The most common side effect of prebiotics is abdominal bloating and discomfort when large doses are consumed. Large amounts of prebiotic provide an abundance of food for a range of gut bacteria and when fermented this can result in an excess of gas.
The more common first generation prebiotics e.g. inulin or fructo-oligosaccharides (FOS) are most prone to this problem. These are classed as FODMAPS (Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols)
The latest generation of prebiotics are more selectively fermented in the gut, by low-gas producing bacteria, avoiding this problem. Such prebiotics based on GOS (galacto-oligosaccharides) are not classed as FODMAPS due to differences in their chemical structure. In all cases it is advisable to stick to the recommended dose on the pack
When taking prebiotics for the first time some individuals may find that it takes a few days for their system to adjust as to the new food source. Symptoms such as tummy gurgling are in the vast majority of cases transitory and are an indication that the gut bacteria are in the process of being re-balanced.