My research objectives are to define antibiotic resistance gene dissemination in the environment, starting in the intestinal environment, 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, 3) disturbances such as antibiotic treatment and Salmonella challenge alter bacterial community structure in different ways, and 4) 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, heat stress, immune modulation, 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.
Dr. Heather Allen
Research Microbiologist, USDA Agricultural Research Service, National Animal Disease Center
Area of Expertise:
B.S., Microbiology, University of Iowa, 2002
Ph.D., Microbiology, University of Wisconsin-Madison, 2009