Projects

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

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Profiling the gastrointestinal microbiota in response to Salmonella: low versus high Salmonella shedding in the natural porcine host - (Peer Reviewed Journal)

Bearson, S.M., Allen, H.K., Bearson, B.L., Looft, T.P., Brunelle, B.W., Kich, J.D., Christopher, T.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. Available: http://authors.elsevier.com/sd/article/S1567134813000956.

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 - (Peer Reviewed Journal)

Allen, H.K., Bunge, J., Foster, J.A., 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 - (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):1-5. Available: http://www.landesbioscience.com/journals/gutmicrobes/article/21288/?nocache=632992022.

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.

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)