Gut Fermentation Syndrome


This causes wind and bloating in the upper abdomen, and sometimes nausea and pain. Some people notice fatigue and brain fag. Bloating and wind after a carbohydrate meal is a good clue. This overlaps with small bowel overgrowth syndrome. It is common but under-diagnosed.


We all have microbes in our lower intestine which have a very useful function (digesting vegetables, producing vitamins and boosting immunity). However they shouldn’t be in the small intestine. Normally they are removed from the small intestine by stomach acid, bicarbonate and enzymes from the pancreas and bile from the gallbladder.

But this can go wrong, especially if we don’t produce enough stomach acid and a chain of reactions follows leading to the digestive processes not working properly. This leads to an overgrowth of microbes. These produce fermentation and produce chemicals such as alcohols, methane and hydrogen sulphide. These cause wind (smelly if there is methane and hydrogen sulphide) and bloating.

The main cause of this overgrowth is the high sugar content of the modern diet which makes it easy for microbes to breed. However lack of stomach acid (from acid-blocking drugs), poor diet and snacks (meaning the stomach never has time to build up enough acid) are also factors. Usually there is an overgrowth of fungi but sometimes it is bacteria.

Drugs, including antibiotics and acid-blocking drugs can make the situation worse. (Typically antibiotics make it worse encouraging fungal overgrowth but paradoxically sometimes make it better if there is bacterial overgrowth.)


This syndrome goes undiagnosed because standard tests typically come back normal or show only minor changes. These includes endoscopy and standard blood tests. Unfortunately there is no easy way of making this diagnosis. The most useful tests are not available on the NHS. Although there is no perfect test for this condition, Biolab Medical Unit do a test for organic acids in the urine which gives a useful measure of both bacterial and fungal infection (typically arabinase and tartaric acid are increased with fungal infection) and this is probably the most useful test. Biolab also do a SIBO (small intestinal bacterial overgrowth) breath test which will identify bacterial overgrowth. Another test they do is D lactate in the blood which also suggests bacterial infection. Other useful tests include comprehensive digestive stool analysis and hydrogen sulphide in the urine (which suggests bacterial infection).

What to Do

The first step is keeping sugar very low combined with a low refined carbohydrate (white flour, white rice, chips, cooked potatoes). Usually it is best to remove yeasty foods like cheeses, marmite, alcohol and mushrooms.

Ideally stop acid-blocking drugs if you are taking them (not always easy as rebound acidity can happen once they are stopped or reduced). Reduce them gradually.

Have a long gap, ideally at least 12 hour between your last food (or alcohol) at night and the first food in the morning, to allow acid levels to build up. Avoiding snacks also helps.

If the main cause is fungal then a course of antifungal drugs such as fluconazole 50mg daily for a few weeks may be given. (But you will need a blood test to check your liver with a long course). Sometimes Nystan powder can be very useful and can be obtained from specialist chemists. Typically the dose is built up slowly. This is beyond the scope of this leaflet. Antibiotics are sometimes needed for bacterial infections. These are all prescriptions drugs. An alternative is over the counter anti-fungals such as dida (Holland & Barrett, Amazon) which may help.

Dr Myhill recommends large doses of vitamin C, especially at night as this can help kill harmful microbes. Taking betaine with meals often helps. Vitamin C kills both harmful bacteria and fungi. Start with Vitamin C 2-3 grams at night. Some people will need to build up to bowel tolerance (to the point where it causes loose stools) and then reducing the dose slightly. Use until symptoms settle. (Dr Myhilll also recommends that if you use betaine which is acidic then to also take magnesium carbonate 1 gram 90 minutes after meals). Probiotics are beneficial as are fermented foods like kefir.