Is Your ‘IBS’ Actually SIBO?
Written by Jessica Diakoumakos, Naturopath (BHSc Naturopathy) · Emba Wellness, Melbourne · Updated 16.04.2026
IBS (Irritable Bowel Syndrome) is a functional diagnosis — it describes symptoms rather than their cause. Research suggests that up to 80% of people diagnosed with IBS may actually have SIBO (Small Intestinal Bacterial Overgrowth), a condition caused by an excessive amount of bacteria in the small intestine. SIBO is diagnosed through a lactulose breath test measuring hydrogen and methane gas, and is treatable with a root-cause naturopathic approach including herbal medicine, targeted dietary changes, and probiotic therapy.
Struggling with bloating, unpredictable digestion, and the classic "IBS" label — but not getting any real answers?
You're not alone. And more importantly, you're not imagining it.
The problem isn't that your gut is broken beyond explanation. The problem is that IBS isn't actually a diagnosis — it's a description. It tells you what is happening, but not why. And in my experience, "why" is exactly what most people with persistent gut symptoms have never been properly asked.
One of the most common answers I find when we start investigating — through testing, clinical assessment, and a functional lens — is SIBO.
What Is IBS — and Why It's Not Enough of an Answer
IBS (Irritable Bowel Syndrome) affects approximately 11% of the global population, making it one of the most commonly diagnosed gastrointestinal conditions worldwide (Lovell & Ford, 2012). Symptoms include bloating, abdominal pain, diarrhoea, constipation, or a combination of both.
But IBS is what's called a functional diagnosis — a label applied to a cluster of symptoms when no structural abnormality is found on standard testing. A normal colonoscopy, normal blood tests, and normal imaging can all coexist with significant, daily gut symptoms. This is not because the symptoms aren't real. It's because the tools used to rule out serious disease aren't designed to identify the functional and microbial drivers that are often responsible.
IBS tells you what your gut is doing. It doesn't tell you what's causing it.
What Is SIBO?
SIBO stands for Small Intestinal Bacterial Overgrowth. It refers to an excessive proliferation of bacteria in the small intestine — a part of the digestive tract that should contain relatively few bacteria compared to the colon.
When bacteria migrate into or proliferate in the small intestine, they begin fermenting carbohydrates that would normally be absorbed further down the digestive tract. This fermentation produces gas — hydrogen, methane, or hydrogen sulfide — which causes the classic SIBO symptom picture:
Bloating — typically worsening throughout the day and after meals
Abdominal discomfort or cramping
Diarrhoea, constipation, or alternating between both
Excessive gas and flatulence
Nausea or early satiety
Brain fog and fatigue — driven by bacterial toxins and gut-brain axis disruption
Research shows that up to 80% of people diagnosed with IBS may actually have underlying SIBO — a staggering overlap that has significant implications for how these conditions are treated (Ghoshal et al., 2020; Pimentel et al., 2003). A 2003 study by Pimentel et al. in The American Journal of Gastroenterology found that normalising lactulose breath test results — indicating resolution of SIBO — was directly correlated with improvement in IBS symptoms. In other words, when the SIBO resolved, so did the IBS.
“IBS is not a life sentence — it’s often a sign that something specific is going on in the gut that hasn’t been properly investigated yet.”
The Three Types of SIBO — and Why It Matters
Not all SIBO is the same. There are three distinct types, each producing different gases and presenting with different symptom patterns — and each requiring a different treatment approach.
Hydrogen-Dominant SIBO
Hydrogen-producing bacteria are typically associated with diarrhoea-predominantsymptoms. Hydrogen gas speeds up gut motility, which is why people with hydrogen SIBO often experience loose or urgent stools, cramping, and frequent bowel movements. Treatment protocols targeting hydrogen-dominant SIBO focus on reducing hydrogen-producing bacterial species while supporting motility and gut lining integrity.
Methane-Dominant SIBO
(IMO — Intestinal Methanogen Overgrowth) Methane is produced not by bacteria but by archaea — a distinct category of microorganism. Methane gas slows gut motility, which is why methane-dominant presentations are typically associated with constipation, bloating, and a feeling of incomplete evacuation. Because archaea are not technically bacteria, standard antibiotic protocols are often less effective for IMO — treatment requires a different approach targeting these methane-producing organisms specifically.
Hydrogen Sulfide SIBO
Hydrogen sulfide-producing bacteria produce a gas associated with the characteristic rotten egg smell, sulfuric flatulence, and a mixed or unpredictable symptom picture. Hydrogen sulfide SIBO is the least well understood of the three types and can be more difficult to identify on standard breath testing — some specialist labs offer specific hydrogen sulfide testing where standard breath tests may not capture it clearly.
