Rifaximin for SIBO: How to Improve Its Effectiveness with PHGG and Natural Support
Living with SIBO (Small Intestinal Bacterial Overgrowth) can feel like living with a rebellious flatmate. One day your digestion is tolerable, the next it’s all bloating, pain, and brain fog—no matter how “healthy” your meals are. For many people, antibiotics like Rifaximin are the first option their doctor suggests.
And while Rifaximin can be very effective, it’s rarely the whole answer. Recurrence rates are high, symptoms often creep back, and many people end up cycling through multiple rounds without lasting relief.
Here’s the good news: research shows Rifaximin works far better when it’s supported by Partially Hydrolysed Guar Gum (PHGG) and other natural strategies that help repair the gut environment. And if you’re vegan or plant-rich, there are specific ways to support your digestion that align with your ethics as well as your health.
In this article, I’ll break down:
What Rifaximin is and how it works for SIBO
Why it often isn’t enough on its own
How PHGG dramatically improves outcomes
The role of natural medicines in reducing recurrence
How a holistic approach creates sustainable recovery
What is Rifaximin and How Does It Work for SIBO?
SIBO happens when bacteria that are normally quite happy living in the large intestine wander upstream into the small intestine, where they don’t belong. The result? Gas, bloating, reflux, abdominal pain, diarrhoea, constipation, fatigue, even skin issues and mood symptoms.
Rifaximin is a non-absorbed antibiotic—meaning it stays in the gut rather than travelling through the bloodstream. That’s a huge advantage because it can reduce bacterial overgrowth locally without affecting the whole body.
Studies show that Rifaximin can be effective at reducing symptoms, particularly in people with hydrogen-dominant SIBO (the type most associated with diarrhoea and bloating). It’s generally well tolerated, with fewer side effects than systemic antibiotics.
Why Rifaximin Alone May Not Be Enough
For all its strengths, Rifaximin isn’t a magic bullet. Relapse rates can be 40–70% within nine months if nothing else changes. Why? Because SIBO isn’t just about bacteria—it’s about the environment that allowed the bacteria to migrate upstream in the first place.
Some reasons Rifaximin fails long-term include:
Impaired motility: The “housekeeper wave” (migrating motor complex) that sweeps bacteria down the gut isn’t working properly.
Underlying conditions: Hypochlorhydria (low stomach acid), IBS, adhesions, or hypothyroidism can all contribute.
Weakened microbiome: Killing bacteria without restoring healthy balance leaves the gut vulnerable to recurrence.
Inflammation and stress: A reactive nervous system worsens motility and barrier function.
This is why so many people experience that frustrating cycle: initial relief, then symptoms creeping back.
PHGG: The Secret Partner That Boosts Results
Enter Partially Hydrolysed Guar Gum (PHGG)—a gentle prebiotic fibre derived from guar beans. Unlike some fibres that worsen bloating in SIBO, PHGG is usually well tolerated in small amounts and has been shown in clinical trials to boost Rifaximin’s effectiveness.
One study found that Rifaximin alone eradicated SIBO in about 62% of patients. But when combined with PHGG, eradication jumped to 85%. That’s a significant difference.
Why does PHGG help?
It enhances motility, keeping food and bacteria moving in the right direction.
It supports beneficial bacteria like bifidobacteria and lactobacilli, which crowd out harmful species.
It’s low-fermenting, so less likely to cause bloating compared with other prebiotics.
It helps create a more stable gut environment after antibiotics, reducing recurrence.
For vegans, PHGG can be an especially supportive option because it doesn’t conflict with a plant-rich lifestyle and helps address the fibre-tolerance issues that often come with SIBO.
Natural Supports That Enhance Rifaximin’s Effectiveness
If antibiotics are the demolition crew, natural supports are the builders who come in to repair, reinforce, and restore. Without this step, the “house” (your gut) remains vulnerable.
Here are the areas I focus on in clinic:
1. Diet During and After Treatment
During Rifaximin: Some practitioners suggest a reduced-fermentation diet (like a modified low FODMAP) to minimise fuel for bacteria. Others prefer to feed bacteria during treatment to draw them out for the antibiotic to hit. The approach depends on your type of SIBO.
After treatment: Slowly reintroduce diverse plant foods to rebuild resilience. Diversity is key to long-term gut health.
2. Motility Support
Because impaired motility is a root cause of SIBO recurrence, this step is essential. Options include:
Ginger – shown to stimulate gastric emptying.
Iberogast – a herbal liquid blend with pro-motility effects.
Lifestyle – eating at regular intervals (not grazing), gentle yoga twists, vagus nerve activation through humming, gargling, or breathwork.
3. Anti-Inflammatory Nutrients
Ongoing gut inflammation worsens sensitivity and motility. Natural anti-inflammatories can help:
Curcumin – reduces intestinal inflammation.
Omega-3 fatty acids – from Ahiflower, flax, and chia for vegans, support gut barrier function and reduce cytokine activity.
4. Microbiome Restoration
Probiotics are tricky in SIBO—some strains worsen symptoms. But carefully chosen options, like Saccharomyces boulardii (a probiotic yeast), can help reduce recurrence. Postbiotics and PHGG also play a role here.
