What Is SIBO?
SIBO stands for small intestinal bacterial overgrowth — and if you've been struggling with bloating, erratic bowel habits, and symptoms that seem to get worse no matter what you eat, it's worth knowing about.
In my clinic, SIBO is one of the most common root causes I find underlying IBS. Research suggests that up to half of people diagnosed with IBS have SIBO when properly tested — yet it's still frequently missed or misdiagnosed.
So what is it, exactly?
SIBO occurs when bacteria that normally live in your large intestine migrate up and establish themselves in your small intestine — in numbers they shouldn't be. It's not about bad bacteria doing bad things; it's about the bowel bacteria in the wrong place.
Your small intestine should be a relatively quiet environment — it's where nutrients are absorbed, and it needs to stay clean enough to do that job properly. The large intestine, by contrast, is a fermentation factory with an enormous bacterial population that helps break down fibre and waste. When large intestinal bacteria end up in the small intestine, the fermentation process starts happening in the wrong place — and that's where the symptoms begin.
Why Does Location Matter So Much?
The small intestine contains roughly 10³ to 10⁵ bacteria per millilitre of content — a relatively sparse population. The large intestine can contain up to 10¹¹ to 10¹² bacteria per millilitre. That's a difference of several orders of magnitude.
When bacteria colonise the small intestine in excessive numbers, they start competing with you for your food — particularly carbohydrates and sugars. They ferment these foods and produce gas. And unlike the large intestine, which is designed to handle fermentation, the small intestine isn't built for it.
Types of SIBO: Hydrogen, Methane (IMO) and Hydrogen Sulfide
Not all SIBO is the same, and the type of gas being produced matters — both for your symptoms and for how it's treated.
Hydrogen-dominant SIBO is the most common type. Hydrogen gas is produced by bacteria fermenting carbohydrates in the small intestine. It tends to be associated with diarrhoea-predominant symptoms.
Methane — or more accurately, IMO (Intestinal Methanogen Overgrowth) is worth understanding correctly. Methane is produced not by bacteria but by single-celled organisms called archaea — specifically Methanobrevibacter smithii. This is why the condition has been renamed IMO. Methane slows gut motility, which is why IMO tends to be associated with constipation and bloating that is slow to shift.
Hydrogen sulfide (ISO — Intestinal Sulfide Overproduction) is a third type that's now recognised and worth knowing about. Hydrogen sulfide is produced by sulfur-metabolising bacteria — such as Bilophila wadsworthia and Desulfovibrio species — and can contribute to diarrhoea, urgency, and that characteristic "rotten egg" smell.
The hydrogen sulfide breath test isn't currently available in Australia, so when I suspect ISO in a client, I use a comprehensive stool test to look for overgrowths in these sulfur-metabolising strains. If your hydrogen and methane results come back normal but you're still symptomatic, this is often the next piece to investigate.
Many people have a combination of gas types, which is why testing matters.
How These Gases Cause Your Symptoms
The excess gas produced by bacterial fermentation is the direct cause of most SIBO symptoms. The bloating, the distension, the cramping — that's fermentation happening in a place it shouldn't.
Beyond the immediate discomfort, there's a deeper layer of damage that explains why SIBO creates such wide-ranging symptoms:
Damage to the intestinal lining. The microvilli — tiny finger-like projections that line your small intestine and absorb nutrients — become damaged by ongoing bacterial activity and inflammation. This contributes to leaky gut (intestinal hyperpermeability), where the gut wall becomes more porous than it should be.
Malabsorption. When the microvilli are compromised, you absorb nutrients less efficiently. This is why people with longstanding SIBO often develop deficiencies in B12, iron, and fat-soluble vitamins like A, D, E and K.
MMC disruption. The migrating motor complex (MMC) is your gut's housekeeper — a wave of muscular contractions that sweeps through the small intestine between meals, clearing debris and bacteria. SIBO can impair the MMC, and a damaged MMC makes SIBO worse. Stress and eating too frequently also interrupt this cleaning wave, which is why grazing between meals often makes SIBO symptoms worse.
Systemic effects. When the gut barrier becomes leaky, undigested food particles and bacterial byproducts cross into the bloodstream. Depending on your individual susceptibilities, this can drive symptoms far beyond the gut — joint pain, skin flares, brain fog, headaches, and fatigue.
SIBO Symptoms
People with SIBO typically experience some combination of:
- Bloating and abdominal distension (often worse as the day goes on)
- Excess gas — flatulence and/or burping
- Cramping or abdominal discomfort
- Constipation and/or diarrhoea (or alternating between the two)
- Symptoms that worsen with fibre, beans, onion, garlic, or starchy foods
- Indigestion and nausea
- Fatigue
Beyond the digestive system, SIBO may also contribute to:
- Reflux / GORD
- Headaches and migraines
- Food intolerances that seem to be expanding over time
- Nutritional deficiencies (B12, iron, vitamin D)
- Low mood and brain fog
- Skin conditions — eczema, rosacea, breakouts
- Joint pain
- Hormonal imbalance
The longer SIBO has been present, the more likely it is that food intolerances will expand — because the gut lining has had more time to become compromised. If you're finding that your list of "safe foods" is shrinking, that's a sign the underlying issue needs addressing, not just managing.
