Treating has the purpose of restoring balance amongst micro-organisms in the gut. In order to do that, it is necessary to decrease the overgrown population to normal numbers. There is no need to completely get rid of them, and the truth is that we do not want to do that either. With the right numbers, they benefit us in many ways. Moreover, it is impossible to eradicate all of them since they are too versatile. A simple culling is enough. To do that, you need to do as follows:
1. We restrict our intake of sugars, thus depriving the microbe of its favourite food (and ours!).
2. We use medication to further reduce the microbial population.
3. We replace the fermenting microbe with friendly bacteria.
4. We use nutritional supplements to help our immune systems.
The only difference between the treatment of yeast and bacterial fermentation is in the use of medication. The principles of diet, microbial replacement and nutritional supplement are the same.
Drug treatment for gut fermentation
The choice of drug is dictated by the organism we are dealing with. Yeast can be tackled head-on with anti-fungal drugs, whereas we must take a more subtle approach with bacterial overgrowth.
The most effective medicine for the treatment of yeast fermentation is nystatin, a powerful anti-fungal drug. This is taken, ideally, in the form of a powder. All other preparations of nystatin are sugar-laden. Fortunately, nystatin is also a very safe drug, and can be taken in large doses without ill effects. It: safety and efficacy stem from the fact that its absorption into the body is negligible. This serves our purpose well. We want it to stay in the gut.
Some patients complain that nystatin makes them feel ill, and there is no doubt that a minority of these are genuinely intolerant to the drug itself. But most of the symptoms attributed to nystatin actually come from the dying yeast colonies. Yeast cell; burst when they die, and their contents spill out into the gut. Some of these substances are toxic to us, and they give rise to flu-like symptoms, such as headache, fatigue, and aches and pains in the muscles. These die-off reactions, as they're called, can be minimised by starting with very small doses of nystatin, with gradual increases until therapeutic (effective) levels are reached. Starting the diet a week before the nystatin will also help, for this will (slightly) reduce yeast populations in itself. Nystatin is a prescription-only medicine, so discuss its use with your doctor.
A word about other anti-fungals
Nystatin is the most suitable medication for yeast fermentation, but some patients (a minority) are intolerant to it. They get symptoms even when they observe the dosing precautions just described. These require an alternative anti-fungal. All such treatments are prescription-only medicines. They are absorbed into the bloodstream, and are therefore less effective than nystatin in the treatment of fermentation. They are very effective for the treatment of infection, however. The use of these drugs should be discussed with your doctor. Some individuals and health food shops sell stuff which is supposedly anti-fungal. The truth is, this limits the ability of yeast to grow, but it doesn't kill it off. If you have a significant overgrowth you will need a 'killer', not a 'limiter'. Once the overgrowth is controlled, then by all means use these yeast-limiting agents to prevent a recurrence.