Comparisons of microbiomes in conventional and alternative poultry production systems

Authors: Rothrock, Michael

Submitted to: Poultry Science Association Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/28/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary: With the advent of new sequencing technologies and platforms, entire microbiomes are more easily characterized than ever before, while initially used more as a surveying tool to determine what microbial taxa (and their relative abundance) comprise various microbiomes, using microbiome data in a more applied manner is essential to make it more applicable to the poultry industry. While the US poultry industry is dominated by commercial, conventional management practices, upwards of 20% of the market is now comprised of poultry products produced using alternative management systems (e.g. organic, all natural, pastured). Therefore, is it not only essential that we use applied microbiomic analysis of poultry microbiomes throughout the various conventional poultry production environments, but they should also be applied to the diverse environments in these alternative management systems. For this symposium talk, I will review the applied microbiome studies that we have been performed on the different environments of the conventional poultry production system (hatchery, live production, processing plant), and then present similar data from pastured poultry flock management systems. While general trends and taxa comparisons will be discussed, applying these microbiome tools to address food safety issues will be highlighted. Also to be stressed will be the need to link this data to other important metadata (e.g. management data, physiochemistry, cultural data) to truly unlock the potential of these datasets to address the complex issues facing our increasingly diverse poultry industry.

Technical Abstract: With the advent of new sequencing technologies and platforms, entire microbiomes are more easily characterized than ever before, while initially used more as a surveying tool to determine what microbial taxa (and their relative abundance) comprise various microbiomes, using microbiome data in a more applied manner is essential to make it more applicable to the poultry industry. While the US poultry industry is dominated by commercial, conventional management practices, upwards of 20% of the market is now comprised of poultry products produced using alternative management systems (e.g. organic, all natural, pastured). Therefore, is it not only essential that we use applied microbiomic analysis of poultry microbiomes throughout the various conventional poultry production environments, but they should also be applied to the diverse environments in these alternative management systems. For this symposium talk, I will review the applied microbiome studies that we have been performed on the different environments of the conventional poultry production system (hatchery, live production, processing plant), and then present similar data from pastured poultry flock management systems. While general trends and taxa comparisons will be discussed, applying these microbiome tools to address food safety issues will be highlighted. Also to be stressed will be the need to link this data to other important metadata (e.g. management data, physiochemistry, cultural data) to truly unlock the potential of these datasets to address the complex issues facing our increasingly diverse poultry industry.