5 Common Mistakes Made When Treating SIBO (Small Intestinal Bacterial Overgrowth)

Small Intestinal Bacterial Overgrowth (SIBO) is now widely recognised as a leading contributor to chronic digestive complaints—particularly among those diagnosed with IBS. Despite greater awareness and access to testing, many individuals find themselves stuck in a cycle of temporary relief followed by relapse.

In our clinical experience at The Autoimmune Clinic, this is often due to missteps in how SIBO is diagnosed, treated, and followed up. Below are five of the most common mistakes we see, and how a more strategic approach can support better, longer-lasting outcomes.

1. Focusing Solely on Killing Bacteria Without Addressing the Underlying Cause

Most treatments for SIBO—whether pharmaceutical (e.g. rifaximin) or herbal (e.g. berberine, oregano oil)—are designed to kill the overgrown bacteria in the small intestine. While this can reduce the bacterial load and ease symptoms, it does not resolve the underlying cause.

Common root contributors include:

• Impaired gut motility (e.g. due to vagus nerve dysfunction, hypothyroidism, or post-infectious damage)

• Structural issues such as adhesions or ileocaecal valve dysfunction

• Long-term use of acid-suppressing medication

• Previous food poisoning or gastrointestinal infections

• Chronic stress or trauma impairing the enteric nervous system

Without identifying and addressing these drivers, recurrence is likely. A sustainable approach requires ongoing support for motility (often through prokinetics or vagal tone work), nervous system regulation, and lifestyle factors that influence digestive health.

2. Not Retesting After Treatment to Confirm Resolution

A frequent mistake is assuming that one round of treatment has “cured” the problem without any follow-up testing. While symptom improvement is promising, it does not always indicate full clearance of the overgrowth.

Many individuals experience partial relief but continue to struggle with low-grade symptoms, or relapse shortly after stopping treatment. In some cases, the overgrowth persists or shifts into a different pattern (e.g. hydrogen converting to methane production).

Re-testing via a breath test (usually with lactulose or glucose) about 10 to 14 days after finishing antimicrobials allows practitioners to:

• Confirm whether the overgrowth has resolved

• Identify persistent or new gas patterns

• Tailor the next phase of care appropriately

Without this step, treatment may end too early, leading to recurrence and prolonged frustration.

3. Not Considering Other Conditions That Mimic SIBO – Such as SIFO

Symptoms of SIBO—bloating, cramping, altered bowels—are non-specific and can be caused by several different gastrointestinal imbalances. A key one often overlooked is Small Intestinal Fungal Overgrowth (SIFO).

SIFO involves fungal organisms, most commonly Candida, growing excessively in the small intestine. It may develop after repeated antibiotic use, in individuals with suppressed immunity, or in the context of mould/mycotoxin exposure.

Clues pointing to SIFO rather than (or in addition to) SIBO include:

• Worsening symptoms with antimicrobial treatment

• Persistent bloating despite negative SIBO tests

• Sugar cravings or history of thrush

• Reactions to fermented or yeasty foods

Other conditions that can mimic SIBO include bile acid diarrhoea, pancreatic enzyme insufficiency, parasitic infections, and chronic constipation. A narrow focus on bacteria alone may miss these other important contributors to dysbiosis and gut dysfunction.

A thorough assessment—including stool analysis, symptom history, and potentially antifungal trials—can help refine the clinical picture.

4. Overusing Restrictive Diets and Failing to Reintroduce Foods

While short-term dietary strategies such as the low FODMAP diet or the SIBO Bi-Phasic protocol can offer symptomatic relief, staying on restrictive diets long-term can be counterproductive.

Potential consequences of prolonged restriction include:

• Loss of microbial diversity in the colon

• Nutrient deficiencies (e.g. B vitamins, fibre, polyphenols)

• Increased food fear and reduced tolerance

• Worsening constipation or fatigue

A better approach is to use dietary restriction strategically during active treatment, followed by careful reintroduction of foods to rebuild diversity and tolerance. This often needs to be done gradually, with digestive support in place, and ideally with practitioner guidance.

Remember, the goal is not to remain on a “SIBO-safe” diet forever, but to restore flexibility and resilience in the digestive system over time.

5. Assuming One Round of Treatment Is Enough

SIBO often requires a phased and repeated approach to achieve full resolution. Studies suggest relapse rates are high—especially if underlying causes are not fully addressed. One round of rifaximin or herbals may help reduce symptoms but is rarely curative on its own.

A complete treatment roadmap may include:

• Preparation: Reducing inflammation, supporting digestion and nervous system regulation

• Treatment: Antimicrobials or antibiotics tailored to the gas type and symptom pattern

• Repair: Gut healing (e.g. with nutrients, probiotics, nervous system support)

• Rebuild: Restoring a diverse microbiome, dietary expansion

• Maintenance: Long-term motility support and relapse prevention

Treatment must be personalised, layered, and monitored—rather than rigidly timed or protocolised.

SIBO is not just a bacterial issue; it is a reflection of broader dysfunction within the gut ecosystem and often the nervous system as well. A targeted treatment may bring relief, but without looking deeper, symptoms frequently return.

If you’ve had limited success with past SIBO protocols, consider whether any of the above factors might be contributing. At The Autoimmune Clinic, we take a comprehensive and personalised approach to gut health, guiding clients through all phases of recovery with careful attention to root cause, resilience, and long-term function.

If you’re ready to explore this further, please reach out to book an appointment or a discovery call with one of our practitioners.

Further Resources

For more insights on SIBO, including common causes, treatment options, and mistakes to avoid, you can watch our clinic director, Muriel Wallace-Scott, discuss this topic on Instagram:

Watch the video here