Functional medicine treatment for SIBO

Why SIBO often relapses

In conventional care, SIBO is commonly managed with antibiotics such as rifaximin, sometimes combined with dietary restriction. While this can reduce bacterial load and improve symptoms in the short term, recurrence is common when underlying contributors remain unaddressed. Many people find their symptoms return after treatment ends, even when the initial approach seemed to work.

In our clinical experience, several things often contribute: poor gut motility, where the small intestine’s natural self-cleaning wave slows, and bacteria accumulate; low stomach acid, which removes one of the body’s main defences against overgrowth; nervous system dysregulation from chronic stress; structural changes such as adhesions from surgery or inflammation; an unsettled microbiome that makes re-establishment more likely once treatment stops and many other causes.

Getting rid of the overgrowth is only part of the solution. If the conditions that allowed it to develop are still there, symptoms may return.

Our approach to SIBO treatment

Care starts with a root-cause approach to understanding why overgrowth developed and what’s been allowing it to return. We look at your symptom history, how previous treatment went, and what hasn’t resolved, then interpret breath testing and any other relevant investigations to build a clear picture before deciding how to proceed.

Depending on your presentation, care may include:

Restoring motility
The gut has a built-in cleaning cycle that sweeps bacteria through between meals, but in most people with SIBO, this is not working as it should. The first step is working out what has slowed it down. Common contributors include:

• Autonomic nerve damage from a prior gut infection
• Thyroid dysfunction
• Blood sugar instability
• Eating patterns that suppress fasting-state MMC activity
• Structural factors affecting intestinal movement
• Reduced vagal tone from chronic stress or prior illness

Supporting the nervous system
The autonomic nervous system directly influences gut movement and the acid, enzymes, and bile the gut produces to break down food.

• Vagal nerve stimulation, through practices such as slow diaphragmatic breathing, cold water to the face, and humming, is one way to support this
• Sleep, regular movement, and mindfulness practices may also be recommended depending on your presentation

Supporting gastric acid
Stomach acid is one of your body’s main defences against bacteria surviving in the small intestine, and is assessed early. Where acid production is low, whether from long-term PPI use or natural decline, supporting it back toward a healthy level helps remove one of the conditions that allowed overgrowth to take hold.

Reducing bacterial load
Targeted botanical or pharmaceutical agents are selected according to the dominant gas type. Herbal antimicrobials can reduce the bacteria causing harm while being gentler on the beneficial species than antibiotics tend to be. ‘Pathobionts’ are bacteria that cause harm only when they’re in the wrong place or present in excessive numbers, and targeted botanical agents are often well-suited to addressing them selectively.

Commonly used options include:

• Oregano oil
• Berberine
• Allicin
• Pomegranate husk
• Garlic

Oregano oil, in particular, has a stronger action on beneficial species and should be used carefully.

Where bacterial biofilm is present, antimicrobial agents alone are often insufficient. Biofilm is a protective structure that bacteria build around themselves, making it harder for antimicrobial agents to reach them. Biofilm-disrupting agents, including specific enzymes and N-acetyl cysteine (NAC), may be used alongside antimicrobials to improve effectiveness.

During bacterial die-off, the debris released as bacteria die can pass through a compromised gut lining and temporarily worsen symptoms. Binding agents such as activated charcoal or bentonite clay may be used to reduce absorption of these substances during treatment.

In cases where SIBO has not responded to antimicrobial treatment, an elemental diet (a short course of pre-digested liquid nutrition that bypasses normal digestion entirely) is an effective alternative. Because nutrients are absorbed before bacteria can ferment them, the overgrowth is effectively starved. This is typically used as a short course of two to three weeks.

Repairing the intestinal lining
Where bacterial activity has compromised the gut barrier, targeted nutritional support helps repair the lining and calm the immune activity behind food intolerances and broader symptoms.

This typically includes nutrients that support lining repair and immune regulation, including:

• Zinc
• Vitamin A
• Essential fatty acids
• Vitamin D

Rebuilding the microbiome
Once bacterial load has been reduced, probiotic and prebiotic support is introduced to re-establish beneficial species and support short-chain fatty acid production. Timing and strain selection matter. Certain probiotics introduced before motility is restored can worsen symptoms rather than help.

Digestive enzymes may also be used where digestive function remains compromised.

Addressing diet
Diet plays a supporting role throughout SIBO treatment, primarily by reducing the fermentable carbohydrates that bacteria feed on.

• Low-FODMAP, the specific carbohydrate diet, or SIBO-specific dietary protocols can reduce symptom burden during treatment, but prolonged carbohydrate restriction can deplete beneficial bacterial species and reduce microbial diversity, which can set back the microbial recovery you’re working toward
• Identifying food intolerances that have developed as a result of gut lining damage is also part of preventing symptoms from returning

How we investigate SIBO and digestive symptoms

While SIBO breath testing may be appropriate, it isn’t automatically the starting point for everyone. In some cases, SIBO testing is indicated. In others, broader testing such as comprehensive stool analysis, coeliac screening, inflammatory markers, or metabolic and hormonal assessments may be more relevant. Testing is selected based on your unique health picture to ensure investigations are relevant and likely to guide your treatment plan, and may include:

• SIBO breath testing
• Coeliac screening
• Food sensitivity tests
• Digestive function tests (stomach acid adequacy and transit time)
• Microbiome testing
• Organic acid testing in some cases
• Assessment of thyroid function, blood sugar regulation, and other systemic factors affecting gut motility

WHAT PATIENTS SAY