SIBO Treatment: Your Personalised Plan

Getting rid of SIBO (Small Intestinal Bacterial Overgrowth) requires a multi-pronged approach, and it's one of my core areas of specialisation. The first step is confirming the diagnosis and identifying the type — hydrogen-dominant, methane-dominant (now called IMO — Intestinal Methanogen Overgrowth), or hydrogen sulphide. This matters because the treatment protocols differ.

The conventional first-line treatment is antibiotics — typically rifaximin, or rifaximin combined with neomycin for methane-dominant cases. Herbal antimicrobials (including berberine, oregano oil, and allicin) are a well-evidenced alternative that I use with many clients. But here's the critical piece: antibiotics or antimicrobials alone are rarely sufficient long-term. SIBO has an underlying cause — whether that's impaired gut motility, reduced stomach acid, structural issues, or a history of gut infection — and addressing that cause is essential to prevent recurrence.

I've completed the SIBO Masterclass with Nirala Jacobi, Australia's leading SIBO clinician, and bring that specialist knowledge to every SIBO client. If you suspect SIBO, book a free Strategy Session to discuss testing and next steps.

The SIBO diet aims to reduce fermentable carbohydrates that feed bacteria in the small intestine — the goal is to starve the overgrowth rather than feeding it. This makes high-FODMAP foods problematic for most people with SIBO: garlic, onion, leeks, wheat and rye products, legumes, lactose-containing dairy, and certain fruits like apples, pears, and stone fruits are typically restricted during the treatment phase.

Some SIBO protocols use a more intensive diet — like the Specific Carbohydrate Diet (SCD) or Bi-Phasic Diet — that removes most fermentable carbohydrates temporarily. Added sugars, alcohol, and highly processed foods should also be minimised, as they provide ready fuel for bacteria.

Importantly, SIBO dietary restriction is meant to be therapeutic and temporary — not a permanent way of eating. Once the overgrowth is treated and the gut is rebalanced, many foods can be reintroduced. I guide my clients through both the restriction phase and the reintroduction process to avoid unnecessary long-term limitation.

A SIBO flare-up typically involves a dramatic increase in digestive symptoms, often appearing or worsening shortly after eating. The hallmark symptom is intense bloating — often severe enough to make clothing uncomfortable and visible to others — accompanied by abdominal pain or cramping. Excessive gas, belching, diarrhoea, constipation (particularly in methane-dominant SIBO), or a combination of both are common.

Unlike IBS flares, which can be more generalised, SIBO flares often have a clear timing pattern: symptoms tend to worsen throughout the day and after meals, particularly meals containing fermentable carbohydrates. Fatigue, brain fog, and nausea during flares are also frequently reported by my clients.

If you're experiencing regular flares despite dietary management, it may indicate that the underlying SIBO hasn't been fully treated or has recurred. Recurrence is common with SIBO — this is why addressing the root cause and implementing motility support is as important as the treatment itself.

SIBO doesn't occur randomly — it develops when the body's defence mechanisms against bacterial overgrowth in the small intestine are impaired. The most fundamental trigger is poor gut motility, specifically dysfunction of the Migrating Motor Complex (MMC) — the housekeeping wave that sweeps bacteria through the small intestine between meals. When the MMC is impaired (often following a gut infection or injury), bacteria accumulate.

Common underlying triggers include a history of food poisoning or gastroenteritis (post-infectious IBS/SIBO is well-documented), low stomach acid (which allows bacteria from the mouth and food to survive into the small intestine), structural issues like adhesions or diverticula, hypothyroidism, diabetes, and the regular use of medications like proton pump inhibitors or opioids that slow gut motility.

Understanding your personal underlying trigger is essential for preventing SIBO from recurring — treating the overgrowth without addressing what caused it means it's highly likely to come back. This is a key focus of the work I do with SIBO clients.

Changes in bowel habits are often one of the most distressing aspects of SIBO, and the pattern depends on which type you have. Hydrogen-dominant SIBO tends to be associated with diarrhoea — loose, frequent, urgent stools, often pale or floating (indicating fat malabsorption). Methane-dominant SIBO (IMO) is more typically associated with constipation, slow transit, and hard, difficult-to-pass stools.

Floating, pale, foul-smelling stools are a sign of fat malabsorption — something that occurs when SIBO interferes with bile acids and digestive enzymes in the small intestine. Undigested food in stools and significant bloating alongside bowel changes are also common. These aren't just uncomfortable — they indicate your body isn't absorbing nutrients properly, which has wider health implications.

If you've noticed these kinds of changes, it's worth proper investigation. SIBO can be accurately tested using a breath test, and the results guide the treatment approach.

SIBO is aggravated by anything that feeds the bacteria in the small intestine or impairs the gut's ability to clear them. From a dietary perspective, fermentable carbohydrates — particularly high-FODMAP foods, sugars, and refined carbohydrates — are the biggest provocateurs. Alcohol also feeds bacterial growth and impairs gut motility.

Beyond diet, stress is a major aggravating factor because it impairs the MMC (the gut's housekeeping mechanism), slows motility, and reduces stomach acid — all of which worsen bacterial overgrowth. Medications that slow gut motility (like opioids or some antidepressants) and acid-suppressing medications (proton pump inhibitors) are well-documented aggravators of SIBO.

Interestingly, eating too frequently — without adequate fasting windows between meals — prevents the MMC from doing its work. One of the things I often recommend for SIBO clients is building adequate gaps between meals, particularly leaving 12+ hours overnight, to support gut motility and bacterial clearance.

