What is SIBO? Why Bacteria in the Wrong Place Changes Everything About Your Gut
- Apr 20
- 10 min read
Bloating that builds through the day no matter what you eat. A food tolerance picture that keeps changing. Fatigue that sleep does not touch. Digestive discomfort that has become so normal you have stopped mentioning it to your doctor.
If this sounds familiar, I want to introduce you to a condition that is far more common than most people realise, and that frequently goes undiagnosed for years.
It is called SIBO. Small intestinal bacterial overgrowth. And while the name sounds technical, what it describes is actually straightforward: bacteria that belong in your large intestine have migrated into and colonised your small intestine, where they do not belong and where their presence causes a cascade of problems that extend well beyond the gut.
Understanding why bacteria end up in the wrong place, what they do when they get there, and what it takes to address it properly is where I want to start. Because SIBO is not just a gut problem. It is a whole-body problem. And it is one that is genuinely addressable when approached correctly.
SIBO occurs when bacteria that belong in the large intestine migrate into the small intestine. The result is not just bloating. It is a cascade of systemic effects that most people, and many practitioners, do not connect to their gut.
Understanding the Geography
Your digestive tract is not a uniform environment. Different sections have very different bacterial populations, and this is intentional. The stomach and small intestine are meant to be relatively low in bacteria, partly maintained by stomach acid, bile, digestive enzymes, and a specialised motility pattern called the migrating motor complex. The large intestine, by contrast, is home to trillions of bacteria and is designed for exactly that.
When bacteria from the large intestine make their way into and establish themselves in the small intestine, the environment changes fundamentally. The small intestine is where the majority of nutrient absorption takes place. It is not equipped to handle large bacterial colonies fermenting food as it arrives. When it has to, the results are predictable.
A 2023 epidemiological review published in World Journal of Gastroenterology found that SIBO is detected in 33.8% of patients with gastrointestinal complaints who undergo breath testing, making it a significant finding in symptomatic populations. The review also noted that among patients with irritable bowel syndrome, prevalence estimates from breath testing range from 30% to 85% depending on the study population, suggesting substantial overlap between IBS diagnoses and undetected SIBO (Efremova et al., World Journal of Gastroenterology, 2023).
These numbers suggest that a significant proportion of people who have been told they have IBS, or whose digestive symptoms have never been fully explained, may in fact, have SIBO.
What SIBO Actually Does
When bacteria ferment food in the small intestine, they produce gas, primarily hydrogen and methane, depending on the type of bacteria involved. This fermentation happens rapidly, often within an hour or two of eating, which is why SIBO bloating tends to be progressive across the day rather than appearing only after specific foods.
The gas produced causes distension, pressure, pain, and altered motility, which can manifest as diarrhoea, constipation, or an unpredictable combination of both. The pattern varies depending on whether hydrogen-producing or methane-producing bacteria are dominant, and this distinction matters both for understanding symptoms and for treatment.
But the effects of SIBO do not stop at gas and bloating. Bacterial overgrowth in the small intestine disrupts nutrient absorption directly. The bacteria compete with the host for nutrients, particularly vitamin B12, fat-soluble vitamins, and iron. This is why fatigue, anaemia, and nutritional deficiencies are common in SIBO presentations that have been present for some time.
The bacterial presence also drives intestinal inflammation, which over time compromises the integrity of the intestinal lining. This is the mechanism behind increased intestinal permeability, commonly referred to as leaky gut, which allows bacterial byproducts and partially digested food particles to enter the bloodstream and drive systemic inflammation.
From here, the effects of SIBO reach the brain via the gut-brain axis, contributing to cognitive symptoms, mood changes, and anxiety that many women with SIBO experience but rarely connect to their digestive picture.
Why Food Intolerances Keep Changing
One of the most diagnostically useful features of SIBO, and one of the most frustrating for those living with it, is the changing nature of food reactions.
In true food allergy, the immune system reacts to a specific food protein in a consistent, predictable way. The same food causes the same reaction, every time. But in SIBO, the problem is not the food. It is the bacterial environment reacting to the food. And because that environment changes over time, the reactivity changes with it.
Foods high in fermentable carbohydrates, the FODMAP foods, tend to cause the most significant reactions because they provide the most substrate for bacterial fermentation. But almost any food can become problematic when the bacterial load is high enough. This is why some women with SIBO find themselves progressively eliminating more and more foods in search of safe options, only to find that the list of safe foods keeps shrinking.
This is an important clinical distinction. Eliminating foods addresses the symptom but not the cause. SIBO requires the bacterial environment to be addressed directly.
Why Does SIBO Develop?
SIBO is not bad luck. It develops when the mechanisms that normally prevent bacterial migration and overgrowth in the small intestine are compromised. Understanding which of these mechanisms is impaired in an individual case is essential, because SIBO has a high recurrence rate when the underlying cause is not addressed alongside treatment. Some of these include:
• The migrating motor complex (MMC). This is the gut's internal cleaning mechanism, a series of electrical waves that sweep through the small intestine during fasting periods to push bacteria, food residue, and debris toward the large intestine. The MMC only operates when the gut is not actively digesting, which is why constant snacking, eating very close together, or conditions that impair gut motility disrupt this critical housekeeping function.
