POULTRY-RELATED MICROBIOME CHANGES FROM EMBRYONIC DEVELOPMENT TO FINAL PRODUCT: A SINGLE PASTURED-RAISED FLOCK FARM-TO-FORK ANALYSIS

Authors: Rothrock, Michael; LOCATELLI, AUDE - Oak Ridge Institute For Science And Education (ORISE); HIETT, KELLI - Former ARS Employee; CAUDILL, ANDREW - University Of Georgia

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/16/2017
Publication Date: 7/9/2017
Citation: Rothrock Jr, M.J., Locatelli, A., Hiett, K.L., Caudill, A.J. 2017. POULTRY-RELATED MICROBIOME CHANGES FROM EMBRYONIC DEVELOPMENT TO FINAL PRODUCT: A SINGLE PASTURED-RAISED FLOCK FARM-TO-FORK ANALYSIS (abstrect). FEMS 2017 Congress. FEMS7-0636.

Interpretive Summary: Background: 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. Objective: 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. Methods: 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. Conclusions: 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.

Technical Abstract: Background: 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. Objective: 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. Methods: 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. Conclusions: 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.