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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 #291443

Title: The poultry-associated microbiome: network analysis and farm-to-fork characterizations

item Oakley, Brian
item MORALES, CESAR - Former ARS Employee
item Line, John
item Berrang, Mark
item Meinersmann, Richard - Rick
item TILLMAN, GLENN - Former ARS Employee
item Wise, Mark
item SIRAGUSA, GREGORY - Former ARS Employee
item Hiett, Kelli
item Seal, Bruce

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/20/2013
Publication Date: 7/21/2013
Citation: Oakley, B., Morales, C., Line, J.E., Berrang, M.E., Meinersmann, R.J., Tillman, G.E., Wise, M., Siragusa, G., Hiett, K.L., Seal, B.S. 2013. The poultry-associated microbiome: network analysis and farm-to-fork characterizations. Federation of European Microbiological Societies Microbiology. July 21-25, 2013. Leipzig, Germany.

Interpretive Summary:

Technical Abstract: Background: As the source of a majority of emerging infectious diseases, animal-associated microbiomes represent a nexus of food safety, animal health, and public health. Objectives and Methods: To profile poultry-associated microbiomes and important pathogens at various stages of commercial poultry production from farm to consumer, high-throughput sequencing (HTS) was combined with novel quantitative-PCR assays and network analysis of HTS microbiome data. Conclusions: 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 2-4 times lower than fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses 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 multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were encountered in on-farm samples. Network analysis revealed a majority of Campylobacter sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. Characterizing the poultry microbiome across a series of farm-to-fork samples demonstrates the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.