The latest on SIBO & natural strategies

Quick Summary

Small Intestinal Bacterial Overgrowth (SIBO) occurs when too many bacteria colonise the small intestine, causing uncomfortable digestive symptoms like bloating, gas, and altered bowel habits. This condition results from a combination of factors, including impaired gut motility, low stomach acid, and structural abnormalities. Recent research has identified specific bacterial and archaeal species responsible for different SIBO subtypes, each producing distinct gases—hydrogen, methane, or hydrogen sulphide—that correlate with specific symptoms. Natural treatment strategies, including herbal antimicrobials, probiotics, targeted dietary approaches, and lifestyle modifications, have shown remarkable success in managing SIBO while addressing its root causes. However, SIBO is a complex condition that requires proper diagnosis and professional guidance—working with an experienced naturopathic practitioner is essential for safe, effective treatment.

This article covers the most recent scientific research findings and natural treatment strategies for SIBO

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SIBO

Small Intestinal Bacterial Overgrowth (SIBO) occurs when too many bacteria colonise the small intestine, causing uncomfortable digestive symptoms like bloating, gas, and altered bowel habits

Topics Covered in This Article -

• Understanding SIBO: – The mechanisms behind bacterial overgrowth and why your small intestine becomes overrun

• The Key Microbes in SIBO – Identifying the specific bacteria and archaea responsible for your symptoms

• Natural Antimicrobial Treatments – How herbal medicines compare to antibiotics for eradicating SIBO, and why you need to be cautious

• Probiotics and Prebiotics – Using beneficial microbes and targeted fibres to restore balance

• Dietary Strategies for SIBO – Personalised eating approaches to reduce symptoms and prevent recurrence

• Lifestyle Gut Support Measures – The easy things - natural prokinetics, meal timing, and holistic strategies to keep SIBO from returning

Understanding SIBO: What Goes Wrong in Your Gut

Your small intestine is meant to be a relatively clean neighbourhood compared to your large intestine. Under normal circumstances, a combination of stomach acid, bile, digestive enzymes, immune defences, and rhythmic cleansing waves called the migrating motor complex (MMC) keeps bacterial populations low in this part of your digestive tract. But when these protective mechanisms fail, bacteria begin to accumulate where they shouldn't be, leading to SIBO.

The problems start when these excess bacteria begin fermenting the carbohydrates from your meals. This fermentation process produces gases—primarily hydrogen, methane, and hydrogen sulphide—that cause the characteristic bloating, distension, and discomfort that SIBO sufferers know all too well. Methane gas is particularly troublesome because it actually slows down intestinal movement, contributing to constipation and creating a vicious cycle where slowed transit allows even more bacterial overgrowth.

Beyond the uncomfortable gas and bloating, these bacteria cause real nutritional problems. They consume nutrients meant for you, including vitamin B12, and they interfere with bile acids, which are essential for fat absorption. This interference can lead to fat malabsorption, resulting in greasy stools, weight loss, and deficiencies in fat-soluble vitamins like A, D, E, and K. Some people develop anemia, experience significant fatigue, or notice cognitive issues like "brain fog" due to the chronic low-grade inflammation triggered by bacterial toxins and increased intestinal permeability.

Several underlying factors set the stage for SIBO. Impaired gut motility is perhaps the most common condition; conditions like diabetes-related nerve damage, hypothyroidism, scleroderma, or chronic use of opioid medications can slow the intestinal waves that normally sweep bacteria downward. Structural abnormalities like small bowel diverticula, strictures, surgical adhesions, or even a malfunctioning ileocecal valve (which normally prevents colonic bacteria from migrating backward into the small intestine) create pockets where bacteria can flourish. Antibiotics, which are often life-saving medicines, are non-specific antimicrobials, meaning they kill the bad, the good and everything in between. Regardless of how necessary they may be, antibiotics are disruptive to gut microbes.

Low stomach acid is another major contributor. Your stomach acid serves as a crucial first line of defence against microbes you ingest with food. When acid production is insufficient—whether due to aging, autoimmune conditions, or the widespread use of proton pump inhibitors for heartburn—more bacteria survive the journey into your small intestine. Similarly, pancreatic enzyme deficiency or reduced bile flow removes other antimicrobial defences, creating a more hospitable environment for bacterial proliferation.

The Key Culprits: Microbes Involved in SIBO

Understanding which microbes are causing your SIBO is increasingly important for targeted treatment. Recent DNA sequencing studies have revealed that SIBO isn't just about "too many bacteria"—it's about the wrong types of bacteria taking over.