SIBO is a master of disguise — its symptoms overlap significantly with several other conditions, which is one reason it's frequently missed or misdiagnosed. The most common misdiagnosis is IBS: bloating, diarrhoea, constipation, and abdominal pain are present in both. Research suggests that up to 80% of people with IBS may actually have SIBO as an underlying driver — which is why I always assess for SIBO when working with IBS clients.

Other conditions that can look like SIBO include coeliac disease, inflammatory bowel disease (Crohn's or colitis), histamine intolerance, food intolerances (particularly lactose and fructose), gastroparesis, and even thyroid disorders that affect gut motility. Functional dyspepsia can also produce similar upper gut symptoms.

Getting an accurate diagnosis is the starting point for effective treatment — which is why I take a thorough approach to assessment rather than treating assumed diagnoses. A SIBO breath test is a relatively straightforward way to confirm or rule out overgrowth.

The 'SIBO belly' is a phrase many of my clients use before they have a diagnosis — they describe a belly that looks and feels pregnant by the end of the day despite eating normally, that distends rapidly after meals, and that produces constant rumbling, gurgling, and gas. The bloating in SIBO can be quite dramatic — significantly more severe than typical IBS bloating — because it's driven by active fermentation of carbohydrates by bacteria in the small intestine.

The bloating is often accompanied by a feeling of pressure, tightness, or being 'stuck', and can range from uncomfortable to genuinely painful. Upper abdominal fullness and nausea, particularly after meals, are also characteristic. Many people describe feeling well in the morning and progressively worse throughout the day as food moves through and is fermented by the bacteria.

If this description resonates with you, it's worth investigating for SIBO. It's a pattern I've seen hundreds of times, and it responds very well to proper targeted treatment.

Untreated SIBO isn't just uncomfortable — over time it can have significant consequences for nutritional status and overall health. The bacteria in the small intestine compete with you for nutrients and interfere with normal absorption. Fat-soluble vitamins (A, D, E, K) and B12 are commonly depleted in chronic SIBO. Iron deficiency anaemia and magnesium deficiency are also well-documented. Protein malabsorption can affect energy, immunity, and muscle maintenance.

Chronic SIBO also maintains intestinal permeability ('leaky gut'), contributing to systemic inflammation, food intolerances, skin problems, brain fog, and fatigue. Over the long term, the ongoing inflammatory burden can affect liver function and potentially contribute to autoimmune conditions.

It's also worth noting that untreated SIBO tends to worsen over time as the overgrowth establishes itself more firmly and the gut environment becomes increasingly imbalanced. Early treatment is easier and more effective than treating a long-established overgrowth — so if you suspect SIBO, don't put it off.

Probiotics alone cannot cure SIBO, but they do have a useful role in a comprehensive treatment plan. Research on probiotics for SIBO shows mixed results — some strains appear to help reduce bacterial overgrowth and improve symptoms, while others are contraindicated (particularly in methane-dominant cases or IMO, where adding more bacteria can worsen symptoms).

This is why I assess carefully before recommending probiotics to anyone with suspected or confirmed SIBO. Used at the wrong time or with the wrong strains, probiotics can actually make SIBO symptoms worse. Used appropriately — particularly during the post-treatment phase to help restore a healthy microbiome and prevent recurrence — they can be a valuable part of the protocol.

The main treatments for SIBO are antimicrobials (herbal or pharmaceutical), dietary changes, and motility support. Probiotics are a supportive adjunct, not a standalone cure. If you've been taking probiotics for gut symptoms without improvement, it may be worth investigating whether SIBO is present.

This is one of the most common questions I hear, and the honest answer is: it varies significantly. An initial treatment course — whether antibiotic or herbal antimicrobial — typically runs for 2–4 weeks. Many people experience significant symptom improvement within this period. However, this doesn't mean SIBO is 'fixed.'

Full recovery — including healing the gut lining, restoring a healthy microbiome, reintroducing a broader diet, and most importantly addressing the underlying cause — typically takes 3–6 months of active support. Without addressing the underlying cause, recurrence rates for SIBO are high (research suggests 40–80% recurrence within 12 months for antibiotic treatment alone). This is why my approach focuses equally on preventing recurrence as on treating the active overgrowth.

I work with SIBO clients through my 8-Week Gut Fix Program, which covers the treatment phase and the foundational work for long-term remission. Book a free Strategy Session to discuss what's involved: vibrantnutrition.com.au.

The gold-standard test for SIBO is a hydrogen/methane breath test. You consume a sugar solution (lactulose or glucose) and breath samples are taken at regular intervals over 2–3 hours. If bacteria in the small intestine ferment the sugar and produce hydrogen and/or methane gas, this will be detected in the breath. The pattern and timing of the gas response indicates both the presence and type of SIBO.

Clinically, the symptoms I look for that suggest SIBO include: significant bloating that worsens throughout the day and after meals; excessive gas or belching; alternating diarrhoea and constipation; brain fog, fatigue, and nutritional deficiencies disproportionate to diet; and IBS symptoms that haven't responded to standard dietary management. A history of food poisoning or a gut infection that marked the onset of gut symptoms is also a strong clinical indicator.

I can arrange breath testing for clients as part of an assessment. If you recognise your symptoms in this description, a breath test can give us a clear diagnostic picture to work from. Book a free Strategy Session to discuss testing options: vibrantnutrition.com.au.