You can have more than one type simultaneously — which is why breath test interpretation and a clinically informed treatment protocol matters far more than a generic "gut protocol."
How SIBO Is Diagnosed
SIBO is diagnosed through a lactulose breath test — a non-invasive test that measures the hydrogen and methane gases produced by bacteria in the small intestine as they ferment a solution of lactulose.
The test involves:
Preparing with a specific low-fermentation diet the day before
Fasting overnight before the test
Drinking a lactulose solution in the morning
Collecting breath samples at regular intervals over two to three hours
The results show the pattern and timing of gas production — which tells us not just whether SIBO is present, but which type and how far into the small intestine the overgrowth is occurring.
Test kits are shipped directly to your home anywhere in Australia and returned by post — no clinic visit required. Results are interpreted in full during your consultation.
A positive breath test, interpreted in the context of your symptoms and clinical history, allows for a precise, targeted treatment plan rather than a generic approach.
What a Naturopathic Approach to SIBO Looks Like
In clinic, SIBO is one of the conditions I see most frequently — often in clients who have been managing "IBS" for years without ever having proper testing. The key is accurate diagnosis first. Without knowing which type of SIBO is present, treatment is guesswork. Once we have breath test results, the protocol becomes precise — and that precision is what makes the difference between another round of gut supplements that don't work and a treatment plan that actually resolves the overgrowth.
Something I want to be upfront about: my approach to SIBO is more conservative than what you'll read in a lot of naturopathic SIBO content online. I don't go straight to herbal antimicrobials as a first step. Here's why.
Herbal antimicrobials — oregano oil, berberine, allicin, neem — are effective at reducing bacterial overgrowth, but they are not selective. They can't distinguish between the bacteria that shouldn't be in your small intestine and the beneficial species that are critical to your gut ecosystem. For someone who already has a fragile, depleted microbiome — which many people with long-standing gut symptoms do — leading with aggressive antimicrobial therapy can cause more disruption than it resolves.
My preference is to start by creating conditions in the gut where beneficial bacteria can thrive and pathogenic overgrowth is less likely to take hold, before considering anything more targeted. This approach takes longer, but it tends to produce more durable outcomes and is considerably gentler on a gut that's already under strain.
Step 1 — Prepare the Terrain
Before any antimicrobial intervention, I focus on supporting the foundational conditions for gut health — stomach acid adequacy, digestive enzyme support, and gut motility. The migrating motor complex (MMC) — the wave-like contractions that sweep the small intestine clean between meals — is one of the primary mechanisms that prevents bacterial overgrowth from recurring. Many people with SIBO have impaired MMC function, often from chronic stress, previous gut infections, or nervous system dysregulation. Supporting MMC function through meal spacing, prokinetic herbs, and nervous system support creates an environment that's less hospitable to overgrowth before we introduce anything more aggressive.
Step 2 — Address the Root Cause
SIBO doesn't develop in a vacuum. Common underlying contributors include low stomach acid, impaired gut motility, hypothyroidism, adhesions from abdominal surgery, chronic stress, and a history of antibiotic use. A treatment plan that doesn't identify and address these factors risks recurrence — which is one of the most common frustrations for people who've been treated for SIBO before, sometimes multiple times. This is why I spend significant time in the initial consultation understanding what created the conditions for overgrowth in the first place.
Read more about how antibiotics affect your gut microbiome.
Step 3 — Targeted Dietary Support
Dietary modification during SIBO treatment is highly individual and often counterintuitive. What helps one person can worsen another — high-FODMAP foods can feed hydrogen-producing bacteria, while sulfur-containing foods may exacerbate hydrogen sulfide SIBO. At the same time, overly restrictive diets that eliminate too many plant foods can further deplete microbiome diversity, which is the opposite of what we want long-term. I work with clients to find a targeted approach that reduces fermentation load without unnecessarily restricting the dietary diversity that supports a resilient microbiome.
Step 4 — Selective Antimicrobial Support Where Appropriate
Once the terrain has been prepared and root causes addressed, targeted antimicrobial support may be introduced where indicated — but selectively and strategically, not as a blanket first response. The protocol is guided by breath test results, symptom pattern, and how the gut has responded to the preparatory phase. In some cases, particularly for methane-dominant SIBO or IMO, pharmaceutical options may also be discussed in collaboration with your GP.