The most consistently identified troublemakers belong to the Enterobacteriaceae family—organisms that normally live in your colon but have migrated northward into your small intestine. This family includes species like Escherichia coli, Klebsiella pneumoniae, and various Enterococcus species. These bacteria are considered "disruptor" species because they crowd out the beneficial strict anaerobes that should be present in small amounts in the small intestine. Research shows that an increased abundance of these Enterobacteriaceae strongly correlates with SIBO diagnosis and symptom severity, particularly bloating and urgency.

Many of these bacteria are hydrogen producers—they ferment carbohydrates and produce hydrogen gas as a byproduct. Excess hydrogen is what's measured on SIBO breath tests, and it tends to correlate with diarrhea-predominant symptoms because hydrogen can actually speed up intestinal transit. People with hydrogen-dominant SIBO often experience loose stools, urgency, and significant bloating shortly after meals.

Then there's the methane story, which is actually quite different. Methane isn't produced by bacteria at all—it's made by archaea, ancient microorganisms that are technically in a different domain of life. The primary culprit is Methanobrevibacter smithii, which consumes hydrogen and carbon dioxide to produce methane gas. This condition is now sometimes called Intestinal Methanogen Overgrowth (IMO) rather than methane SIBO.

Methane has a dramatically different effect than hydrogen—it slows intestinal motility, leading to constipation. Research confirms that people with constipation-predominant IBS who test positive for methane on breath tests have higher levels of M. smithii in their stool, and their methane levels directly correlate with how slowly food moves through their system. About 30% of adults harbor these methane-producing archaea, which explains why some people test negative for hydrogen but positive for methane—these are distinct microbial profiles requiring different treatment approaches.

The newest piece of the puzzle is hydrogen sulfide (H₂S). Certain bacteria, particularly sulfate-reducing species like Desulfovibrio and some Fusobacterium species, consume hydrogen to produce hydrogen sulfide gas. This gives off a characteristic rotten egg smell and has been linked to diarrhea and abdominal pain. H₂S wasn't measured in older SIBO tests, but newer three-gas breath tests can now detect it. Studies from 2022 show that IBS patients with high H₂S on breath tests have increased levels of these sulfur-producing microbes and tend toward diarrhea symptoms.

These different gas producers actually interact in complex ways. Hydrogen producers feed substrate to both methane and H₂S producers. If methanogens flourish, they consume so much hydrogen that breath tests might show near-zero hydrogen readings despite significant overgrowth—a "flatline" result that can be misleading. Research suggests that methane producers and H₂S producers tend to be inversely related; when one dominates, it can suppress the other. This explains why different SIBO patients experience such different symptoms—it depends on which microbes have taken over their small intestine.

Why Professional Diagnosis Matters

Given the complexity of these different microbial patterns and their overlapping symptoms with other digestive conditions, proper diagnosis is essential. SIBO can mimic or co-exist with irritable bowel syndrome, inflammatory bowel disease, celiac disease, and food intolerances. Without appropriate testing and clinical assessment by an experienced practitioner, you might be treating the wrong condition entirely—or missing underlying causes that need to be addressed. Self-diagnosis based on symptoms alone often leads to unnecessary dietary restrictions and delayed appropriate treatment, or you could make things worse.

Garlic, thyme and oregano in your daily diet can help balance your gut microbes, and in specific doses and forms can help to treat SIBO.

Natural Antimicrobial Treatments

The good news is that natural antimicrobial agents have gained significant scientific validation as alternatives to pharmaceutical antibiotics for treating SIBO. Plant-derived compounds offer broad-spectrum antibacterial and antifungal effects without promoting antibiotic resistance as aggressively as conventional antibiotics.

Herbal antimicrobials that have shown particular promise include oregano oil (rich in the compound carvacrol), garlic extract (containing allicin), neem, berberine-containing herbs like goldenseal and Berberis species, and thyme. Recent high-quality studies demonstrate that herbal therapy can match the effectiveness of Rifaximin, the most commonly prescribed antibiotic for SIBO. In clinical trials, herbal combinations including oregano and berberine formulas achieved breath test normalisation rates comparable to Rifaximin's 50-60% success rate.

What's particularly interesting is that patients who failed to respond to rifaximin have shown success with herbal treatments in follow-up attempts, suggesting herbs can rescue difficult SIBO cases. The herbal antimicrobials appear to work by reducing overall bacterial load while favouring rebalancing of the microbiome—similar to antibiotics but with a gentler, more selective effect.