How Common Is SIBO?
SIBO is more common than most GPs realise. Research and clinical experience consistently show a strong connection between SIBO and IBS — current meta-analyses suggest that approximately one-third to over half of people with IBS test positive for SIBO, depending on the diagnostic method used. It's considered significantly under-diagnosed because mild cases may have few obvious symptoms, and moderate cases overlap considerably with other gut conditions.
What Causes SIBO?
There's rarely a single cause — for most people, SIBO develops from a combination of factors that reduce the gut's ability to keep bacteria in their proper place. Understanding your contributing factors is essential for preventing it from coming back.
Triggers and risk factors include:
- Post-infectious gut dysmotility — a bout of food poisoning or gastroenteritis is one of the most common triggering events. The bacteria C. jejuni can trigger an autoimmune response that damages the MMC.
- Chronic stress — lowers stomach acid and impairs the MMC, both of which allow bacteria to overgrow
- Low stomach acid (hypochlorhydria) — including from H. pylori infection or prolonged use of proton pump inhibitors (PPIs) or antacids
- Abdominal surgery — appendectomy, hysterectomy, or any surgery that causes adhesions can alter gut motility and structure
- Hypothyroidism and poor blood sugar regulation — both slow gut transit and predispose to overgrowth
- Underlying gut conditions — coeliac disease (especially if not fully resolving on a gluten-free diet), Crohn's disease, and ulcerative colitis all increase risk
- Ileocecal valve dysfunction — this valve between the small and large intestine acts as a barrier; if it's not closing properly, bacteria can migrate upward
- Certain medications — antibiotics (which alter the microbiome), narcotics (which slow motility), and the oral contraceptive pill
- Gastroparesis — delayed stomach emptying creates an environment that encourages bacterial overgrowth
- Structural issues — small bowel diverticulosis, adhesions, or previous gastric bypass surgery
- Diet — a diet high in processed foods, refined carbohydrates, and excess sugar provides an ideal food source for bacterial overgrowth
- Alcohol — even moderate intake has been associated with changes in gut motility and bacterial populations relevant to SIBO
- Herbicide exposure — glyphosate has been shown to have antimicrobial properties that may selectively affect gut bacteria; while the direct link to SIBO in humans is still emerging, it's a consideration worth noting for people with high dietary exposure
Is SIBO Contagious?
No — SIBO is not contagious and cannot be passed from one person to another. The bacteria involved are your own naturally occurring gut bacteria that have migrated where they shouldn't be. Unlike a bacterial infection caused by an external pathogen, SIBO is an internal imbalance. The environment in your gut — your motility, stomach acid levels, immune function, and anatomy — is what creates the conditions for it to develop. Addressing those underlying factors is the key to lasting resolution.
What Foods Trigger SIBO Symptoms?
Food isn't the cause of SIBO — but it absolutely affects how severe your symptoms are while SIBO is present. Certain foods feed the bacteria and make the fermentation (and therefore the gas) worse:
- High FODMAP foods (fermentable carbohydrates like onion, garlic, apple, wheat, legumes)
- Sugar alcohols (xylitol, sorbitol, mannitol — common in "diet" products)
- Lactose in dairy products
- Fructose (including large amounts of fruit)
- Starchy carbohydrates like bread, pasta, rice, potatoes
This is why people with SIBO often feel better when they reduce these foods — but dietary restriction alone isn't treatment. It manages symptoms without addressing the underlying overgrowth.
Testing for SIBO
The standard way to test for SIBO is with a breath test. It's non-invasive, simple to do at home, and gives us a lot of useful information.
You'll prepare with a one-day dietary preparation and then drink a test substrate (lactulose, glucose or both). You collect breath samples every 20 minutes over 2–3 hours. The test measures the hydrogen and methane gas in your breath — gases produced by bacteria, not by your own metabolism.
The results tell us:
- Whether SIBO is present
- Approximately where in the small intestine the overgrowth is located
- Which gas type is being produced (hydrogen, methane/IMO)
What if the breath test comes back negative but symptoms persist? This is where hydrogen sulfide comes in. Hydrogen sulfide isn't detectable on a standard breath test, and the specialised H2S breath test isn't currently available in Australia.
Instead, when I suspect hydrogen sulfide is a factor, I use a comprehensive stool test to look for overgrowths of sulfur-metabolising bacteria — organisms like Bilophila wadsworthia, Desulfovibrio species, and Fusobacterium. Elevated levels of these bacteria, combined with the right symptom picture (diarrhoea, urgency, that distinctive rotten egg smell), give us enough to work with clinically.
