Dietary intake may cause variable bacterial prevalence in the gastrointestinal tract. The objective of this research was to determine the prevalence of Enterobacteriaceae in the cecum and feces following flaxseed and buckwheat supplemented diets. Seventy-two C57BL/6J male mice were randomly assigned to a diet group and fed for eight weeks: high fat (45% Kcal fat); 10% whole flaxseed (45% Kcal fat); 6% defatted flaxseed (45% Kcal fat); 4% flaxseed oil (45% Kcal fat); 10% buckwheat (45% Kcal fat); and low fat (16% Kcal fat). Significant differences in the prevalence of Enterobacteriaceae in the cecum (p < 0.0348) and feces post treatment (p < 0.0033) were observed. The groups with the highest prevalence of Enterobacteriaceae were whole flaxseed, buckwheat, and defatted flaxseed. The groups with the lowest prevalence were flaxseed oil and high fat. Our results indicated that a positive relationship exists between high fermentable fiber diets and Enterobacteriaceae proliferation.