A 2024 randomised trial in Spain compared standard SIBO therapy (rifaximin plus diet) against an integrative approach that added herbal antimicrobials, probiotics, and prebiotic fibre to the rifaximin and dietary treatment. Both groups saw reduced breath test gas levels, but the integrative group had significantly higher clinical remission rates, especially for methane-predominant SIBO. Patients in the integrative group reported better relief from bloating and constipation, even when gas levels on breath tests were similar between groups. This suggests that herbs and probiotics contribute to symptom improvement through mechanisms beyond just reducing bacterial numbers—perhaps by modulating inflammation, strengthening the gut barrier, or favourably shifting the microbial community composition.

For those seeking to avoid antibiotics altogether, herbal antimicrobials can serve as primary therapy for mild to moderate SIBO. They're also valuable as adjuncts after antibiotic courses to reduce recurrence rates. The typical treatment protocol involves taking herbal antimicrobial combinations for 4-6 weeks, often rotating between different formulas to prevent bacterial adaptation. However, this should always be done under the guidance of a practitioner to avoid causing harm.

Self-prescribing diets or herbal antimicrobials can make things worse - and may miss something more serious.

The Risks of Self-Prescribing Herbal Antimicrobials

While these research findings are encouraging, it's crucial to understand that herbal antimicrobials are powerful medicines, not benign supplements you can casually experiment with. Self-prescribing antimicrobial herbs without proper guidance can lead to several problems:

• First, choosing the wrong herbs or incorrect dosages for your specific SIBO subtype can be ineffective at best and potentially harmful at worst. Methane-dominant SIBO, for instance, often requires different herbal protocols than hydrogen-dominant SIBO, and what works for one person may worsen symptoms in another. The herbs that target archaea are different from those that work best on hydrogen-producing bacteria.

• Second, herbal antimicrobials can cause significant die-off reactions when bacteria are killed rapidly, releasing toxins that make you feel worse before you feel better. Without proper guidance on managing these reactions—through appropriate dosing schedules, binders, and supportive therapies—many people abandon effective treatment protocols prematurely, thinking the herbs are making them worse.

• Third, taking antimicrobial herbs for too long or at incorrect doses can disrupt your beneficial gut bacteria just as antibiotics can, potentially creating new imbalances or making SIBO worse. An experienced naturopathic practitioner knows how to balance antimicrobial treatment with gut restoration strategies to prevent this.

• Finally, herbs can interact with medications, affect underlying health conditions, or be contraindicated in pregnancy, liver disease, or other situations. What seems "natural" isn't always safe for everyone.

Probiotics and Prebiotics: Fighting Fire with Fire

It might seem counterintuitive to add bacteria when you're already dealing with too many bacteria, but consuming beneficial microorganisms—probiotics—has proven remarkably effective in SIBO treatment. Good bacteria can compete with problematic microbes for resources and attachment sites, enhance gut barrier function, produce antimicrobial compounds, and modulate immune responses to favour a healthier microbial balance.

The probiotic with perhaps the strongest evidence is Saccharomyces boulardii, which is actually a beneficial yeast rather than a bacterium. This distinction is important because being a yeast means it's unaffected by antibiotics and can be taken simultaneously during antibiotic therapy without being killed off. A 2020 trial on SIBO in systemic sclerosis patients (a condition frequently complicated by SIBO) found that S. boulardii alone achieved a 33% eradication rate with significant symptom relief, compared to only 25% with the antibiotic metronidazole alone. When S. boulardii was combined with metronidazole, the eradication rate jumped to 55%—clear evidence of synergy.

Even more impressive results came from a study on cirrhotic patients with SIBO, where a three-month course of S. boulardii achieved an 80% clearance rate compared to just 23% in the placebo group. These patients also experienced reduced complications like ascites, demonstrating that probiotics can deliver tangible clinical improvements beyond just normalising breath tests.

Bacterial probiotics containing Lactobacillus and Bifidobacterium species have also shown benefits; however, it’s important to be prescribed specific strains of these species. You can’t just take any old probiotic off the shelf. Pediatric data and case series indicate that probiotic therapy leads to partial or complete symptom resolution in a majority of children with SIBO and can help maintain longer-term remission when given in repeated courses. While probiotics alone may not completely cure SIBO in every case, they consistently reduce symptoms like abdominal pain and bloating, and when used after antimicrobial treatment, they help restore normal flora and prevent rapid relapse.

