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Heather Allen
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Heather K. Allen
National Animal Disease Center
Research Microbiologist
Phone (515) 337-7207
Fax (515) 337-7428
P.O. Box 70
1920 Dayton Ave.
Ames, IA 50010

B.S. University of Iowa (hons.), Microbiology, 2002
Ph.D. University of Wisconsin-Madison, Microbiology, 2009
Postdoc- National Animal Disease Center, 2011

Research Interests:
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.

Analyzing environmental reservoirs of antibiotic resistance genes using high-throughput techniques.

Defining swine gut microbiota resilience and recovery in response to diet and disturbances.

Developing non-antibiotic feeding strategies in swine, including of potential probiotic bacteria that produce butyrate.

Honors and Awards:
2015  Herbert L. Rothbart Early Career Scientist Award recipient for the Agricultural Research Service, USDA

2014  Outreach, Diversity, and Equal Opportunity Award recipient for the Midwest Area, ARS, USDA

2012-2015 Agricultural Expert, Annual Iowa Youth Institute of the World Food Prize

Laboratory Personnel:
Technicians -  Jennifer Jones, Biological Science Lab Tech.
Post doc -  Nichole Ricker
Grad Students, ISU Julian Trachsel, Phil Colgan 

Recent Publications: Complete list of published work:


  1. Trachsel, J., D. O. Bayles, U. Y. Levine, T. Looft, and H. K. Allen. 2016. Function and diversity of bacterial butyryl-coA:acetate transferases from the swine gut microbiota. Appl Environ Microbiol.
    82(22):6788-6798. doi: 10.1128/AEM.02307-16
  2. Allen, H.K., An, R., Handelsman, J., Moe, L. 2015. A response regulator from a soil metagenome enhances resistance to the beta-lactam antibiotic carbenicillin in Escherichia coli. PloS One. doi: 10.1371/journal.pone.0120094
  3. Allen H. K. and S. T. Abedon. 2014. Virus ecology and disturbances: impact of environmental disruption on the viruses of microorganisms. Front Microbiol. 5:700. doi: 10.3389/fmicb.2014.00700
  4. Looft T.*, H. K. Allen *, Casey T. A., Alt D. P., Stanton T. B. 2014. Carbadox has both temporary and lasting effects on the swine gut microbiota. Front Microbiol. 5:276. doi: 10.3389/fmicb.2014.00276.
  5. Allen H. K. 2014. Antibiotic resistance gene discovery in food-producing animals. Curr Opin Microbiol. 19:25-29.
  6. Allen H. K., Stanton T. B. 2014. Altered egos: antibiotic effects on food animal microbiomes. Annu Rev Microbiol. 68:297-315.
  7. Allen H. K., Trachsel J., Looft T., Casey T. A. 2014. Finding alternatives to antibiotics. Ann N Y Acad Sci. 1323:91-100.
  8. Bearson, B.*, H. K. Allen*, B. W. Brunelle, I. S. Lee, S. R. Casjens, and T. B. Stanton. 2014. The agricultural antibiotic carbadox induces phage-mediated gene transfer in Salmonella. Front Microbiol. 5:52. doi: 10.3389/fmicb.2014.00052.
  9. Looft, T., H. K. Allen, B. L. Cantarel, U. Y. Levine, D. O. Bayles, D. P. Alt, B. Henrissat, and T. Stanton. 2014. Bacteria, phages, and pigs: The effects of in-feed antibiotics on the microbiome at different gut locations. ISME J. doi: 10.1038/ismej.2014.12.