• Stomach acid. Adequate gastric acid is a primary defence against bacterial overgrowth. Acid kills bacteria before they can establish in the small intestine. Long-term use of proton pump inhibitors (PPIs), low stomach acid associated with ageing or chronic stress, and H. pylori infection all compromise this protection.
• Previous gut infection. Gastroenteritis, food poisoning, and other gut infections can damage the interstitial cells of Cajal, the pacemaker cells of the gut responsible for MMC function. Post-infectious SIBO is a well-established phenomenon and one reason why gut symptoms that begin after a stomach bug or bouts of food poisoning deserve investigation.
• Thyroid dysfunction. The thyroid regulates gut motility. Hypothyroidism, including subclinical presentations, slows transit throughout the digestive tract and is a recognised risk factor for SIBO.
• Structural changes. Altered anatomy from abdominal surgery, adhesions, or a dysfunctional ileocecal valve, the valve between the small and large intestine, can predispose to SIBO by allowing bacterial backflow or impairing transit.
• Chronic stress. The gut-brain axis runs in both directions. Chronic psychological and physiological stress disrupts gut motility via the autonomic nervous system, reducing MMC function and altering the gut environment in ways that favour bacterial overgrowth. A 2024 population-based study published in PMC analysed over 1.6 million COVID-19 patients and found a significantly increased risk of SIBO diagnosis in the 12 months following COVID-19 infection across all adult age groups. The risk was progressive over time, becoming distinctly significant by 6 months and highest at 12 months post-infection. This finding suggests that post-viral gut motility disruption may be an important emerging driver of SIBO presentations in the current clinical landscape (PMC, 2024).
How is SIBO Diagnosed and Treated?
SIBO is diagnosed via a breath test, a simple and non-invasive test that measures hydrogen and methane gas produced by bacterial fermentation in the small intestine following ingestion of a specific sugar substrate. The pattern of gas production across the test indicates the type and location of bacterial overgrowth and informs treatment selection.
Treatment for SIBO involves three parallel tracks. First, reducing the bacterial load through targeted antimicrobial therapy. Second, supporting gut motility so that the MMC can resume its housekeeping function and prevent rapid bacterial recolonisation. Third, addressing the underlying cause, whether that is low stomach acid, thyroid dysfunction, chronic stress, dietary habits that impair the MMC, or structural factors.
Without addressing the underlying cause, SIBO recurrence rates are high. This is one of the most common points of failure in self-directed treatment approaches. Alongside active treatment, dietary modifications are often used to reduce bacterial substrate and symptom load during the treatment phase. These are typically temporary and structured, not a permanent way of eating, and are followed by a careful and supported reintroduction process.
"SIBO is one of the conditions I find most satisfying to work with because the outcomes when it is approached comprehensively are often significant. Women who have been managing bloating, fatigue, and an ever-shrinking list of safe foods for years often see substantial improvement when we identify and address the full picture. The key is treating the bacterial overgrowth and the reason it developed in the first place. Without both, you are fighting the same battle repeatedly. With both, the results tend to be lasting." - Gemma Knaap, Naturopath (BHSc Naturopathy, Certified Natural Fertility Educator, Gut Microbiome Analyst) | Southernwood Apothecary & Clinic | Albany, WA | Telehealth across Australia
SIBO Beyond the Digestive System
Because SIBO drives systemic inflammation, nutrient depletion, and gut-brain axis disruption, its effects are felt well beyond the gut. It is worth naming some of the less obvious presentations, because they are frequently investigated in isolation without the digestive connection being made. These include:
• Brain fog and cognitive difficulty, driven by systemic inflammation and the gut-brain axis.
• Fatigue, from nutritional deficiencies, particularly B12 and iron, and from the inflammatory load.
• Mood changes and anxiety, via the gut-brain axis and the influence of gut bacteria on neurotransmitter production.
• Skin conditions, including rosacea and eczema, which have a documented association with SIBO in the research literature.
• Joint pain, driven by systemic inflammation from intestinal permeability.
• Restless legs syndrome, which has been associated with iron deficiency secondary to SIBO.
If you have been managing a cluster of symptoms across different body systems without a unifying explanation, the gut is always worth investigating.
Putting It All Together
SIBO is one of those conditions that makes an enormous amount of sense once you understand the mechanism. The bloating that builds through the day. The food reactions that keep shifting. The fatigue that has no obvious explanation. The brain fog that nobody has been able to account for. When you understand that bacteria in the wrong place can drive all of this and more, the picture that felt fragmented and confusing starts to come together.
