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United States Department of Agriculture

Agricultural Research Service

Related Topics

Heather Allen
National Animal Disease Center
Research Microbiologist

Phone: (515) 337-7207
Fax: (515) 337-7402
P.O. BOX 70
1920 DAYTON AVE
AMES, IA, 50010

Projects
ANIMAL INTESTINAL MICROBIOMES, FOODBORNE PATHOGENS, AND ANTIMICROBIALS
Appropriated (D)
  Accession Number: 420876

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Antibiotic resistance gene discovery in food-producing animals Reprint Icon - (Review Article)
Allen, H.K. 2014. Antibiotic resistance gene discovery in food-producing animals. Current Opinion in Microbiology. 19:25-29.
Carbadox has both temporary and lasting effects on the swine gut microbiota - (Peer Reviewed Journal)
Looft, T.P., Allen, H.K., Casey, T., Alt, D.P., Stanton, T.B. 2014. Carbadox has both temporary and lasting effects on the swine gut microbiota. Frontiers in Microbiology. DOI: 10.3389/fmicb.2014.00276.
How do agricultural practices impact microbiomes? A case study of antibiotic effects on the swine gut microbiome - (Abstract Only) - (14-May-14)
Finding alternatives to antibiotics Reprint Icon - (Peer Reviewed Journal)
Allen, H.K., Trachsel, J., Looft, T.P., Casey, T. 2014. Finding alternatives to antibiotics. Annals of the New York Academy of Sciences. Available: http://onlinelibrary.wiley.com/doi/10.1111/nyas.12468/abstract.
Altered egos: antibiotic effects on food animal microbiomes Reprint Icon - (Review Article)
Allen, H.K., Stanton, T.B. 2014. Altered egos: antibiotic effects on food animal microbiomes. Annual Review of Microbiology. 68:297-315.
Reduced salmonella fecal shedding in swine administered porcine granulocyte-colony stimulating factor (G-CSF) - (Abstract Only)
Bearson, S.M., Bearson, B.L., Loving, C.L., Allen, H.K., Lee, I.S., Kehrli Jr, M.E. 2014. Reduced salmonella fecal shedding in swine administered porcine granulocyte-colony stimulating factor (G-CSF) [abstract]. In: Proceedings of 114th General Meeting of the American Society for Microbiology, Boston, Massachusetts, May 17-20, 2014. p. 204.
The agricultural antibiotic carbadox induces phage-mediated gene transfer in Salmonella Reprint Icon - (Peer Reviewed Journal)
Bearson, B.L., Allen, H.K., Brunelle, B.W., Lee, I.S., Casjens, S.R., Stanton, T.B. 2014. The agricultural antibiotic carbadox induces phage-mediated gene transfer in Salmonella. Frontiers in Microbiology. 5:1-8.
Bacteria, phages, and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations Reprint Icon - (Peer Reviewed Journal)
Looft, T.P., Allen, H.K., Cantarel, B., Levine, U.Y., Bayles, D.O., Alt, D.P., Henrissat, B., Stanton, T.B. 2014. Bacteria, phages, and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations. Journal of the International Society for Microbial Ecology. 8(8):1566-1576. DOI: 10.1038/ismej.2014.12.
Heat stress: intestinal barrier and immune disruption in pigs - (Abstract Only) - (23-Oct-13)
Gastrointestinal microbiota and porcine immunity: factors that influence salmonella shedding in swine - (Abstract Only)
Bearson, S.M., Knetter, S.M., Allen, H.K., Bearson, B.L., Brunelle, B.W., Huang, T., Looft, T.P., Ramer-Tait, A.E., Nettleton, D., Stanton, T.B., Wannemuehler, M.J., Tuggle, C.K. 2014. Gastrointestinal microbiota and porcine immunity: factors that influence salmonella shedding in swine [abstract]. In: Proceedings of Symposium on Gut Health in Production of Food Animals, Kansas City, Missouri, November 11-13, 2013. p. 12-13.