Prebiotics—fermentable fibres that feed beneficial gut bacteria—require more careful consideration in SIBO. The idea of adding fermentable fibre when bacteria are already over-fermenting foods seems paradoxical, but emerging research shows that strategically selected prebiotics can selectively nourish beneficial microbes that outcompete SIBO-associated bacteria, thereby rebalancing the ecosystem.

Partially hydrolysed guar gum (PHGG) is one example—a gentle, soluble fibre that has improved SIBO treatment outcomes in studies. In pregnant women with subclinical hypothyroidism (a group prone to SIBO), a combination of inulin-based prebiotic fibre and multi-strain probiotics for 21 days eradicated SIBO in 63-71% of cases—higher than the typical 40% eradication rate with antibiotics alone. The prebiotic was thought to stimulate the growth of Bifidobacteria and other protective flora, which suppressed the gas-producing overgrowth. Patients also saw improved absorption of thyroid medication and reduced TSH levels, indicating overall improved gut function.

Caution is warranted with prebiotics in active SIBO—some individuals experience increased gas or bloating initially. However, when used strategically in conjunction with antimicrobials or probiotics, prebiotics like PHGG, inulin, or galacto-oligosaccharides can help "reset" the microbiome and promote long-term microbial balance. The strategy aims not just to kill excess bacteria but to fertilise the gut with food for beneficial microbes so dysbiosis doesn't simply return once treatment stops.

Why Probiotic Selection Requires Expertise

Here's where things get tricky: not all probiotics are helpful for SIBO, and some can actually make symptoms worse. Certain probiotic strains produce D-lactate, which can accumulate and cause neurological symptoms like brain fog and confusion in people with SIBO. Other strains may worsen bloating in some individuals, particularly during active overgrowth.

The timing of probiotic introduction matters enormously. Starting probiotics too early in treatment, at the wrong dose, or choosing inappropriate strains for your SIBO subtype can intensify symptoms and discourage you from an approach that might have worked with proper guidance. Similarly, prebiotics introduced at the wrong time or in excessive amounts can feed the overgrowth rather than helpful bacteria, making you significantly worse.

An experienced naturopathic practitioner understands which probiotic strains work best for different SIBO subtypes, when to introduce them in the treatment timeline, how to dose them appropriately, and how to monitor for adverse effects. They can also determine whether probiotics are appropriate for you at all—in some cases, they may need to be delayed until after antimicrobial treatment is complete.

Dietary Strategies for SIBO Management

Diet plays a crucial role in managing SIBO, both during active treatment and for long-term prevention. The key is personalisation—what works for one person may not work for another, depending on their specific SIBO subtype, symptom pattern, and individual tolerances.

The Modified Low FODMAP Approach

The low FODMAP diet has become well-known for managing IBS symptoms, and it's frequently applied to SIBO as well. FODMAP stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols—types of carbohydrates that are poorly absorbed in the small intestine and readily fermented by bacteria. However, a blanket approach of eliminating all FODMAPs isn't ideal for everyone.

A more sophisticated approach involves testing tolerance to different FODMAP groups individually rather than eliminating everything at once. This diet should be viewed as a short-term strategy, typically lasting 4-8 weeks, not a permanent lifestyle. The goal is symptom reduction during treatment, followed by systematic reintroduction of FODMAP groups to identify specific personal triggers.

Different SIBO subtypes may benefit from different FODMAP modifications. For hydrogen-dominant SIBO (associated with diarrhea), focusing more on restricting fructose and polyols may be helpful. For methane-dominant SIBO (linked to constipation), placing more emphasis on limiting certain fibres and resistant starches might be more appropriate.

Specific Carbohydrate Diet Elements

While the full Specific Carbohydrate Diet (SCD) isn't typically recommended as a first-line approach for SIBO, incorporating elements from it can be valuable. The SCD focuses on restricting complex polysaccharides and disaccharides that may feed bacterial overgrowth while emphasising easily digestible proteins, fats, and carefully selected simple carbohydrates that are absorbed higher in the small intestine.

A hybrid approach that integrates SCD principles with FODMAP concepts can work well for some patients, focusing on the most problematic carbohydrates for each individual rather than imposing blanket restrictions. This maintains nutritional adequacy while reducing fermentable substrate for overgrown bacteria.

The Bi-Phasic Diet Approach

Some practitioners utilise a bi-phasic dietary strategy that involves two distinct phases:

The Reduction Phase (typically 2-4 weeks) is the most restrictive period, removing nearly all fermentable foods. This phase coincides with antimicrobial treatment and is designed to starve overgrown bacteria while reducing symptoms. It's challenging but can dramatically improve comfort during the critical treatment window.

