Animal Science Department


First Advisor

Gary A. Sullivan

Date of this Version



A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy, Major: Animal Science (Meat Science & Muscle Biology), Under the Supervision of Professor Gary A. Sullivan. Lincoln, Nebraska: May 2019.

Copyright (c) 2019 Chad G. Bower


The objective of this study in its entirety was to utilize high next-generation genetic sequencing to evaluate the microbial communities involved with processed meat spoilage. High throughput 16S rRNA gene sequencing on the Illumina MiSeq© platform was used alongside traditional plating methods to characterize the growth and composition of bacterial communities in processed meats. Previous results from this lab indicated a relatively high prevalence of Pseudomonas in cooked, sliced, and vacuum packaged deli meats, which was contrary to conventional wisdom. Therefore, four studies were designed to further evaluate the factors that may influence microbial communities in processed meats. Study 1 aimed to identify differences between the processing environment in which sliced deli-ham is produced, handled, and packaged. Products within the same category description from three separate processors had significantly different bacterial community profiles, however, all had prevalence of Pseudomonas, to varying degrees. Study 2 was designed to determine differences in the bacterial communities of various phases throughout processing, from raw ground beef to cooking, slicing, and applying an antimicrobial or post-lethality treatment. Raw ground beef and sliced bologna had similar bacterial community profiles, having the least microbial diversity with a high prevalence of Pseudomonas, while both cured and uncured links, and bologna with high pressure processing (HPP) or with organic acid salts had a higher proportion of various Firmicutes and Proteobacteria. Study 3 aimed to determine the differences in microbial community composition of sliced bologna caused by different clean-label and traditional antimicrobials. Increased growth and a higher prevalence of Pseudomonas were observed in the control treatment with no antimicrobial, while all antimicrobial treatments had greater microbial diversity, with increased amounts of various organisms compared to the Control. Study 4 aimed to identify differences in the microbial community composition between franks smoked with natural hardwood smoke, dipped in liquid smoke, or unsmoked. Minimal bacterial growth was observed in all three treatments throughout 14 weeks of refrigerated storage, and there were minuscule differences in their bacterial community composition. Differences in the microbial community composition of processed meats are vital to extending the shelf-life of products and further understanding their relationship with meat spoilage.

Advisor: Gary A. Sullivan