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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Poultry Microbiological Safety and Processing Research Unit » Research » Publications at this Location » Publication #287114

Title: The poultry-associated microbiome: network analysis and characterization along the farm-to-fork continuum

item Oakley, Brian
item Morales, Cesar
item Line, John
item Berrang, Mark
item Meinersmann, Richard - Rick
item TILLMAN, GLENN - Food Safety Inspection Service (FSIS)
item WISE, MARK - Biomerieux, Inc
item SIRAGUSA, GREGORY - Danisco Usa, Inc
item Hiett, Kelli
item Seal, Bruce

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 10/1/2012
Publication Date: 10/25/2012
Citation: Oakley, B., Morales, C., Line, J.E., Berrang, M.E., Meinersmann, R.J., Tillman, G.E., Wise, M.G., Siragusa, G.R., Hiett, K.L., Seal, B.S. 2012. The poultry-associated microbiome: network analysis and characterization along the farm-to-fork continuum. Southeastern Branch of the American Society for Microbiology. October 25-27, 2012. Athens, GA.

Interpretive Summary:

Technical Abstract: Agriculture represents an important link between animal-associated microbes and humans as food-borne pathogens continue to be a leading cause of illness and hospitalizations. We combined high-throughput sequencing (HTS), network analysis, and quantitative-PCR (qPCR) assays to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Network analysis focused on the foodborne pathogen Campylobacter revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2-4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and several putative pathogens, including multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were metabolically active and encountered in on-farm samples. These data represent the first HTS-based characterization of poultry-associated microbiomes along the farm-to-fork continuum and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.