The Reintroduction Phase involves gradually adding foods back in a systematic way, testing tolerance to increasingly fermentable foods. This helps identify individual tolerance thresholds and prepares for transition to a more varied, sustainable maintenance diet.

The Elemental Diet: A Powerful Reset

For stubborn cases or when other treatments have failed, the elemental diet offers a remarkably effective option. This is a nutritionally complete liquid formula containing amino acids, simple sugars, vitamins, and fats in their simplest, pre-digested forms. It provides complete nutrition to you while essentially starving bacteria, since there are no complex foods for microbes to ferment.

Classic studies reported that approximately 80% of patients achieved breath test normalisation after a 2-week elemental diet. A 2024 clinical trial using a more palatable elemental formula reported a 100% cure rate in SIBO patients and a 75% cure rate in those with combined SIBO and methane overgrowth after 14 days. Symptoms improved dramatically, and most patients maintained improvement after reintroducing regular foods.

The elemental diet is admittedly very restrictive—you consume only the formula for 2-3 weeks—but it represents a powerful, non-pharmaceutical way to eradicate overgrowth when needed. It should be undertaken with professional guidance.

Practical Dietary Implementation

Successful dietary management involves several practical strategies:

• Food and symptom journaling helps identify personal triggers and tolerance patterns

• Gradual modifications rather than sudden dramatic changes reduce stress and improve adherence

• Focusing on permitted foods rather than restrictions makes the diet feel less punishing

• Choose nutrient-dense options within restricted categories to maintain nutritional status

• Meal spacing matters—leaving 4-5 hours between meals supports the migrating motor complex, those cleansing waves that sweep bacteria through the intestines

• Overnight fasting of at least 12 hours encourages gut housekeeping

Transitioning to Long-Term Eating

A critical aspect of dietary management is transitioning to a sustainable long-term eating pattern that supports microbial diversity, provides adequate prebiotic fibres for gut health, maintains symptom control, prevents SIBO recurrence, and supports overall well-being. This typically involves gradually reintroducing more variety and fermentable fibres as tolerance improves, while avoiding excess simple sugars and processed foods that create a highly fermentable environment.

The goal isn't to stay on a restrictive diet forever—it's to calm the system during treatment, identify true triggers, and then expand to the most diverse, nutrient-rich diet you can tolerate.

The Dangers of DIY Dietary Approaches - a word of caution

This is where many well-intentioned SIBO sufferers run into serious trouble. Restrictive diets found online or in books—whether low FODMAP, SCD, or bi-phasic approaches—can cause significant harm when self-implemented without professional oversight.

Overly restrictive diets can lead to nutritional deficiencies, particularly of fibre, vitamins, minerals, and beneficial plant compounds. When maintained too long, they can actually reduce microbial diversity in your gut, making you more vulnerable to digestive issues long-term. Many people become fearful of food, developing disordered eating patterns or orthorexia as their "safe food" list shrinks progressively smaller.

Furthermore, without proper testing and monitoring, you might be restricting the wrong foods entirely. Someone with hydrogen sulphide SIBO, for example, needs different dietary modifications than someone with methane overgrowth. Restricting based on generic SIBO advice might not address your specific situation and could unnecessarily limit your nutrition.

The reintroduction phase is particularly tricky, and where professional guidance becomes invaluable. Reintroducing foods too quickly, in the wrong order, or without understanding your individual tolerance patterns can lead to symptom flares that discourage you from expanding your diet—leaving you unnecessarily restricted for months or years.

Additionally, people often start extreme elimination diets before they've even confirmed a SIBO diagnosis, potentially masking symptoms of other conditions that need different treatment. Some serious health conditions can have digestive symptoms that appear similar to IBS or SIBO - e.g. ovarian cancer, and it is important to first rule these out. The temporary symptom relief from severe restriction can give false confidence that you're "managing" SIBO when you're actually just suppressing symptoms while the underlying problem worsens.

An experienced naturopathic practitioner can personalise dietary approaches based on your breath test results, symptom patterns, nutritional status, other health conditions, and lifestyle factors. They'll ensure you maintain adequate nutrition, guide appropriate timing of restrictions and reintroductions, help you interpret your symptoms during the process, and support your transition back to the most varied diet you can sustain—because that's the ultimate goal.

