During a colon cleansing procedure, harmful toxins and bacteria are removed from the system. This of course brings about complications, specifically, the removal of non-harmful bacteria. There is such a thing as good bacteria, which helps in the smooth and efficient operation of the body. Problem arises when you undergo colon cleansing procedure, since there is no way to simply remove only the harmful bacteria. The good bacteria are also removed as there is no way to make a distinction between the two types of bacteria.