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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.)

Clusters of antibiotic resistance genes enriched together stay together in swine agriculture - (Peer Reviewed Journal)
Johnson, T.A., Stedtfeld, R.D., Wang, Q., Cole, J.R., Hashsham, S.A., Looft, T.P., Zhu, Y., Tiedje, J.M. 2016. Antibiotic resistance genes enriched together stay together: Lessons from swine agriculture. mBio. 7(2):e02214-02215. doi: 10.1128/mBio.02214-02215.
Complete genome sequence of Coriobacteriaceae Strain 68-1-3, a novel mucus- degrading isolate from the swine intestinal tract - (Peer Reviewed Journal)
(25-Aug-15)
A response regulator from a soil metagenome enhances resistance to the beta-lactam antibiotic carbenicillin in Escherichia coli - (Peer Reviewed Journal)
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. 10(3):e0120094. DOI: 10.1371/journal.pone.0120094.
Editorial on virus ecology and disturbances: impact of environmental disruption on the viruses of microorganisms     Reprint Icon - (Other)
Allen, H.K., Stephen, A.T. 2014. Editorial on virus ecology and disturbances: impact of environmental disruption on the viruses of microorganisms. Frontiers in Microbiology. 5(700). Available: http://journal.frontiersin.org/researchtopic/1525.
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.
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.
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: 8/26/2016
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