SIBO Explained: Why You Are Bloated No Matter What You Eat
Do you wake up with a flat stomach and end the day looking six months pregnant?
Does bloating build steadily through the day regardless of what you eat? Do you feel fine on an empty stomach but uncomfortable within twenty minutes of eating almost anything? Have you tried cutting out gluten, dairy, sugar, and fibre, only to still feel distended, gassy, or fatigued after meals?
This pattern is one of the most common reasons patients present to our Robina clinic, and it often points toward small intestinal bacterial overgrowth, or SIBO.
SIBO is frequently treated as a simple problem with a simple fix: kill the bacteria, take a probiotic, move on. In practice, it is rarely that straightforward. SIBO is usually a downstream consequence of something else going wrong in the gut. Treating the overgrowth without addressing why it developed is one of the main reasons people relapse within months of finishing treatment.
What is SIBO?
The small intestine is normally home to relatively low numbers of bacteria compared to the large intestine. This design allows nutrients to be absorbed efficiently before food reaches the colon, where the bulk of your microbiome resides.
SIBO occurs when bacteria that normally belong in the large intestine migrate into, or overgrow within, the small intestine. These bacteria ferment carbohydrates before they can be properly digested and absorbed, producing excess gas as a by-product.
Two gases are typically implicated. Hydrogen is associated with loose stools, urgency, and diarrhoea-predominant symptoms. Methane is produced by archaea rather than bacteria and is associated with constipation, slower transit, and bloating that feels heavier and more persistent. Some people produce a mix of both, and a smaller group produce elevated hydrogen sulfide, which is linked to sulphur-smelling gas and a distinct symptom pattern of its own.
Common symptoms of SIBO
← Scroll to see full table
| Pattern | Common symptoms |
|---|---|
| Digestive | Bloating that worsens through the day, abdominal distension, excessive gas, belching |
| Bowel habits | Diarrhoea, constipation, or alternating between the two |
| Post-meal | Discomfort or bloating within 20 to 90 minutes of eating, particularly after carbohydrate-containing meals |
| Nutrient related | Fatigue, low iron, low B12, unexplained weight loss or difficulty gaining weight |
| Systemic | Brain fog, joint aches, skin flare-ups, food reactions that seem to expand over time |
A useful clinical clue is the pattern of distension. Many people with SIBO describe a flat stomach on waking that progressively distends as the day goes on. This differs from bloating that is constant regardless of eating, which points toward other mechanisms.
What causes SIBO?
SIBO is a symptom of an underlying problem, not usually a standalone diagnosis. Several mechanisms allow bacteria to overgrow in the small intestine.
Impaired motility and the migrating motor complex
Between meals the gut runs a cleansing wave called the migrating motor complex, which sweeps residual food and bacteria toward the colon. When this mechanism is damaged or under-functioning — often following food poisoning, a virus, or chronic stress — bacteria are not cleared effectively and can accumulate in the small intestine.
Low stomach acid
Stomach acid is one of the body's main defences against bacterial overgrowth. Long-term use of acid-suppressing medication, chronic stress, or ageing can all reduce acid output and allow more bacteria to survive into the small intestine than would normally be the case.
Structural issues
Adhesions from previous surgery, a slow ileocecal valve, diverticula, or anatomical narrowing can create pockets where bacteria stagnate and multiply rather than moving through to the large intestine as they normally would.
Reduced digestive enzyme or bile output
Bile has antimicrobial properties in the small intestine. Reduced bile flow — often linked to gallbladder issues or sluggish liver function — can allow bacterial overgrowth to establish and persist in an environment that would normally be hostile to it.
Nervous system dysregulation
Digestive motility, stomach acid secretion, and bile release are all under vagal and parasympathetic control. A nervous system stuck in a sympathetic, high-alert state may under-drive these functions, setting the stage for SIBO to develop or return after treatment.
Underlying conditions
Hypothyroidism, connective tissue disorders, diabetes, coeliac disease, and prior abdominal surgery are all recognised risk factors for SIBO. Identifying and addressing these is often a necessary part of a complete treatment approach.
Why treating SIBO alone often fails
This is the piece most patients have not been told.
Antimicrobial herbs, antibiotics such as rifaximin, and elemental diets can all reduce bacterial load and provide genuine symptom relief. Many patients feel significantly better within weeks of starting treatment.
But if the underlying driver (whether that is poor motility, low stomach acid, structural narrowing, or nervous system dysregulation) is never addressed, the small intestine has no reason to stay clear. Recurrence rates after standard SIBO treatment are reported to be high, and repeated rounds of antimicrobials without addressing the root cause can further disrupt the broader microbiome.
This is why a functional medicine approach asks two questions rather than one. What is driving the bacterial overgrowth? And how do we clear it while restoring the mechanisms that are meant to prevent it recurring?
How is SIBO diagnosed?
The most common non-invasive test is a breath test, which measures hydrogen and methane gas after consuming a lactulose or glucose substrate. Elevated gas at specific time points indicates bacterial fermentation occurring earlier in the digestive tract than expected.
Breath testing has limitations and is not perfect in every case, so results are always interpreted alongside symptom history, bowel pattern, prior antibiotic and PPI use, and other functional testing such as stool analysis where relevant.
Does this sound like you?
SIBO symptoms overlap significantly with IBS, which is one reason it is frequently missed or misdiagnosed for years. The pattern of symptoms — particularly when and how bloating occurs — is often more informative than the symptoms themselves.
