Felines are increasingly at risk for infections of multi-drug resistant bacteria in the US, and mounting evidence exists that raw meat diets (marketed as “natural”) expose cats and their owners to numerous pathogens. Also, no standard methods are established to verify the animal source label claims of commercial diets. The goal of this study is to profile the bacterial and parasite microbiome of raw and conventional feline diets in order to determine if additional pathogens and/or antimicrobial resistance (AMR) mechanisms of concern are present. Using a combination of novel and well-established next-generation sequencing (NGS) approaches, we will conduct three targeted metagenomic analyses on each sample in order to characterize their 1.) bacterial and parasite population contained in the sample, 2.) resistome and 3.) vertebrate mitochondrial 16S. Rather than enriching for particular types of bacteria and following with subtyping, we will start with a wider net to give an unbiased picture of the microbial population and follow with specific tests to confirm findings. We will use a different next-generation sequencing approach for each aim, which will also provide important data on the utility of these methods for larger investigations.