Skip to main content
ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Egg and Poultry Production Safety Research Unit » Research » Publications at this Location » Publication #339620

Research Project: Reduction of Invasive Salmonella enterica in Poultry through Genomics, Phenomics and Field Investigations of Small Multi-Species Farm Environments

Location: Egg and Poultry Production Safety Research Unit

Title: A Combined 16S Microbiome and Culture-Based Analysis of Foodborne Pathogens Throughout the Entire Lifecycle of A Single Pastured-Raised Broiler Flock

item Rothrock, Michael
item LOCATELLI, AUDE - Department Of Energy
item HIETT, KELLI - Former ARS Employee
item CAUDILL, ANDREW - University Of Georgia

Submitted to: Poultry Science Association Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/5/2017
Publication Date: 7/6/2017
Citation: Rothrock Jr, M.J., Locatelli, A., Hiett, K., Caudill, A. 2017. A Combined 16S Microbiome and Culture-Based Analysis of Foodborne Pathogens Throughout the Entire Lifecycle of A Single Pastured-Raised Broiler Flock. Poultry Science Association Meeting Abstract. p. 536.

Interpretive Summary:

Technical Abstract: While conventionally grown poultry continues to dominate the U.S. poultry industry, there is an increasing demand for locally-grown, “all natural” alternatives. Unfortunately, limited research has been done on this type of poultry management practice, and thus many of these management effects on the environment, poultry products, and human health is unknown. The use of next generation sequencing allows for not only the gross (e.g. community structure) but also fine-scale (e.g. genera abundances) examination of complex microbial communities. Utilizing these technologies can provide a better understanding of the poultry microbiome and how it changes throughout a flock’s life cycle to better elucidate not only the overall microbial ecology of these communities, but specifically the ecology of the foodborne pathogens inherent within poultry production. Broiler samples were taken during the entire flock life cycle, including Hatchery, Brood, Pasture, Processing, and Final Product, as well as samples from other farm animals in close contact with the broilers. Genomic DNA was extracted, 16S microbiomic profiles were generated (Illumina MiSeq), and microbiomes were analyzed and compared using QIIME 1.91 to determine how microbiomes shifted throughout production continuum, as well as what environmental or management factors may be influencing these shifts. Salmonella, Campylobacter, and Listeria were isolated from environmental samples, especially during the Processing and Final Product stages. Significant microbiome shifts occurred during the life cycle of this broiler flock, with microbiomes clustering based on sample type and stage of production continuum. Additionally, while this flock was considered “free-range” with access to and contact with other farm animals, the poultry fecal microbiomes remained distinct from the non-poultry animals throughout their lives.