Blood tests can't diagnose SIBO directly, but they're a valuable part of the picture — checking for nutritional deficiencies (particularly B12, iron, and vitamin D), thyroid function, and inflammatory markers.
SIBO Treatment: A Multi-Step Approach
There's no single pill that fixes SIBO — and this is where a lot of people get frustrated if they've only been offered a short antibiotic course. Effective treatment requires addressing the overgrowth and the conditions that allowed it to develop in the first place. Without the latter, relapse rates are high.
Here's how I approach it with clients:
1. Stop Fuelling the Fire
Reduce the foods that feed bacterial overgrowth — either with an elimination diet, a low-FODMAP approach, the Bi-Phasic SIBO diet, or in some cases, an elemental diet. This doesn't cure SIBO, but it reduces symptoms and slows the overgrowth while we work on the root causes.
2. Test to Confirm
Breath testing confirms SIBO is present, identifies the gas type, and helps determine where in the small intestine the overgrowth is occurring. Testing takes the guesswork out of treatment.
3. Targeted Antimicrobials
Based on your test results and clinical picture, we use either herbal antimicrobials (such as oregano oil, allicin, berberine, or neem — at the indicated dose chosen specifically for the gas type present). The protocol is tailored — hydrogen and methane/IMO require different approaches.
4. Address Motility and Stress
Restoring proper gut motility is essential. Prokinetics (herbal or pharmaceutical) support the MMC in doing its job. Addressing stress — which directly suppresses stomach acid and the MMC — is equally important. This might look like targeted nervous system support, sleep improvements, or simply changing meal frequency.
5. Heal the Gut Lining
Once the overgrowth is reduced, we focus on repairing the gut lining — reducing intestinal permeability, calming inflammation, and beginning to reintroduce foods.
6. Rebalance the Microbiome
Restoring a healthy microbial community in the large intestine reduces the risk of relapse and improves long-term gut resilience. This phase involves targeted probiotics and prebiotic foods, tailored to what your gut needs.
7. Address the Root Cause
This is the most important step for preventing recurrence. Is it low stomach acid? Hypothyroidism? An ileocecal valve issue? Post-infectious MMC damage? Identifying and correcting the underlying driver is what makes the difference between one round of treatment and a lasting resolution.
Is SIBO Linked to Other Health Conditions?
Yes — SIBO has been associated with a number of conditions that can either contribute to it or be worsened by it:
Irritable Bowel Syndrome (IBS), Inflammatory Bowel Disease (Crohn's and ulcerative colitis), coeliac disease (particularly in those not responding to a gluten-free diet), type 2 diabetes (where autonomic neuropathy affects gut motility), gastroparesis, chronic pancreatitis, scleroderma and other connective tissue conditions, hypochlorhydria, and previous abdominal surgery.
Having one of these conditions doesn't mean you'll develop SIBO — but it does raise your risk and makes testing a worthwhile investigation.
Working With a SIBO Specialist
After 16 years working with gut health clients, the thing I see most consistently is this: people who've been told "it's just IBS" have often had undiagnosed SIBO for years. They've tried elimination diets, probiotics, and fibre supplements — and nothing has stuck because the root cause hasn't been addressed.
SIBO is treatable. Most of my clients see significant improvement within a few weeks when we follow the right steps in the right order.
If you're experiencing symptoms that sound familiar here — especially bloating that gets worse through the day, unpredictable bowel habits, and foods that used to be fine that are now a problem — it's worth looking into.
Book a Free Gut Fix Strategy Session
If you'd like to understand whether SIBO could be at the root of your symptoms, I'd love to help you work it out. In a free Gut Fix Strategy Session, we'll go through your symptoms and history and I'll walk you through the testing and treatment options that make sense for your situation.
Book your free Gut Fix Strategy Session here
Or call 1300 16 75 72 — leave a message with reception and I'll call you back.
References
- Ford AC, et al. "Small Intestinal Bacterial Overgrowth in Irritable Bowel Syndrome: Systematic Review and Meta-Analysis." Clinical Gastroenterology and Hepatology, 2009. PubMed
- Pimentel M, et al. "ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth." American Journal of Gastroenterology, 2020.
- Rezaie A, et al. "Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders." American Journal of Gastroenterology, 2017. DOI: 10.1038/ajg.2017.138
- Pimentel M, et al. "Methane and the Gastrointestinal Tract." Digestive Diseases and Sciences, 2013. DOI: 10.1007/s10620-013-2581-2
- Rao SSC, Bhagatwala J. "Small Intestinal Bacterial Overgrowth: Clinical Features and Therapeutic Management." Clinical and Translational Gastroenterology, 2019.
- Mayo Clinic. "Small Intestinal Bacterial Overgrowth (SIBO)." mayoclinic.org