A flat stomach in the morning that progressively distends through the day, particularly after carbohydrate-containing meals, is a pattern that warrants breath testing. This differs from constant bloating unrelated to food intake, which points toward different underlying mechanisms.
The history is equally important — food poisoning, antibiotic use, chronic PPI use, abdominal surgery, or a prolonged period of high stress often precedes the onset of SIBO symptoms by weeks or months.
Flat in the morning.
Bloated by evening.
A functional medicine approach to SIBO
Confirm and characterise the overgrowth
Breath testing to identify whether the pattern is hydrogen dominant, methane dominant, or mixed, since this shapes the treatment approach and determines which organisms are likely involved.
Reduce the bacterial load
Herbal antimicrobials, elemental diet approaches, or referral for pharmaceutical treatment where appropriate, matched to the individual case and the type of overgrowth identified on testing.
Identify the underlying driver
Assessment of motility, stomach acid function, bile flow, thyroid function, prior abdominal history, and nervous system regulation — because the bacteria came back for a reason and that reason needs to be identified.
Support the terrain during treatment
Appropriate dietary modification during active treatment without defaulting to unnecessary long-term restriction, alongside support for the gut lining and nutrient status where testing indicates deficiency.
Restore the mechanisms that prevent recurrence
This is the step that is most often skipped. Supporting the migrating motor complex with appropriate meal spacing, addressing stomach acid where indicated, and calming a nervous system stuck in high alert are all central to keeping SIBO from returning after treatment.
Reintroduce food diversity
Once symptoms and testing improve, food variety is gradually restored. Long-term restrictive diets can reduce microbiome diversity and are not the end goal — a diverse, resilient microbiome is.
Practical first steps
These points are for general educational purposes and do not replace personalised clinical assessment.
Notice your pattern
Track whether bloating builds through the day, whether it is worse with certain carbohydrates, and whether bowel habits lean toward loose, constipated, or both. The pattern is often more informative than the symptoms alone.
Look at your history
Food poisoning, a course of antibiotics, chronic PPI use, abdominal surgery, or a period of high stress often precedes the onset of SIBO symptoms by weeks or months.
Avoid indefinite restriction
Cutting out FODMAPs or fibre can reduce symptoms short term but is not a diagnosis or a long-term solution on its own. Long-term restriction can reduce microbiome diversity.
Space your meals
Frequent snacking does not allow the migrating motor complex to run its cleansing cycle between meals. Allowing 4 to 5 hours between eating occasions is generally considered supportive of normal motility.
Get properly assessed
Breath testing and a thorough case history give a far clearer picture than guessing from symptoms alone. The type of gas pattern identified on testing shapes the approach significantly.
When to seek professional assessment
The key takeaway
SIBO is a real and investigable condition, but it is rarely the whole story. Bacterial overgrowth is usually a sign that motility, stomach acid, bile flow, or nervous system regulation has broken down somewhere upstream.
Clearing the bacteria is an important step. Understanding and addressing why the overgrowth happened in the first place is what determines whether it stays away.
At Wave Functional Health we work with patients who have already tried antimicrobials, elimination diets, or a course of rifaximin, only to see symptoms return. If you are dealing with persistent bloating, altered bowel habits, or a SIBO diagnosis that keeps coming back, a deeper functional medicine assessment may help identify what is driving it.
Frequently asked questions
SIBO stands for small intestinal bacterial overgrowth. It occurs when bacteria that normally live in the large intestine overgrow in the small intestine, fermenting carbohydrates and producing excess gas that leads to bloating, discomfort, and altered bowel habits.
A common pattern is a flat stomach in the morning that progressively distends through the day, particularly after eating carbohydrates. This differs from bloating that is constant regardless of food intake, which points toward different underlying mechanisms.
The most common test is a breath test measuring hydrogen and methane gas after a lactulose or glucose substrate. Results are interpreted alongside symptom history and, where relevant, other functional testing such as comprehensive stool analysis.
SIBO is usually a downstream consequence of poor gut motility, low stomach acid, reduced bile flow, structural issues, or nervous system dysregulation. If the underlying driver is not identified and addressed, the small intestine has no reason to stay clear once antimicrobial treatment ends.
Usually not. A structured low-FODMAP or elimination approach can help manage symptoms during active treatment, but long-term restriction can reduce microbiome diversity and is not considered a long-term solution on its own. The goal is to address the drivers that make certain foods problematic, not to avoid them indefinitely.
Stress influences digestive motility, stomach acid secretion, and bile release — all of which normally help prevent bacterial overgrowth. A nervous system stuck in a high-alert state may under-drive these functions, making nervous system regulation an important part of both treatment and prevention of recurrence.
References
Pimentel M, et al. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. American Journal of Gastroenterology. 2020.
Rao SSC, Bhagatwala J. Small Intestinal Bacterial Overgrowth: Clinical Features and Therapeutic Management. Clinical and Translational Gastroenterology. 2019.
Achufusi TGO, et al. Small Intestinal Bacterial Overgrowth: Comprehensive Review of Diagnosis and Management. Cureus. 2020.
Takakura W, Pimentel M. Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: An Update. Frontiers in Psychiatry. 2020.
Persistent bloating that keeps coming back
deserves a proper investigation.
At Wave Functional Health we look at gut motility, stomach acid function, bile flow, microbiome balance, nutrient status, and nervous system regulation together — because SIBO is rarely just about the bacteria.
Book a ConsultationDr Matt le Roux is a chiropractor and functional medicine practitioner at Wave Functional Health, Suite 326, 34-36 Glenferrie Drive, Robina QLD 4226. He works with patients across the Gold Coast and internationally via telehealth.