Gut Fermentation Syndrome

        This goes under a variety of names such as upper fermenting gut, fungal-type dysbiosis and small intestinal overgrowth syndrome (SIBO).


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.


        The key finding is gas and wind and hence abdominal swelling.



        We have billions of microbes in our lower intestine. These have a very useful functions: digesting fibre we can’t digest, producing vitamins, producing anti-inflammatory compounds such as butyrate, controlling harmful bacteria and fungi and boosting immunity. However, in the small intestine they shouldn’t be there, at least in any number. Normally acid from the stomach, bicarbonate and enzymes from the pancreas and bile from the gallbladder remove these microbes from the small intestine. In addition, beneficial microbes (which outnumber the harmful ones by 9:1) keep the harmful ones in check.

        Overgrowth off fungi is the commonest cause of this syndrome and this has been called fungal-type dysbiosis. This syndrome was first recognised by Hurst in 1931. The treatment given at the time was carbohydrate restriction, vitamins, betaine and pancreatic enzymes.

        The main reason gut fermentation develops is too much sugar and refined carbohydrates in the diet which provides perfect food for harmful bacteria and fungi.

          Other causes are poor diet (especially processed food) and snacks (meaning the stomach never has time to recover and build up enough acid). Sometimes the overgrowth is of fungi and sometimes it is pathogenic bacteria.

          Drugs, including antibiotics, steroids, non-steroid anti-inflammatory drugs such as ibuprofen (NSAIDs) and acid-blocking drugs can make the situation worse.

          Sugar, artificial sweeteners, sugar alcohols (as in chewing gum), emulsifiers (in processed foods), alcohol and chlorinated water can all add to the problem.

Gut fermentation syndrome is typically associated with leaky gut syndrome. This allows poorly digested food particles to enter the blood stream, triggering allergic reactions and the release of inflammatory chemicals.


This syndrome often goes undiagnosed because standard tests typically come back normal or show only minor changes.

          Endoscopy tends to be normal or show minor changes. Standard blood test will also be normal. A major clue is poor response to an exclusion diet. Unfortunately there is no perfect way of making this diagnosis (one of the reasons it is under-diagnosed). In my experience most gastroenterologists are not familiar with this problem.

Tests are unfortunately not available on the NHS and there is no perfect test.

A test for organic acids in the urine, from Great Plains Laboratory, gives a useful measure of both bacterial and fungal infection (typically arabinase and tartaric acid are increased with fungal infection).

There are also breath tests for SIBO (small intestinal bacterial overgrowth) which can 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).




        DIET: The first step is a diet very low sugar, low refined carbohydrate (low in white flour, white rice, chips and potatoes) which starves the harmful microbes. Usually it is best to remove yeasty foods like cheeses, marmite, alcohol and mushrooms. This needs to be done for a minimum of 8 weeks.

ANTI-MICROBIALS: 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 during a longer 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 used but this needs care as many antibiotics make matters worse.

 Dr Myhill recommends large doses of vitamin C, especially at night as this can help kill harmful microbes (see htpps:// Taking betaine with meals often helps. Vitamin C kills both harmful bacteria and fungi, so using Vitamin C up to bowel tolerance (when it will cause loose stools) and then slightly reducing the dose is a simple and effective strategy. Use it until symptoms settle. (Dr Myhilll also recommends that if you use betaine which is acidic then it may be best to take magnesium carbonate 1 gram 90 minutes after meals to balance this).


Probiotics (see separate leaflet)

Fermented foods: sauerkraut, kefir, unpasteurised cheeses.


Ideally stop acid-blocking drugs if taking them – not always easy as rebound acidity which can happen when they are stopped or reduced. Reduce them gradually. Avoid harmful drugs where possible: steroids, antibiotics, NSAIDs


          This has been shown to reduce friendly bacteria and make pathogenic bacteria more harmful.