5. Nervous System Regulation
The gut and nervous system are deeply connected. Chronic stress shuts down motility and drives inflammation. Supporting nervous system health is as important as dietary change.
Breathwork, meditation, somatic practices.
Trauma-informed approaches such as Rapid Core Healing and Family Constellations, which I integrate in my work, to address deeper emotional stressors that perpetuate gut dysfunction.
A Holistic Naturopathic Approach
What I see so often is this divide:
Doctors prescribe Rifaximin, maybe diet advice, and send patients on their way.
Naturopaths or integrative practitioners use herbs and food plans but may not incorporate antibiotics where they’re genuinely helpful.
Trauma therapists work beautifully with the nervous system but may miss the physical side—like motility, nutrient depletion, or microbial imbalance.
The result? Many people fall between the cracks.
The reality is that SIBO is multi-layered. Addressing it sustainably requires integration: medical tools like Rifaximin plus natural medicine plus emotional healing. That’s the approach I bring as a naturopath specialising in vegan health—bridging the best of evidence-based natural care with trauma-informed nervous system support. I fully support my clients in choosing Rifaxamin in conjunction with natural medicines if this is the approach they determine best for them.
Should You Consider Rifaximin for SIBO?
Rifaximin can be very effective, but it’s not for everyone.
Most effective for: hydrogen-dominant SIBO, moderate to severe cases, and sometimes in methane-dominant SIBO when combined with neomycin.
Less essential for: mild cases that respond to herbal antimicrobials and diet.
Best results: when paired with PHGG and natural supports that address motility, microbiome repair, and inflammation.
If you’re plant-based, the decision can feel even more complex, especially if you’ve been told “just cut out beans forever.” That’s not a sustainable solution, nor is it nutritionally sound. Supporting your gut so you can tolerate plant foods again is possible—but it requires a thoughtful plan.
Summary: Building Long-Term Gut Resilience
Rifaximin is a valuable tool for SIBO, but it’s not the finish line. Without addressing motility, inflammation, microbiome repair, and nervous system health, relapse is common.
PHGG has been shown to dramatically improve eradication rates, making it a key partner in treatment. And natural medicines—from ginger and curcumin to omega-3s and somatic support—help build the long-term resilience your gut needs.
You don’t have to choose between “conventional” and “natural.” The most effective path is often both, integrated in a way that works for your body and values.
Final Thought
Healing from SIBO isn’t just about wiping out bacteria—it’s about restoring harmony in the gut ecosystem. Like tending a garden, it takes clearing the weeds, planting the right seeds, nourishing the soil, and creating an environment where healthy growth flourishes.
Rifaximin can clear space. PHGG and natural supports help the garden grow back stronger. And with the right holistic care, you can move beyond the cycle of relapse and into genuine, sustainable gut health.
By Camilla Brinkworth BHSc Naturopathy, Grad Cert Human Nutrition – Vegan Naturopath, Nutritionist & Trauma-Informed Practitioner
I specialise in supporting vegans and plant-rich eaters with complex health issues like SIBO, IBS, and PMDD. My approach combines evidence-based naturopathy, plant-based nutrition, and trauma-informed therapies such as Rapid Core Healing and Family Constellations. Having walked my own long healing path, I offer compassionate, practical guidance to help you restore your health without compromising your values.
Frequently Asked Questions (FAQs)
1. How effective is Rifaximin for SIBO?
Rifaximin is one of the most researched antibiotics for SIBO, particularly for hydrogen-dominant cases. Clinical trials show it can significantly reduce bacterial overgrowth, but relapse is common if underlying causes aren’t addressed. Pairing it with gut-supportive strategies like PHGG and natural therapies can improve long-term results.
2. Why combine Rifaximin with PHGG?
PHGG (Partially Hydrolyzed Guar Gum) is a gentle prebiotic fibre that has been shown in studies to improve Rifaximin’s effectiveness. It helps reduce relapse rates, supports healthy gut bacteria, and improves bowel regularity—making it an ideal partner for SIBO treatment.
3. Can natural medicine support SIBO treatment?
Yes. Herbal antimicrobials, anti-inflammatory nutrients, and motility-supporting supplements can work alongside or after Rifaximin. Naturopaths often use herbs such as oregano, berberine, or neem, plus magnesium and bitters for motility. These support long-term healing and reduce recurrence.
4. Is Rifaximin safe for vegans?
Rifaximin itself is vegan-friendly, but recovery depends on dietary choices. A plant-rich diet with low-fermentation foods during treatment can support healing. Adding PHGG and plant-based anti-inflammatories, such as turmeric and ginger, may further improve outcomes.
5. What happens if SIBO comes back after Rifaximin?
Recurrence is common because SIBO often stems from deeper issues like motility problems, stress, or low stomach acid. If symptoms return, a holistic plan—including diet adjustments, prokinetics, stress reduction, and sometimes repeat or alternative treatment—can be more effective long-term.
6. Can I take probiotics with Rifaximin for SIBO?
Some probiotics can worsen bloating in SIBO if introduced too early. However, spore-based probiotics or strains shown to reduce gas may be introduced after Rifaximin. PHGG helps prepare the gut environment so probiotics can colonise more effectively.