Food Safety Research Information Office
Title:Animal Intestinal Microbiomes, Foodborne Pathogens, and Antimicrobials
Objective:

1. Identify and characterize intestinal ecological niches and their impact on foodborne pathogen survival, persistence, colonization, or virulence. In a broader systematic approach, evaluate the interactions among environmental influences (e.g., management, production) and ecological niches on phenotypic and genotypic characteristics and food safety.

2. Evaluate the effects of antimicrobials on intestinal microbiomes, and on the expression and transmission of virulence, fitness, and antimicrobial resistance genes in culture and the host.

3. Develop a functional metagenomic approach to identify gene products that inhibit foodborne pathogen growth, interfere with virulence gene expressions, or reduce antimicrobial resistance (and enhance food safety).

4. Assess role of commensal intestinal bacteria in evolution, persistence, or transmission of resistance genes. Evaluate novel strategies for reducing antimicrobial resistant organisms and resistance genes.

5. Evaluate the effects of environmental influences (e.g., management, production), ecological niches and vaccine strategies on phenotypic and genotypic characteristics of Campylobacter (specifically in turkeys).

More Info:
Approach: Research to control Campylobacter in turkeys will be pursued by subfractionating, identifying and characterizing microbial species in turkey ceca which are potential Campylobacter antagonists. Cecal populations will be subfractionated in vivo by antibiotic applications and dexamethasone induced stress. Potentially useful species will initially be associated with Campylobacter reductions in vivo and confirmed in vitro by using co-cultures. Two other approaches for controlling Campylobacter will be tested: dietary additives (prebiotics and probiotics) and a prime-boost vaccination strategy using C. jejuni surface membrane protein CjaA expressed in a recombinant strain of attenuated Salmonella. The commensal anaerobe Megasphaera elsdenii will be used as an archetype intestinal bacterium to identify common antibiotic resistance genes and transfer mechanisms in the intestinal tract and to test M. elsdenii as a site for tetracycline resistance gene evolution in that ecosystem. In a probiotic type attempt, a mix of five antibiotic sensitive M. elsdenii strains will be used to block the transmission of antibiotic resistant strains from mother sow to offspring pigs. Metagenomic, culture, and PCR methods will be used to assess the effects of dietary antibiotics (ASP250, carbadox, and other antibiotics) on swine and turkey microbiomes. Specific areas of research will include the influence of subinhibitory antibiotics on the production of Salmonella bacteriophages carrying fitness or virulence genes and on phage mediated gene transfer between Salmonella strains (transduction). These studies will be carried out with Salmonella Typhimurium strains in culture and in a mouse model. Functional metagenomics assays involving recombinant E. coli and Salmonella strains containing reporter plasmids will be used to identify gene products which either affect Salmonella virulence or are inhibitory for Salmonella growth.
Funding Source:United States Department of Agriculture (USDA), Agricultural Research Service (ARS)
Type:Appropriated
Start Date:2010
End Date:2015
Project Number:3625-31320-003-00
Accession Number:420876
Institutions:USDA/ARS - Midwest Area
Investigators:Allen, Heather
Casey, Thomas
Looft, Torey
Stanton, Thaddeus
Project Reports:2013 Annual Report
2012 Annual Report
2011 Annual Report
Published Journal
Articles USDA
ARS (NP 108):
Bacteria, phages, and pigs: The effect of in-feed antibiotics on bacterial membership, metabolic potential, and phages in different gut locations
Looft TP, Allen HK, Cantarel B, Levine UY, Bayles DO, Alt DP, Henrissat B, Stanton TB .
J Int Soc Microbial Ecol. 2014 Feb 13. [Epub ahead of print]
Colostral antibody-mediated and cell-mediated immunity contributes to innate and antigen-specific immunity in piglets
Bandrick M, Ariza-Nieto C, Baidoo SK, Molitor TW.
Dev Comp Immunol. 2013 Nov 16;43(1):114-20.
Butyrate-producing bacteria, including mucin degraders, from the swine intestinal tract
Levine UY, Looft TP, Allen HK, Stanton TB .
Appl Environ Microbiol. 2013 Jun;79:3879-81.
The modulating role of dissolved organic matter on spatial patterns of microbial metabolism in Lake Erie sediments
Bouzat JL, Hoostal MJ, Looft T.
Journal of Great Lakes Research. 2013 Jun;39(2):344-51.
Cloacibacillus porcorum sp. nov., a mucin-degrading bacterium from the swine intestinal tract and emended description of the genus Cloacibacillus
Looft T, Levine UY, Stanton TB.
Int J Syst Evol Microbiol. 2013 Jun;63:1960-6.
A call for antibiotic alternatives research
Stanton TB.
Trends Microbiol. 2013 Mar;21(3):111-3.
Treatment, promotion, commotion: Antibiotic alternatives in food-producing animals
Allen HK, Levine UY, Looft T, Bandrick M, Casey TA.
Trends Microbiol. 2013 Mar;21(3):114-9.
Estimation of viral richness from shotgun metagenomes using a frequency count approach
Allen HK, Bunge J, Foster JA, Bayles DO, Stanton TB.
BMC Microbiome. 2013 Feb 4;1:5.
Mitsuokella jalaludinii inhibits growth of Salmonella enterica serovar Typhimurium
Levine UY, Bearson SM, Stanton TB.
Vet Microbiol. 2012 Sep 14;159(1):115-22.
Collateral effects of antibiotics on mammalian gut microbiomes
Looft T, Allen HK.
Gut Microbes. 2012 Sep;3(5):463-7.
Estimating population diversity with CatchAll
Bunge J, Woodard L, Böhning D, Foster JA, Connolly S, Allen HK.
Bioinformatics. 2012 Apr 1;28(7):1045-7.
Estimating population diversity with unreliable low frequency counts
Bunge J, Böhning D, Allen H, Foster JA.
Pac Symp Biocomput. 2012;:203-12.
Antibiotics in feed induce prophages in swine fecal microbiomes
Allen HK, Looft T, Bayles DO, Humphrey S, Levine UY, Alt D, Stanton TB.
MBio. 2011 Nov 29;2(6):.
Chlortetracycline-resistant intestinal bacteria in organically raised and feral Swine
Stanton TB, Humphrey SB, Stoffregen WC.
Appl Environ Microbiol. 2011 Oct;77(20):7167-70.
Non-journal publications:
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.
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.
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.
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.
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.
Food Safety Categories:On-Farm Food Safety
Methodology
Pathogen Biology
Farm-to-Table categories:On-farm food production
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