There is now very clear evidence that Crohns Disease always has a dysbiosis of the colonic bacteria. This means that there are more bad than good bacteria within the colon. What is not known as yet is whether this is helping to cause the Crohns problem or whether it is a result of the disease. However, what is now apparent is that making a major effort to change this bacterial makeup is a logical potential therapeutic goal. The following articles from major academic centers speak directly to this issue, mentioning prebiotics as a possible agent.
New therapeutic options for inflammatory bowel disease
Another article that addresses this issue of modulation of the gut microbiome as a therapeutic measure in inflammatory bowel disease.
Changing the gut flora in inflammatory bowel disease