My research objectives are to define the diversity of antibiotic resistance genes in the swine gut and to discover efficacious alternatives to in-feed antibiotics. To this end, I am interested in the effect of ecosystem disturbances on the swine intestinal microbiome to inform potential non-antibiotic microbiome modulation strategies. With my collaborators I have discovered that 1) the swine gut microbiota harbors diverse antibiotic resistance genes regardless of antibiotic treatment, 2) antibiotic resistance genes are co-selected that confer resistance to antibiotics not administered , and 3) certain in-feed antibiotics induce phage-mediated gene transfer in the swine gut microbiome and in Salmonella enterica serovar Typhimurium. Current analyses of other disturbances on the swine gut microbiome include Salmonella challenge, heat stress, and dietary feed additives. In addition to high-throughput DNA sequence analysis, anaerobic microbiology is employed to culture beneficial microbes with therapeutic potential, such as butyrate-producing bacteria.