Dynamic phages in the swine gut ecosystem - (Abstract Only)
Allen, H.K., Looft, T.P., Bayles, D.O., Alt, D.P., Stanton, T.B. 2013. Dynamic phages in the swine gut ecosystem [abstract]. Molecular Genetics of Bacteria and Phage Meeting. p. 94.
The agricultural antibiotic carbadox induces generalized transducing phage in multidrug-resistant Salmonella enterica serovar Typhimurium DT104 - (Abstract Only)
Bearson, B.L., Brunelle, B.W., Allen, H.K., Bayles, D.O., Stanton, T.B. 2013. The agricultural antibiotic carbadox induces generalized transducing phage in multidrug-resistant Salmonella enterica serovar Typhimurium DT104. Abstracts of the 2013 Molecular Genetics of Bacteria and Phages Meeting, August 6-10, 2013, Madison, Wisconsin. p. 95.
Gene expression changes in the swine microbiota with the in-feed antibiotic carbadox - (Abstract Only)
Looft, T.P., Allen, H.K., Severin, A., Levine, U.Y., Bayles, D.O., Alt, D.P., Stanton, T.B. 2013. Gene expression changes in the swine microbiota with the in-feed antibiotic carbadox. [abstract]. 113th General Meeting, American Society for Microbiology. p. 200.
Butyrate-producing bacteria, including mucin degraders, from the swine intestinal tract - (Peer Reviewed Journal)
Levine, U.Y., Looft, T.P., Allen, H.K., Stanton, T.B. 2013. Butyrate-producing bacteria, including mucin degraders, from the swine intestinal tract. Applied and Environmental Microbiology. 79(12):3879-3881. Available: http://aem.asm.org/content/79/12/3879.long.
Profiling the gastrointestinal microbiota in response to Salmonella: low versus high Salmonella shedding in the natural porcine host Reprint Icon - (Peer Reviewed Journal)
Bearson, S.M., Allen, H.K., Bearson, B.L., Looft, T.P., Brunelle, B.W., Kich, J.D., Tuggle, C.K., Bayles, D.O., Alt, D.P., Levine, U.Y., Stanton, T.B. 2013. Profiling the gastrointestinal microbiota in response to Salmonella: low versus high Salmonella shedding in the natural porcine host. Infection, Genetics and Evolution. 16:330-340.
The agricultural antibiotic carbadox induces prophage and antibiotic resistance gene transfer in multidrug-resistant salmonella enterica serovar typhimurium DT104 - (Abstract Only)
Bearson, B.L., Brunelle, B.W., Allen, H.K., Bayles, D.O., Stanton, T.B. 2013. The agricultural antibiotic carbadox induces prophage and antibiotic resistance gene transfer in multidrug-resistant salmonella enterica serovar typhimurium DT104. Abstracts of the 113th General Meeting of the American Society for Microbiology, May 18-21, 2013, Denver, Colorado. Paper No. #M-1103.
Antibiotics and gene transfer in swine gut bacteria - (Popular Publication)
Allen, H.K. 2012. Antibiotics and gene transfer in swine gut bacteria. Feedinfo News Service. Available: http://www.feedinfo.com.
Estimation of viral richness from shotgun metagenomes using a frequency count approach Reprint Icon - (Peer Reviewed Journal)
Allen, H.K., Bunge, J., Foster, J.A., Bayles, D.O., Stanton, T.B. 2013. Estimation of viral richness from shotgun metagenomes using a frequency count approach. BMC Microbiome. 1(5). Available: http://www.microbiomejournal.com/content/1/1/5.
Treatment, promotion, commotion: Antibiotic alternatives in food-producing animals Reprint Icon - (Peer Reviewed Journal)
Allen, H.K., Levine, U.Y., Looft, T.P., Bandrick, M.M., Casey, T. 2013. Treatment, promotion, commotion: Antibiotic alternatives in food-producing animals. Trends in Microbiology. 21(3):114-119.
Collateral effects of antibiotics on mammalian gut microbiomes - (Peer Reviewed Journal)
