as the Australian College of Naturopaths or the Australian Functional Medicine Association.
Experience with Breath Tests	Ensure they have performed >50 tests and can interpret complex results.
Integrated Care	Providers who collaborate with dietitians, gastroenterologists, and pharmacists can offer comprehensive support.
Patient Reviews	Check for consistent positive feedback on symptom improvement and clear communication.

If you’re unsure whether a practitioner is qualified, consult the Naturopath Vs Functional Medicine Doctor Overlap Or Competition resource for guidance on selecting the right specialist for your needs [5].

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8. Practical Tips & FAQs

Question	Answer
Can I do a breath test at home?	Yes, but ensure you follow strict prep guidelines and use a reputable kit.
What if I’m pregnant?	Breath tests are safe, but antibiotics may be contraindicated; discuss alternatives with your GP.
How long does remission last?	Many patients maintain remission for 3–6 months; relapse can occur if underlying risk factors persist.
Is a low‑FODMAP diet necessary forever?	Typically, a low‑FODMAP diet is used during the acute phase; a personalised re‑introduction plan follows.
Can probiotics help?	Some strains may help, but evidence is limited; use them under professional guidance.

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Conclusion

SIBO is a common yet often overlooked contributor to gut discomfort and systemic symptoms. Breath testing—particularly glucose or lactulose breath tests—provides a reliable, non‑invasive diagnostic route. Once confirmed, a combination of targeted antibiotics, dietary modification, and gut‑healing strategies can restore normal gut function. Functional medicine and naturopathic practitioners in Australia frequently collaborate, offering a comprehensive, patient‑centred approach that addresses both the microbiological and lifestyle factors driving SIBO. By preparing adequately, choosing an experienced provider, and following a structured treatment plan, patients can achieve lasting relief and improved quality of life.

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Further reading: Naturopathic Diagnostic Testing What S Real What S Hype.

Further reading: Gut Health And Ibs How Naturopaths Test And Treat Differently.

Further reading: Uncover Naturopathic Diagnostic Testing What S Real What S Hype Fallback Jpg.

Further reading: Find Out How Gut Health And Ibs How Naturopaths Test And Treat Differently Openai Jpg.

References

1. How To Test For SIBO: Your Ultimate Guide | IFDW — ifdw.org — https://ifdw.org/blogs/gut-health-magazine/how-to-test-for-sibo
2. How To Test For Sibo | IFDW Institute for Digestive Wellbeing | IFDW Institute for Digestive Wellbeing — ifdw.org — https://ifdw.org/pages/how-to-test-for-sibo
3. What Is the Best SIBO Test? – Functional Nutrition Answers — functionalnutritionanswers.com — https://www.functionalnutritionanswers.com/best-sibo-test/
4. Hydrogen Sulfide SIBO: How to Test and Treat – Preserv Wellness — preservwellness.com — https://preservwellness.com/hydrogen-sulfide-sibo/
5. SIBO Testing: Is It Worth It? — planetnaturopath.com — https://www.planetnaturopath.com/sibo-testing/
6. A Functional Medicine SIBO Protocol: Testing and Treatment — rupahealth.com — https://www.rupahealth.com/post/a-functional-medicine-sibo-protocol
7. SIBO Treatment and Testing: A Functional Medicine Approach – Restorative Health Solutions — restorativehealthsolutions.com — https://restorativehealthsolutions.com/blog/gut-health/sibo-treatment-functional-medicine-approach/
8. Nudge Blog – How to Check for SIBO: 4 Common Tests and What to Expect — nudgeibs.com — https://www.nudgeibs.com/blog/post/how-to-check-for-sibo-4-common-tests-and-what-to-expect