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

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.

A call for antibiotic alternatives research - (Peer Reviewed Journal)

Stanton, T.B. 2013. A call for antibiotic alternatives research. Trends in Microbiology. 21(3):111-113.

Poultry intestinal microbiota (turkeys; chickens) – animal health and food safety perspectives - (Book / Chapter)

Levine, U.Y., Stanton, T.B. 2012. Poultry intestinal microbiota (turkeys; chickens) – animal health and food safety perspectives. Encyclopedia of Metagenomics [serial online]. Available: http://www.springerreference.com/docs/html/chapterdbid/303274.html.

Cloacibacillus porcorum sp. nov.,–a mucin-degrading bacterium from the swine intestinal tract - (Peer Reviewed Journal)

Looft, T.P., Levine, U.Y., Stanton, T.B. 2012. Cloacibacillus porcorum sp. nov.,–a mucin-degrading bacterium from the swine intestinal tract. International Journal of Systematic and Evolutionary Microbiology. Available: http://ijs.sgmjournals.org/content/early/2012/10/02/ijs.0.044719-0.full.pdf+html.

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.

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.

Mitsuokella jalaludinii inhibits growth of Salmonella enterica serovar Typhimurium - (Peer Reviewed Journal)

Levine, U.Y., Bearson, S.M., Stanton, T.B. 2012. Mitsuokella jalaludinii inhibits growth of Salmonella enterica serovar Typhimurium. Veterinary Microbiology. 159(1-2):115-122.

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.

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.

Exploring the impacts of antibiotics on the microbial communities in the swine intestinal tract - (Abstract Only)

Looft, T.P., Stanton, T.B. 2011. Exploring the impacts of antibiotics on the microbial communities in the swine intestinal tract [abstract]. 71st Annual Meeting of the North Central Branch of the American Society for Microbiology. October 7-8, 2011. Des Moines, Iowa. 62:136.

Mitsuokella jalaludinii inhibits growth of Salmonella enterica serovar Typhimurium - (Abstract Only)

Levine, U.Y., Bearson, S.M., Stanton, T.B. 2011. Mitsuokella jalaludinii inhibits growth of Salmonella enterica serovar Typhimurium [abstract]. 71st Annual Meeting of the North Central Branch of the American Society for Microbiology. October 7-8, 2011, Des Moines, Iowa. 60:147.

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.

Chlortetracycline - resistant intestinal bacteria in organically-raised and feral swine - (Peer Reviewed Journal)

Stanton, T.B., Humphrey, S.B., Stoffregen, W.C. 2011. Chlortetracycline - resistant intestinal bacteria in organically-raised and feral swine. Applied and Environmental Microbiology. 77(20):7167-7170.