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United States Department of Agriculture

Agricultural Research Service

Research Project: Animal Intestinal Microbiomes, Foodborne Pathogens, and Antimicrobials Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Bacteria, phages, and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations - (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. DOI: 10.1038/ismej.2014.12.
Colostral antibody-mediated and cell-mediated immunity contributes to innate and antigen-specific immunity in piglets - (Peer Reviewed Journal)
(06-Nov-13)
Heat stress: intestinal barrier and immune disruption in pigs - (Abstract Only)
(23-Oct-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.
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.
Spatial patterns of microbial community composition within Lake Erie sediments - (Peer Reviewed Journal)
Bouzat, J., Hostel, M., Looft, T.P. 2013. Spatial patterns of microbial community composition within Lake Erie sediments. Journal of Great Lakes Research. 39(2):344-351.
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.
A call for antibiotic alternatives research     Reprint Icon - (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 and emended description of the genus Cloacibacillus - (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 and emended description of the genus Cloacibacillus. International Journal of Systematic and Evolutionary Microbiology. 63:1960-1966.
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.
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. Available: http://bioinformatics.oxfordjournals.org/content/28/7/1045.long.
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.
Last Modified: 4/18/2014
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