Lifestyle and Gut Support Measures

Beyond antimicrobials and diet, several natural strategies address the root causes of SIBO and help prevent recurrence.

Natural Prokinetics for Motility

Since impaired gut motility is a key factor in SIBO development, strategies to enhance intestinal movement are crucial for prevention. While pharmaceutical prokinetics are sometimes prescribed, natural options also show promise.

Ginger root and its extracts have proven pro-motility effects and are frequently recommended, often taken at bedtime to stimulate the migrating motor complex during overnight fasting. Some studies suggest that integrating ginger helps reduce SIBO relapse rates compared to no motility support.

Other herbal blends like Iberogast, which contains bitter herbs, may support gastric emptying and coordinated intestinal contractions. While research is still emerging, clinical experience suggests these natural prokinetics can play a valuable role in maintaining results after successful treatment.

Meal Timing and Spacing

How and when you eat matters as much as what you eat. Avoiding grazing and instead leaving 4-5 hour gaps between meals allows the migrating motor complex to properly sweep the intestines. Think of these cleansing waves as your gut's housekeeping service—they only work effectively during fasting periods between meals.

Overnight fasting of at least 12 hours is also encouraged, giving your digestive system a prolonged period to perform its cleansing functions. This meal spacing approach reduces available substrate for bacteria and encourages the gut's natural cleansing mechanisms, theoretically lowering the risk of SIBO returning.

Physical Activity

Regular physical activity serves as another natural pro-motility aid. Even light walking can stimulate intestinal transit, and some research suggests it may help normalize breath test results faster. Movement benefits gut motility through multiple mechanisms, including direct mechanical stimulation, stress reduction, and nervous system effects on intestinal function.

Gut-Healing Support

Holistic SIBO management often includes supporting the gut environment directly. Nutrients like L-glutamine are used to repair the intestinal lining after inflammation, potentially alleviating increased intestinal permeability ("leaky gut") and improving nutrient absorption. Some clinicians report improvements in bloating and stool consistency when glutamine is added to treatment regimens.

For those with evidence of bile acid or digestive enzyme insufficiency contributing to SIBO, supplementation with bile acids or digestive enzymes may be helpful, though this should be individualized rather than routinely recommended.

Probiotics that produce butyrate, a short-chain fatty acid, may help reduce inflammation and strengthen the intestinal barrier—an active area of ongoing research.

Addressing Underlying Causes

Successfully treating SIBO long-term requires identifying and addressing underlying causes. This might include:

• Optimising thyroid function if hypothyroidism is present

• Managing diabetes and blood sugar control to prevent neuropathy

• Reviewing medications that may impair motility or reduce stomach acid

• Addressing structural issues through appropriate medical care

• Supporting adequate stomach acid production (sometimes with supplemental betaine HCl, under professional guidance)

Stress Management and the Gut-Brain Axis

Don't underestimate the role of stress in SIBO. Stress can interfere with gut motility and immune function through the gut-brain axis, potentially aggravating bacterial overgrowth. Mind-body practices like yoga, mindfulness meditation, or acupuncture have shown benefits in IBS research and are commonly extrapolated to SIBO care to help normalise nervous system signalling to the gut.

By combining targeted antimicrobial treatments with these supportive strategies, many people report not only relief from abdominal pain and bloating but also improvements in energy, mood, and overall wellness as gut health is restored.

Finding Hope in a Holistic Approach—With Professional Guidance

SIBO can be a frustrating condition, often requiring multiple treatment attempts and ongoing management. However, the growing body of research on natural treatment strategies offers real hope. Herbal antimicrobials, probiotics, prebiotics, elemental diets, and lifestyle modifications all have solid scientific evidence supporting their use.

What makes the natural approach particularly valuable is that it addresses not just the bacterial overgrowth itself but the underlying imbalances that allowed SIBO to develop in the first place. By supporting motility, enhancing digestive function, modulating the immune system, and gradually restoring a balanced microbiome, these strategies aim for lasting improvement rather than just temporary symptom suppression.

However—and this cannot be emphasised enough—SIBO is not a condition to self-treat. The complexity of SIBO, with its various subtypes, overlapping symptoms with other conditions, potential underlying causes, and need for individualised treatment protocols, makes professional guidance essential.

An experienced naturopathic practitioner brings several critical elements to your care:

• Accurate diagnosis through appropriate testing, ensuring you're actually dealing with SIBO and not another condition with similar symptoms. They'll also help identify which subtype you have (hydrogen, methane, or hydrogen sulphide dominant), as this fundamentally changes the treatment approach.

