Metagenomics is the analysis of entire communities of microbes. The ability to perform this analysis, such as via 454- pyrosequencing, could lead to a more comprehensive understanding of the gut microbiome and could be used to aid in the development of effective dietary therapies and products to help maintain health and wellness for both humans1-4 and companion animals.5-7 It is increasingly recognized that gastrointestinal (GI) microflora has a strong impact on the health of cats and dogs8 and that gut microbiome populations can be altered in GI disease4-10 Prior research has confirmed alterations in intestinal microflora in cats with GI disease.11,12 Microbial communities based on 16S rDNA sequence data can be analyzed on multiple fecal samples simultaneously utilizing 454-pyrosequencing with bar-coded primers to amplify particular 16S sequences.