Assessing Commercial and Alternative Poultry Processing Methods using Microbiome Analyses

Authors: Rothrock, Michael

Submitted to: International Poultry Scientific Forum
Publication Type: Abstract Only
Publication Acceptance Date: 11/17/2017
Publication Date: 1/29/2018
Citation: Rothrock Jr, M.J. 2018. Assessing Commercial and Alternative Poultry Processing Methods using Microbiome Analyses. International Poultry Scientific Forum. p. M121.

Interpretive Summary: Assessing poultry processing methods/strategies has historically used culture-based methods to assess bacterial changes or reductions, both in terms of general microbial communities (e.g. total aerobic bacteria) or zoonotic pathogens of interest (e.g. Salmonella, Campylobacter). The advent of next generation sequencing technology has greatly expanded out ability to "dive deep" into the microbiota of poultry processing and assess how different processing methods or strategies may be affecting these poultry-associated microbiota. 16S microbiome analysis using the QIIME pipeline was used to look at strategies used in conventional and small-scale poultry processing plants effect the different types of microbiomes within those environments. Within the conventional poultry processing plant, microbiome analysis was performed to see how microbial populations change within the major processing water tanks (scalder, chiller) throughout a typical processing day, and how water sampling methods effect those microbiomes. Work performed within the small-scale poultry operation setting assessed how different processing/butchering methods u(e.g. small USDA-inspected facilities versus on-farm butchering, removing versus keeping on skin) affect the cecal and post-processing whole carcass rinse microbiomes, and how product storage method (fresh, refrigerated, frozen) affected the final product whole carcass rinse microbiomes. In all cases, microbiome data not only showed changes within the overall microbial community, but shifts in bacterial pathogens (e.g. Salmonella, Campylobacter, Listeria) were also able to be observed. Lastly, data will also be shown that demonstrates how taking a combination culture-based and microbiome approach can help determine the efficacy of new interventions within the processing plant environment. These results highlight the use and utility of microbiome analyses within the poultry processing environment, and how linking it with culture-based analyses can be an important tool for researchers and industry stakeholders in the future.

Technical Abstract: Assessing poultry processing methods/strategies has historically used culture-based methods to assess bacterial changes or reductions, both in terms of general microbial communities (e.g. total aerobic bacteria) or zoonotic pathogens of interest (e.g. Salmonella, Campylobacter). The advent of next generation sequencing technology has greatly expanded out ability to "dive deep" into the microbiota of poultry processing and assess how different processing methods or strategies may be affecting these poultry-associated microbiota. 16S microbiome analysis using the QIIME pipeline was used to look at strategies used in conventional and small-scale poultry processing plants effect the different types of microbiomes within those environments. Within the conventional poultry processing plant, microbiome analysis was performed to see how microbial populations change within the major processing water tanks (scalder, chiller) throughout a typical processing day, and how water sampling methods effect those microbiomes. Work performed within the small-scale poultry operation setting assessed how different processing/butchering methods u(e.g. small USDA-inspected facilities versus on-farm butchering, removing versus keeping on skin) affect the cecal and post-processing whole carcass rinse microbiomes, and how product storage method (fresh, refrigerated, frozen) affected the final product whole carcass rinse microbiomes. In all cases, microbiome data not only showed changes within the overall microbial community, but shifts in bacterial pathogens (e.g. Salmonella, Campylobacter, Listeria) were also able to be observed. Lastly, data will also be shown that demonstrates how taking a combination culture-based and microbiome approach can help determine the efficacy of new interventions within the processing plant environment. These results highlight the use and utility of microbiome analyses within the poultry processing environment, and how linking it with culture-based analyses can be an important tool for researchers and industry stakeholders in the future.