Growing evidence suggests that microbiota in the human gastrointestinal tract play a crucial role in mediating the effects of foods on colonic health and host metabolism. The large bowel ecosystem is known to be perturbed in humans and animals fed high-fat diets and conversely to be protected by fermentable oligosaccharides. We examined the ability of largely fermentable dietary fiber from broccoli ( Brassica oleracea L. var. italica ) and minimally fermented microcrystalline cellulose to buffer against the effects of high-fat intakes. The results showed that high fat lowered food intakes and therefore fiber intake by 27%. The addition of fermentable oligosaccharide to the diet was shown to be beneficial to some microbiota in cecum, altered cecal short-chain fatty acids, and increased the colon crypt depth and the number of goblet cells per crypt in high- and low-fat diets. Although, the fat level was the predominant factor in changes to the large bowel ecosystem, we have shown that broccoli fiber conferred some protection to consumption of a high-fat diet and particularly in terms of colon morphology.