Epidemiologic studies have demonstrated variations in the incidence of colon cancer between populations and socioeconomic groups. Differences in dietary habits have been implicated in the risk of developing colon cancer. Diet appears to influence our colonic microflora. Such variations may allow for future utilization of the fecal flora as markers for screening and diagnosis of colon cancer. The composition of the diet not only dictates the available substrates for the flora but also helps to establish predictable and competitive relationships between intestinal bacteria. To appreciate the significance of populations deemed high and low risk based on host flora, an understanding of several dynamic microbial relationships and metabolites produced is necessary. In this review, we explore the critical relationships between bile acid 7 alpha-dehydroxylation, sulfidogenesis, methanogenesis, and how they relate to carbohydrate and bile acid metabolism. We summarize the chemopreventative, anticarcinogenic, and detoxifying activity of probiotics and prebiotics, as well as potential mechanisms for protection against colon cancer.