Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Food Science (PhD)

Degree Level



Food Science


Steven Ricke

Committee Member

B.J. Bench

Second Committee Member

Michael Johnson

Third Committee Member

Steven Foley

Fourth Committee Member

Young Min Kwon


Food borne-disease, Food Safety, interventions, Microbiology, Microbiota, Next Generation Sequencing, Poultry Processing


The poultry industry and associated regulatory bodies use whole bird carcass (WBC) rinsates to evaluate different stages of broiler processing systems for the prevalence of food-borne pathogens, including Salmonella spp. and Campylobacter spp. Within industry and research groups, the same sample collections are enumerated to determine E. coli, Enterobacteriaceae (EB), and Aerobic Plate Count (APC) microorganisms. Analysis of these indicator microorganisms provides numerical data that can be used to demonstrate the effects of specific process control steps where low occurrences of target pathogens hinder the exclusive use of prevalence data. With the utilization of next generation sequencing (NGS), including analysis of 16s rDNA sequences, a more complete characterization of the microbial communities present (the microbiota) can be identified. Microbiota analysis applied to samples collected within the pre-evisceration stages of a commercial broiler processing facility highlighted shifts in enteric microorganisms that were not fully recognized by traditional microbiological culture methods and provided a better understanding of cross-contamination events within those stages of the process. Additionally, microbiota data provided a more complete evaluation of spoilage and sanitary dress indicator microorganisms which were not identified using the traditional culturing methodologies. In addition to evaluating the processing system, microbiota analysis has also helped to identify how a change in the applied rinse solution could affect downstream microbiological analyses. Cultured microbiological methods indicated significant differences (P ≤ 0.05) in APC levels of the two rinsates, but no significant differences in EB, Salmonella spp. or Campylobacter spp. prevalence. In contrast, beta diversity analysis of the microbiota compositions of the two rinsate types and associated matrices used to assess those levels of microorganisms revealed a marked difference (P < 0.05) at the operational taxonomic unit (OTU) level.