Technical Abstract: The bovine fecal microbiota impact human food safety as well as animal health and nutrition. Although the bacteria of cattle feces has been well characterized using both culture-based and culture independent methods, techniques have been lacking to correlate total community composition with community function. We used pyrosequencing of total community DNA (metagenomics) to describe community composition while also characterizing the functional genes present in beef cattle feces, including genes associated with antibiotic resistance, and bacterial virulence. Results suggest that traditional 16S sequencing using “universal” primers may under-represent Acitinobacteria and Proteobacteria. Over eight percent (8.4%) of the sequences from our beef cattle fecal pool sample could be categorized as virulence genes, including a suite of genes associated with resistance to antibiotic and toxic compounds (RATC). This is a higher proportion of virulence genes than found in Sargasso sea, chicken cecum, and cow rumen samples, but comparable to the proportion found in Antarctic marine derived lake, human fecal, and farm soil samples. The quantitative nature of the metagenomic data, combined with the large number of RATC classes represented in samples from widely different habitats means that metagenomic data can be used to track relative amounts of antibiotic resistance genes in individual animals over time in agriculturally impacted environments, and to generate sample-specific antibiotic resistance gene profiles or fingerprints that can help us to understand the ecology of the microbial communities in each habitat, and the epidemiology of antibiotic resistant gene transport between and among habitats.