When the small intestine is too densely colonised

Healthy state

The gut is colonised very differently along its length. In the stomach and upper small intestine there are usually fewer than a thousand bacteria per millilitre of contents (from a thousand upwards the US guideline speaks of an overgrowth; the threshold used to be a hundred thousand), towards the end of the small intestine it is already millions to hundreds of millions, and in the large intestine hundreds of billions per gram. The small intestine is the absorption zone for nutrients: this is where sugars, protein and fat should be taken up by the body, not by bacteria. The large intestine, by contrast, is the fermentation chamber for what is left.

This separation is not held by a single barrier but by several in series. Saliva already washes bacteria along in the mouth, and in the stomach acid (pH 1 to 3) kills most of them. In the upper small intestine, bile and pancreatic juice inhibit germs, and the gut lining releases its own antibacterial proteins. A mucus layer Mucus layer A gel layer of mucins on the gut wall that keeps bacteria at a distance. In the colon, the inner layer is almost free of microbes. More in the chapter “The mucus layer and additives” and secretory IgA IgA (secretory IgA) The antibody of the mucous membranes. It is released into the gut in large amounts, where it holds germs in the mucus without causing inflammation. More in the chapter “IgA: the antibody that keeps the gut clean, and what vitamin A, D and omega-3 have to do with it”, an antibody on the surface of the lining, keep bacteria away from the gut wall.

The most important mechanical safeguard is the cleansing wave Migrating motor complex A wave of muscle contractions that sweeps the stomach and small intestine empty about every one and a half to two hours when fasting. Eating interrupts it. More in the chapter “Intermittent fasting and meal timing: 16:8, 5:2 and Ramadan”, the migrating motor complex (MMC). About four hours after eating, when the stomach is empty, a strong contraction starts in the stomach and travels over the small intestine to the large intestine, pushing everything ahead of it. The hormone motilin and the gut’s own nervous system control it. After every meal the wave is interrupted and only restarts once the food has been processed. At night it runs undisturbed in several rounds.

At the end of the small intestine sits the ileocaecal valve, the sphincter to the large intestine. It lets contents through but prevents large-intestine bacteria from migrating back into the small intestine. The interplay of acid, bile, immune system, cleansing wave and valve has reserves: if one fails, another usually catches the error. Overgrowth often develops only when several safeguards weaken at the same time.

Disrupted state: causes and effects

In small intestinal bacterial overgrowth Small intestinal bacterial overgrowth (SIBO) Too many bacteria in the small intestine, where normally few live. Bloating and diarrhoea are typical; it is usually diagnosed with a breath test. (SIBO), too many bacteria multiply in the small intestine. The guideline sets the limit at growth of at least a thousand germs per millilitre of small-intestine fluid. The problem is less the type of bacteria than the location: they ferment carbohydrates before the body can absorb them, producing gases, acids and metabolic products that irritate the lining.

Typical are bloating that starts one to two hours after eating, a distended abdomen, abdominal pain, and diarrhoea or constipation. Fibre, onions, legumes and probiotics Probiotics Live microorganisms that are meant to provide a benefit in sufficient amounts. The effect depends on the individual strain. More in the chapter “Using fermented foods well” can make symptoms worse because they give the bacteria even more food. The same symptoms occur with irritable bowel, sugar intolerances or constipation. SIBO therefore cannot be recognised from symptoms alone.

The causes all amount to a failure of the protective layers. Too little stomach acid (acid blockers, stomach lining inflammation) lets more bacteria through. A weak cleansing wave develops after gut infections if lasting damage to the gut’s nerve cells remains, and also with diabetes, scleroderma, an underactive thyroid and under opioids. Operations that bypass a loop of bowel or remove the ileocaecal valve, pouches in the small intestine (diverticula Diverticula Small pouches of the gut lining that bulge through weak spots in the colon wall. When they become inflamed, it is called diverticulitis. More in the chapter “Diverticula, haemorrhoids and fissures: what can go wrong at the end of the gut”), adhesions and narrowings let contents stand still. Pancreatic weakness, coeliac disease Coeliac disease An autoimmune disease in which gluten damages the lining of the small intestine. It is diagnosed with a blood test and usually a biopsy while you are still eating gluten. More in the chapter “Lactose, fructose, gluten: making sense of intolerances” and Crohn’s disease also belong here. With age the risk rises, because stomach acid and gut movement decline and more medications are taken.

The bacteria interfere with digestion itself. They break down bile acids Bile acids Substances made by the liver that make fat digestible. About 95 percent are reabsorbed in the last part of the small intestine; gut bacteria transform the rest. More in the chapter “Bile acids: when bile causes diarrhoea” already in the small intestine, which are then missing for fat digestion. This leads to greasy stools and weight loss and to a deficiency of fat-soluble vitamins. They also consume vitamin B12, while some species produce folate, so the B12 level can be low and the folate level high. If the lining is irritated for a long time, it absorbs iron and other nutrients less well.

SIBO is usually measured with a breath test Breath test After drinking a sugar solution, hydrogen and methane in the breath are measured several times. This can reveal sugar intolerances and signs of bacterial overgrowth. More in the chapter “Gut tests: what they show and what they do not”: you drink a sugar solution, and every 15 to 20 minutes the gas in your breath is measured. If hydrogen rises early, bacteria are apparently fermenting the sugar already in the small intestine. In a meta-analysis Meta-analysis An analysis that combines the results of several studies. It is only as good as the studies it includes. of 14 studies, however, the glucose test detected only about every second actual case (sensitivity 55 per cent), the lactulose test even fewer (42 per cent). False positives are possible, especially with fast gut transit, because then the sugar reaches the large intestine early. The procedures are not uniformly standardised, and the gold standard, a sample from the small intestine, is almost never done.

The gas in the breath test also hints at who is fermenting. Methane does not come from bacteria but from archaea, single-celled organisms that convert hydrogen to methane and slow gut transit. The guideline therefore speaks of a separate form, intestinal methanogen overgrowth IMO (intestinal methanogen overgrowth) Too many methane-producing archaea in the gut, shown by methane of 10 ppm or more on a breath test. Often goes along with constipation. More in the chapter “Hydrogen sulfide and methane: the other gases in the gut” (IMO); it tends to go with constipation. Newer tests also measure hydrogen sulphide, which tends to be linked to diarrhoea; how reliable that is has barely been studied independently. Overgrowth of yeasts in the small intestine is also discussed, but the evidence for it is thin.

An honest assessment belongs here: SIBO is real but probably also too often used as an explanation for unclear symptoms. A positive breath test without an identifiable cause should be read with caution. Symptoms returning after treatment are common and usually suggest that the cause is still there.