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Upper fermenting gut is a common complication of Western diets because they are high in sugars, fruit sugars and starches - i.e. all carbohydrates. If digestion is perfect, then these foods are very useful. However, if we overwhelm our ability to digest with too much carbohydrate, acid blocking drugs, ageing, food allergies and so on, we risk the upper gut switching to a fermenting one - and that carries many problems!
The mainstay and starting point for treatment is always a low carbohydrate, ketogenic diet. This starves the little wretches out. A good sign that the diet has been done well can be seen by looking at the tongue - it should be clean and pink with no crud that can be scraped off. One's teeth should feel glassy smooth because they will be free of bacterial colonies called plaque. Your dentist will be out of a job! However, digestive aids and antimicrobials are additionally helpful and may allow one to be a little more relaxed with the diet. Acid supplements, enzymes, bile salts and vitamin C are all toxic to microbes.
Probiotics are additionally helpful - the idea here is they physically displace unfriendly microbes in the gut. A test which is very useful clinically is the Genova Comprehensive digestive stool analysis. This often shows sensitivities to uva ursi and plant tannins. In addition to other useful information this test gives us a good handle on one's ability to digest and absorb food. The commonest abnormalities are low stomach acid (hypochlorhydria), poor pancreatic function and poor production of bile salts. These problems can be corrected with digestive aids.