Step 5 — Microbiome Restoration
The restoration phase is where long-term outcomes are built. Once overgrowth is addressed, rebuilding microbial diversity through evidence-based probiotic therapy, prebiotic fibre, and targeted dietary diversity is essential for preventing recurrence. This is where Microba microbiome profiling can be particularly valuable — confirming the post-treatment picture and guiding what the microbiome actually needs at that stage, rather than applying a generic protocol.
Read more about Microba microbiome testing at Emba Wellness.
Still Bloated After Doing “Everything Right”?
If you've cut out gluten, tried every probiotic on the shelf, followed all the gut health advice online, and still feel like a balloon by 3pm — this might be your sign.
Persistent gut symptoms that haven't responded to dietary changes alone are worth investigating properly. Not because something is seriously wrong — but because there's almost certainly something specific going on that hasn't been identified yet. And once it is, treatment becomes straightforward.
Frequently Asked Questions
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IBS (Irritable Bowel Syndrome) is a functional diagnosis based on symptoms — it describes what the gut is doing but not why. SIBO (Small Intestinal Bacterial Overgrowth) is a specific condition caused by an excessive amount of bacteria in the small intestine, which can be identified through a breath test. Research suggests up to 80% of people diagnosed with IBS may have underlying SIBO. Identifying and treating SIBO, where present, often resolves symptoms that have been managed as IBS without success.
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The only way to confirm SIBO is through breath testing. Symptoms alone cannot reliably distinguish between IBS and SIBO since they significantly overlap — both can cause bloating, abdominal discomfort, irregular bowel habits, and gas. A breath test, interpreted in the context of your clinical history and symptoms, gives a definitive answer and allows for a targeted treatment approach.
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SIBO bloating is typically characterised by progressive worsening throughout the day — often described as feeling relatively flat in the morning and increasingly distended by the afternoon or evening. It is commonly worse after eating and may be accompanied by visible abdominal distension, gas, abdominal discomfort, and a sensation of pressure or fullness. This pattern of worsening throughout the day, particularly after meals, is a key distinguishing feature from other causes of bloating.
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SIBO is unlikely to resolve without treatment in most cases, particularly if the underlying factors contributing to bacterial overgrowth — such as impaired gut motility, low stomach acid, or dietary patterns that feed overgrowth — are not addressed. Without treatment, symptoms typically persist or worsen over time. The good news is that SIBO is highly treatable with the right protocol, and with appropriate root-cause management, long-term remission is achievable.
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SIBO treatment duration varies significantly depending on the type of SIBO, severity of overgrowth, the underlying causes driving it, and how the gut responds at each stage. My approach is staged rather than a single protocol — beginning with terrain preparation and root cause work before introducing more targeted interventions where needed. This means timelines are genuinely individual. As a general guide, the initial phase of treatment typically runs for six to twelve weeks, with a follow-up breath test after the active treatment phase to confirm whether the overgrowth has resolved. Some clients — particularly those with methane-dominant SIBO or IMO, or with a history of recurrent SIBO — require longer support. The restoration phase following successful treatment is equally important for preventing recurrence and is factored into the overall plan from the beginning.
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Yes. Naturopaths can order SIBO breath testing, interpret results, and provide evidence-based treatment through a staged approach — beginning with gut terrain preparation, motility support, and dietary modification before introducing targeted antimicrobial support where indicated. At Emba Wellness, the treatment approach is tailored to the specific type of SIBO identified on testing and the individual's existing gut health. SIBO testing kits are shipped to your home anywhere in Australia and results are interpreted in detail during your consultation. All consultations are available via telehealth Australia-wide.
Ready to Get Some Real Answers?
As a Microbiome Analyst with specific training in gut health and SIBO, I work with clients across Australia to identify what's actually driving their gut symptoms — through SIBO breath testing, Microba microbiome profiling, and comprehensive functional pathology. If you've been told you have IBS but never had proper testing, this is where to start.
Or learn more about SIBO breath testing and gut health testing at Emba Wellness
References
Ghoshal, U. C., Shukla, R., & Ghoshal, U. (2020). Small intestinal bacterial overgrowth and irritable bowel syndrome: A bridge between functional organic dichotomy. Gut and Liver, 11(2), 196–208. https://doi.org/10.5009/gnl16126
Lovell, R. M., & Ford, A. C. (2012). Global prevalence of and risk factors for irritable bowel syndrome: A meta-analysis. Clinical Gastroenterology and Hepatology, 10(7), 712–721. https://doi.org/10.1016/j.cgh.2012.02.029
Pimentel, M., Chow, E. J., & Lin, H. C. (2003). Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome. The American Journal of Gastroenterology, 98(2), 412–419. https://doi.org/10.1111/j.1572-0241.2003.07234.x
