SIBO Diagnosis: The What, But Not the Why

The small intestine normally carries far fewer bacteria than the large bowel, because its main job is digestion and absorption rather than fermentation × Fermentation Fermentation is the process by which gut bacteria break down certain fibres and carbohydrates. This process produces beneficial compounds such as short-chain fatty acids, but excessive fermentation can also contribute to symptoms such as bloating and gas in some individuals. You can read more here: What Fermented Foods Really Do for Your Gut . In small intestinal bacterial overgrowth (SIBO, an increase in the number of bacteria in the small intestine, or the presence of types usually found further down), bacteria meet food before the body has finished absorbing it. They ferment sugars that would otherwise have been taken up, and the gas they produce is released high in the gut, where it is often felt as bloating, pressure and discomfort within an hour or two of eating. Diarrhoea, constipation or a mixture of both can come with it.

Because these symptoms overlap with irritable bowel syndrome, coeliac disease and several other conditions, SIBO is best thought of as one possible explanation rather than a default one. The timing pattern described in Why Am I Bloated? is often what first points us towards the small intestine.

The usual test is a breath test. You drink a measured sugar solution and breath samples are collected over the following three hours. If bacteria in the small intestine ferment the sugar, they release hydrogen or methane, which is absorbed into the blood and breathed out. The timing and pattern of the rise matter as much as the number, and a methane-dominant result tends to be associated with constipation and slower transit.

In Australia we can measure hydrogen and methane, but not hydrogen sulphide. That limit is worth knowing about, because someone whose gas is mainly sulphide-based can have an apparently normal result despite a convincing story, a pattern I describe in Hydrogen Sulphide and Gut Health. Breath tests are also an indirect measure, so I read them alongside symptoms rather than on their own.

The sugar you drink is called a substrate (the food the bacteria are given to ferment), and the three commonly used are glucose, fructose and lactulose. They are handled differently by the body. Glucose is absorbed early in the small intestine, so it mainly tests the upper part. Lactulose is not absorbed at all and travels the full length of the small bowel, which means it can reveal overgrowth further down but needs careful reading to separate small intestinal from colonic fermentation. Fructose sits somewhere in between, and its absorption varies from person to person.

Because overgrowth can sit in different regions, and because breath tests are an imperfect measure, a single substrate can miss it. Published studies put the sensitivity of a single test at well under 100%, and the figures vary widely between studies. In my practice I often use more than one substrate, because each one is handled differently along the small intestine, and I read the combined pattern alongside your symptoms.

In my practice, treating SIBO has two parts. The first is to reduce the bacteria that have settled in the small intestine, and I do this with herbal antimicrobials chosen because they act on the small intestine without damaging the bacteria further down in the colon, which are doing useful work. The research is limited, although a small trial found herbal protocols performed comparably to the commonly used antibiotic rifaximin.

Feeling better is not the same as having cleared the overgrowth, which is why I like to repeat the breath test afterwards to confirm that it has gone. Treatment needs to be individual, and I would not suggest anyone treat themselves on the basis of symptoms alone.

The second part is working out what allowed the overgrowth in the first place. In my clinical experience a handful of questions come up repeatedly.

Bile acts as a detergent in the small intestine and has antimicrobial properties, so when bile flow is poor, one of the gut’s natural ways of washing bacteria away is weakened.

Stomach acid matters too, because acid destroys many of the bacteria that arrive with food, and long-term use of acid-suppressing medication has been associated with SIBO in studies, although association does not prove cause. If you take this kind of medication, please talk with your prescriber before changing anything, because it is often needed.

Between meals the small intestine is cleared by the migrating motor complex × Migrating Motor Complex (MMC) The migrating motor complex is a repeating pattern of muscular contractions that moves through the stomach and small intestine between meals. It helps clear leftover food, secretions and bacteria towards the large bowel. Eating pauses this cycle, and reduced MMC activity may contribute to bacterial overgrowth in the small intestine. (a repeating wave of muscle activity that sweeps bacteria and debris along towards the colon), which only runs when we are not eating, so constant grazing may interrupt it. How well the rest of the gut moves is covered in Gut Motility: Why Daily Bowel Movements Aren’t Enough.

The ileocaecal valve (the one-way valve where the small intestine joins the large bowel) is meant to stop bacteria drifting backwards, and if it does not work well they may translocate up into the small intestine.

Diet also plays a part, since what we eat shapes what the bacteria have to ferment.

SIBO is notorious for returning, and studies report that recurrence is common. In my experience this usually comes down to one or both of two things. The overgrowth may never have been completely cleared, so that when symptoms eased and treatment stopped, the bacteria that remained had room to bloom and regrow. Or nothing changed in the conditions that allowed the first overgrowth, so the small intestine was just as welcoming as before.

Finding a cause can be genuinely hard, and sometimes only part of the picture becomes clear. Each question answered, whether about bile, acid, motility, the valve or diet, narrows the field and gives the gut a better chance of staying clear. Sudden new food reactions, a pattern I describe in Why Am I Suddenly Sensitive to FODMAPs?, can be another prompt to ask whether the small intestine is involved.

A positive breath test is a useful answer to the question of what is happening in the small intestine. It becomes far more useful when it is followed by the question of why, because that is what decides whether the relief lasts.