• Identification of underlying causes that led to SIBO in the first place—whether it's hypothyroidism, diabetes-related motility issues, medication effects, structural problems, or other factors. Without addressing these root causes, SIBO will likely return no matter how well you treat the immediate overgrowth.

• Personalised treatment protocols that match your specific situation, SIBO subtype, symptom severity, other health conditions, medications, and lifestyle. What works brilliantly for one person might worsen symptoms in another—there's no one-size-fits-all approach to SIBO.

• Safe implementation of herbal antimicrobials, ensuring appropriate herb selection, proper dosing, monitoring for interactions and side effects, and strategies to manage die-off reactions. They can also coordinate with your other healthcare providers if you're taking medications or have other health conditions.

• Nutritional oversight during restrictive dietary phases, ensuring you maintain adequate nutrition while managing symptoms. They'll guide the appropriate timing and sequencing of dietary changes and support successful reintroduction to prevent unnecessarily prolonged restrictions.

• Monitoring and adjustment throughout treatment, interpreting your symptom changes, adjusting protocols as needed, and conducting follow-up testing to confirm resolution. SIBO treatment rarely goes exactly as planned, and having someone who can troubleshoot issues is invaluable.

• Prevention strategies tailored to your specific risk factors, helping you maintain results long-term rather than experiencing repeated relapses.

The information in this article is meant to help you understand SIBO and have informed conversations with your healthcare provider, not to serve as a treatment protocol. While it's valuable to educate yourself about treatment options, attempting to piece together your own protocol from internet research commonly leads to wasted time, money, frustration, and sometimes worsening of your condition.

Working with a knowledgeable naturopathic practitioner who specialises in digestive health gives you the best chance of resolving SIBO safely and effectively. With the right professional guidance, patience, persistence, and an integrative approach rooted in current research, lasting relief and genuine gut healing are entirely possible.

If you're struggling with symptoms that might indicate SIBO—chronic bloating, gas, abdominal discomfort, altered bowel habits, fatigue, or nutrient deficiencies—reach out to an experienced naturopath who can properly assess your situation and guide you toward effective, personalised treatment. Your gut health is too important to leave to guesswork.

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  Tansel, A., & Levinthal, D. J. (2023). Understanding Our Tests: Hydrogen-Methane Breath Testing to Diagnose Small Intestinal Bacterial Overgrowth. Clinical and translational gastroenterology, 14(4), e00567. https://doi.org/10.14309/ctg.0000000000000567

  Redondo-Cuevas, L., Belloch, L., Martín-Carbonell, V., Nicolás, A., Alexandra, I., Sanchis, L., Ynfante, M., Colmenares, M., Mora, M., Liebana, A. R., Antequera, B., Grau, F., Molés, J. R., Cuesta, R., Díaz, S., Sancho, N., Tomás, H., Gonzalvo, J., Jaén, M., Sánchez, E., … Cortés-Rizo, X. (2024). Do Herbal Supplements and Probiotics Complement Antibiotics and Diet in the Management of SIBO? A Randomized Clinical Trial. Nutrients, 16(7), 1083. https://doi.org/10.3390/nu16071083

  Tansel, A., & Levinthal, D. J. (2023). Understanding Our Tests: Hydrogen-Methane Breath Testing to Diagnose Small Intestinal Bacterial Overgrowth. Clinical and translational gastroenterology, 14(4), e00567. https://doi.org/10.14309/ctg.0000000000000567

  Sharabi, E., & Rezaie, A.. (2024). Small Intestinal Bacterial Overgrowth. Current Infectious Disease Reports, 26(11), 227–233. https://doi.org/10.1007/s11908-024-00847-7

  Villanueva-Millan, M. J., Leite, G., Wang, J., Morales, W., Parodi, G., Pimentel, M. L., Barlow, G. M., Mathur, R., Rezaie, A., Sanchez, M., Ayyad, S., Cohrs, D., Chang, C., Rashid, M., Hosseini, A., Fiorentino, A., Weitsman, S., Chuang, B., Chang, B., Pichetshote, N., … Pimentel, M. (2022). Methanogens and Hydrogen Sulfide Producing Bacteria Guide Distinct Gut Microbe Profiles and Irritable Bowel Syndrome Subtypes. The American journal of gastroenterology, 117(12), 2055–2066. https://doi.org/10.14309/ajg.0000000000001997