Looft, T.P., Allen, H.K. 2012. Collateral effects of antibiotics on mammalian gut microbiomes. Gut Microbes. 3(5):463-467.
Profiling the gastrointestinal microbiota in response to Salmonella: low versus high Salmonella shedding in the porcine host - (Abstract Only)
Bearson, S.M., Allen, H.K., Bearson, B.L., Looft, T.P., Brunelle, B.W., Kich, J.D., Bayles, D.O., Alt, D.P., Levine, U.Y., Stanton, T.B. 2012. Profiling the gastrointestinal microbiota in response to Salmonella: low versus high Salmonella shedding in the porcine host [abstract]. American Society for Microbiology General Meeting, June 16-19, 2012, San Francisco, California. p. 3150.
Estimating richness from phage metagenomes - (Abstract Only)
Allen, H.K., Bunge, J., Foster, J.A., Stanton, T.B. 2012. Estimating richness from phage metagenomes [abstract]. American Society for Microbiology General Meeting, June 16-19, 2012, San Francisco, California. Paper No. 2462.
Isolation of unique butyrate-producing bacteria from swine - (Abstract Only)
Levine, U.Y., Looft, T.P., Allen, H.K., Stanton, T.B. 2012. Isolation of unique butyrate-producing bacteria from swine [abstract]. American Society for Microbiology General Meeting, June 16-19, 2012, San Francisco, California. Paper No. 3143.
Estimating population diversity with CatchAll - (Peer Reviewed Journal)
Bunge, J., Woodard, L., Bohning, D., Foster, J.A., Connolly, S., Allen, H.K. 2012. Estimating population diversity with CatchAll. Bioinformatics. 28(7):1045-1047. Available: http://bioinformatics.oxfordjournals.org/content/28/7/1045.long.
In-feed antibiotic effects on the swine intestinal microbiome - (Peer Reviewed Journal)
Looft, T.P., Johnson, T., Allen, H.K., Bayles, D.O., Alt, D.P., Cole, J., Hashsham, S., Stedtfeld, R., Stedtfeld, T., Chai, B., Tiedje, J., Stanton, T.B. 2012. In-feed antibiotic effects on the swine intestinal microbiome. Proceedings of the National Academy of Sciences. 109(5):1691-1696.
Antibiotics in feed induce prophages in swine fecal microbiomes - (Peer Reviewed Journal)
Allen, H.K., Looft, T.P., Bayles, D.O., Humphrey, S.B., Levine, U.Y., Alt, D.P., Stanton, T.B. 2011. Antibiotics in feed induce prophages in swine fecal microbiomes. mBio [serial online]. 2(6). Available: http://mbio.asm.org/content/2/6/e00260-11.
Estimating population diversity with unreliable low frequency counts - (Peer Reviewed Journal)
Bunge, J., Bohning, D., Allen, H.K., Foster, J. 2012. Estimating population diversity with unreliable low frequency counts. Pacific Symposium on Biocomputing (PSB) [serial online]. 17:203-212. Available: http://psb.stanford.edu/psb-online/proceedings/psb12/abstracts/2012_p203.html.
Diverse Phage in the Swine Intestine - (Abstract Only) - (02-May-10)
Metagenomic and 16S rRNA Analyses of Fecal Bacteria of Swine Given Diets Containing Antibiotics - (Abstract Only) - (02-May-10)
Psychrotrophic Strain of Janthinobacterium lividum from a Cold Alaskan Soil Produces Prodigiosin - (Peer Reviewed Journal)
Schloss, P.D., Allen, H.K., Klimowicz, A.K., Mlot, C., Gross, J.A., Savengsuksa, S., Mcellin, J., Clardy, J., Ruess, R.W., Handelsman, J. 2010. Psychrotrophic Strain of Janthinobacterium lividum from a Cold Alaskan Soil Produces Prodigiosin. DNA and Cell Biology. 29(9):533-541.
Investigating the Overlooked Genomes That Impact Animal Health: The Gut Microbiome - (Abstract Only) - (15-Mar-10)
Swine Intestinal Tract Harbors a High Diversity of Butyrate-Producing Bacteria - (Abstract Only) - (11-Mar-10)
Last Modified: 11/27/2014
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