The impact of diet on the microbial composition in the gastrointestinal tract (GIT) has been well documented. However, quantifying the role of the diet in shaping microbial composition in humans has been difficult due to the influence of host genetics and the environment. To test the influence of diets on the GIT microbiome independently of host genotype and environment, two genetically identical co-housed pigs were used in an A-B-A-B design across four 14-day periods using two distinct diets that differed in dietary fiber source, soybean hulls or wheat bran. Shifts in fecal microbiomes were assessed with respect to dietary changes by 454-pyrosequencing analysis using the V3 region of the 16S rRNA genes. Similarity analysis revealed that the GIT microbiome distinctly clustered by diets rather than by individual. Diversity analysis showed that the diet fed had an influence on GIT microbiome diversity, which was host specific. While many bacterial taxa and KEGG orthologs reacted similarly to switches in diet, some bacterial taxa and KEGG orthologs reacted differentially in each of the pigs. While diet changed the GIT microbiome composition of isogenic co-housed pigs, inter-individual variations from epigenetics were not entirely eliminated by the use of cloned pigs.