What I want you to take from this piece is that SIBO is not a life sentence and it is not something you have to manage indefinitely through an ever-shrinking list of safe foods. It is a structural and microbiological problem with a clear investigative pathway and a treatment approach that, when done properly and completely, produces real and lasting results.
The key word is completely. Treating the bacterial overgrowth without identifying and addressing why it developed is the most common reason people find themselves back at square one six months later. A comprehensive approach looks at the full picture, the bacteria, the motility, the underlying drivers, and the gut environment that needs to be rebuilt after treatment.
If you have been living with unexplained digestive symptoms, a diagnosis of IBS that has never fully explained your experience, or a food tolerance picture that keeps getting more complicated, it is worth investigating properly.
I work with women navigating complex gut health presentations via Telehealth across Australia. Consultations are thorough, personalised, and focused on finding and addressing the actual cause rather than managing symptoms indefinitely 🌿
Frequently Asked Questions
What does SIBO feel like?
SIBO typically presents as bloating that builds progressively through the day, often starting relatively flat in the morning and worsening with meals. Other common symptoms include gas, abdominal pain or pressure, diarrhoea, constipation, or an alternating pattern of both, nausea, and a sense of fullness that persists after meals. Beyond the digestive system, fatigue, brain fog, mood changes, and skin conditions are frequently part of the SIBO picture.
How is SIBO tested?
SIBO is diagnosed via a breath test that measures hydrogen and methane gas in exhaled breath following ingestion of a glucose or lactulose substrate. This test can be done at home. The type and timing of gas produced indicates the presence, type, and approximate location of bacterial overgrowth. The test requires a preparation period including dietary restriction and fasting beforehand.
What causes SIBO to keep coming back?
Recurrent SIBO almost always indicates that the underlying cause has not been adequately addressed. The most common reasons for recurrence include impaired migrating motor complex function, low stomach acid, unaddressed thyroid dysfunction, chronic stress disrupting gut motility, structural factors such as a dysfunctional ileocecal valve, and returning to dietary patterns that impair the MMC. A comprehensive treatment approach identifies and addresses the specific underlying factors for the individual, not just the bacterial overgrowth itself.
Can SIBO cause fatigue?
Yes. SIBO causes fatigue through several mechanisms. Bacterial competition for nutrients in the small intestine leads to deficiencies in vitamin B12, iron, and fat-soluble vitamins, all of which are essential for energy production. The systemic inflammation driven by intestinal permeability adds to fatigue. The broader effects of dysbiosis affect mood, motivation, and cognitive function via the gut-brain axis, and this tends to compound the physical exhaustion.
What is the connection between IBS and SIBO?
A substantial proportion of IBS diagnoses may represent undetected SIBO. Research has found positive breath test results consistent with SIBO in 30% to 85% of IBS patients depending on the study population. IBS is a symptom-based diagnosis, meaning it describes a pattern of symptoms without identifying an underlying cause. SIBO is a structural and microbiological cause that can produce exactly the IBS symptom pattern. Where SIBO is identified and treated in someone with an IBS diagnosis, symptom improvement is often significant.
Can a naturopath treat SIBO?
A naturopath can support SIBO investigation and treatment comprehensively, and is often more likely to do so than conventional medical doctors. This includes recommending appropriate breath testing, using herbal antimicrobial protocols alongside gut motility support, addressing the underlying causes of bacterial overgrowth, managing dietary modification during the treatment phase, and supporting the reestablishment of a healthy gut environment after treatment. Professional guidance is important in SIBO management because the treatment approach depends on the type of overgrowth, the underlying drivers, and the individual's overall health context.
References
Efremova, I. et al. (2023). Epidemiology of small intestinal bacterial overgrowth. World Journal of Gastroenterology, 29(22), 3400-3421. https://doi.org/10.3748/wjg.v29.i22.3400
Bushyhead, D. and Quigley, E.M.M. (2022). Small Intestinal Bacterial Overgrowth: Pathophysiology and Its Implications for Definition and Management. Gastroenterology, 163(3), 593-607. https://doi.org/10.1053/j.gastro.2022.04.002
Pimentel, M. et al. (2020). ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. American Journal of Gastroenterology, 115, 165-178. https://doi.org/10.14309/ajg.0000000000000501
PMC. (2024). Progressive Increase in Small Intestinal Bacterial Overgrowth Risk Following COVID-19 Infection: A Global Population-Based Study. https://pmc.ncbi.nlm.nih.gov/articles/PMC12469215/
Shah, A. et al. (2024). Prevalence of SIBO in patients with gastrointestinal symptoms. Journal of Gastroenterology and Hepatology, 39(11), 2308-2318. https://doi.org/10.1111/jgh.16668
NCBI Bookshelf / StatPearls. (2023). Small Intestinal Bacterial Overgrowth. https://www.ncbi.nlm.nih.gov/books/NBK546634/
Tags: SIBO, small intestinal bacterial overgrowth, bloating, gut health, IBS, food intolerances, naturopath, women's health, gut-brain axis, telehealth, Albany WA
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