Although most whole grains are naturally gluten free, many gluten free diets are devoid of these prebiotic, nutrient powerhouses. In an effort to see how eliminating gluten effects the gut microbiome, Spanish researchers assigned ten healthy adults (average age 30) to a gluten free diet for one month, and measured the changes in their gut microbiome. In just one month of eliminating gluten, the good bacteria in their gut significantly decreased, and some harmful bacteria (like E. Coli) increased, although not significantly. This research suggests that those on a medically prescribed gluten free diet should take care to consume foods that are associated with good gut bacteria, such as gluten-free whole grains, fruits, and vegetables.
British Journal of Nutrition. 2009 Oct;102(8):1154-60. (De Palma et al.)