The impact of diet on the microbial composition in the gastrointestinal tract (GIT) has been well documented. The GIT microbiome plays key roles in nutrition including modulation of nutrient uptake and utilization, promotion of GIT development and maturation, and extraction of energy from indigestible non-starch polysaccharides. However, quantifying the role of diet in shaping microbial composition in humans has been difficult. Pigs share a similar GIT anatomy and dietary composition with humans making them an attractive animal model. We used genetically identical co-housed pigs to assess the impact of diets on GIT microbial composition. For this study, the fecal microbiota of two genetically identical co-housed pigs were evaluated when fed diets containing either soybean hulls or wheat bran for 14-days. We found that microbial community composition clustered distinctly by diets with generally higher diversity in the wheat bran group than the soybean hull group. We also identified significant taxonomic differences in the bacterial composition between two different diets. This study allowed us to study the influence of diets on GIT microbiome composition independently of the confounding effects of host genotype and environment.