  Liébana-Castillo, A. R., Redondo-Cuevas, L., Nicolás, Á., Martín-Carbonell, V., Sanchis, L., Olivares, A., Grau, F., Ynfante, M., Colmenares, M., Molina, M. L., Lorente, J. R., Tomás, H., Moreno, N., Garayoa, A., Jaén, M., Mora, M., Gonzalvo, J., Molés, J. R., Díaz, S., … Cortés-Rizo, X.. (2025). Should We Treat SIBO Patients? Impact on Quality of Life and Response to Comprehensive Treatment: A Real-World Clinical Practice Study. Nutrients, 17(7), 1251. https://doi.org/10.3390/nu17071251

  Martyniak, A., Wójcicka, M., Rogatko, I., Piskorz, T., & Tomasik, P. J. (2025). A Comprehensive Review of the Usefulness of Prebiotics, Probiotics, and Postbiotics in the Diagnosis and Treatment of Small Intestine Bacterial Overgrowth. Microorganisms, 13(1), 57. https://doi.org/10.3390/microorganisms13010057

Frequently Asked Questions

• Q: How do I know if I have SIBO or just IBS?

  A: SIBO and IBS share many overlapping symptoms, including bloating, gas, abdominal pain, and altered bowel habits. In fact, research shows a significant subset of IBS patients actually have SIBO as the underlying cause. The key difference is that SIBO can be diagnosed through breath testing that measures hydrogen, methane, and hydrogen sulphide gases produced by bacterial overgrowth in the small intestine. Without proper SIBO testing, you may be managing symptoms without addressing the root cause. Book a free discovery session to discuss whether SIBO breath testing is appropriate for your symptoms.

• Q: What are the best natural treatmen for SIBO

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• Q: Can diet alone cure SIBO?

  A: While diet plays a crucial role in managing SIBO symptoms and preventing recurrence, diet alone rarely eradicates the bacterial overgrowth. Restrictive diets like low FODMAP, specific carbohydrate diet, or bi-phasic approaches can reduce symptoms by limiting fermentable substrates that feed bacteria, but they don't typically eliminate the overgrowth itself. The exception is the elemental diet—a complete liquid formula that has shown 75-100% cure rates in studies. Most successful SIBO treatment protocols combine dietary modifications with antimicrobial therapy (herbal or pharmaceutical), probiotics, and strategies to address underlying causes like impaired gut motility or low stomach acid. Book a free discovery session to explore a comprehensive treatment plan tailored to your needs.

• Q: What causes SIBO and why does it keep coming back?

  A: SIBO develops when protective mechanisms fail, allowing bacteria to accumulate in the small intestine. Common underlying causes include: impaired gut motility (from hypothyroidism, diabetes, or medications), low stomach acid (often from proton pump inhibitors or aging), structural abnormalities (diverticula, strictures, adhesions), ileocecal valve dysfunction, antibiotic use and weakened immunity. SIBO recurrence is common—up to 40-50% within one year—because treating the overgrowth without addressing root causes allows bacteria to proliferate again. Successful long-term management requires identifying and correcting your specific underlying factors, along with appropriate maintenance strategies, including natural prokinetics, meal spacing, and gradual dietary expansion to support healthy gut microbiome diversity.

• Q: How long does it take to treat SIBO naturally?

  A: It depends.

  Natural SIBO treatment timelines vary based on severity, subtype, and underlying causes. Most herbal antimicrobial protocols run 4-6 weeks, while elemental diets typically last 2-3 weeks. However, complete SIBO treatment including antimicrobial therapy, dietary modifications, and gut restoration often takes 2-4 months, with some cases requiring longer. Methane-dominant SIBO (IMO) tends to be more treatment-resistant than hydrogen-dominant SIBO. Follow-up testing at 4-6 weeks after treatment completion confirms eradication. Long-term management focusing on underlying causes, gut motility support, and microbiome restoration continues for several months to prevent SIBO recurrence.

  Because treatment is highly individualised, book a free discovery session to discuss realistic timelines and personalised protocols for your situation.

• Q: The best SIBO naturopath treatment, in Melbourne

  The best, SIBO naturopath treatment is one that treats you as a whole person, who might have other health conditions to be considered at the same time.
  
  That’s what we do as naturopaths - we treat the whole person.
  
  Whilst there is no such thing as a naturopath SIBO specialist, there are some naturopaths who have special interests and gut health is mine.
  
  I work online, and so I am near you - wherever you are. In Melbourne, Sydney, Adelaide, Perth, Darwin or Brisbane - and everywhere in between!