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Evaluation of Microbial Community Dynamics Impacting the Shelf-Life of Processed Meats Chad G

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Evaluation of Microbial Community Dynamics Impacting the Shelf-Life of Processed Meats Chad G University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Theses and Dissertations in Animal Science Animal Science Department 5-2019 Evaluation of Microbial Community Dynamics Impacting the Shelf-Life of Processed Meats Chad G. Bower University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/animalscidiss Part of the Agriculture Commons, and the Animal Sciences Commons Bower, Chad G., "Evaluation of Microbial Community Dynamics Impacting the Shelf-Life of Processed Meats" (2019). Theses and Dissertations in Animal Science. 187. https://digitalcommons.unl.edu/animalscidiss/187 This Article is brought to you for free and open access by the Animal Science Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Theses and Dissertations in Animal Science by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. EVALUATION OF MICROBIAL COMMUNITY DYNAMICS IMPACTING THE SHELF-LIFE OF PROCESSED MEATS by Chad G. Bower 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 EVALUATION OF MICROBIAL COMMUNITY DYNAMICS IMPACTING THE SHELF-LIFE OF PROCESSED MEATS Chad G. Bower, Ph.D. University of Nebraska, 2019 Advisor: Gary A. Sullivan 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. iv ACKNOWLEDGEMENTS I would like to thank my supervisory committee for providing guidance throughout my project and for challenging me to develop my skills as a scientist and professional. I would like to thank my advisor, Dr. Gary Sullivan, for giving me the opportunity to study meat science for the past six years and helping me translate my hands-on experience into scientific skills. I would like to thank all of my fellow grad students who have come and gone during my years at the University of Nebraska. Whether it be banding together to get a project done, or hanging out on weekends to blow off steam, the students I have been fortunate enough to study with are second to none. To our support staff, especially Sherri Pitchie, Tommi Jones, and Calvin Schrock, I can honestly say nothing would get done in this place without your help. Lastly, to the students in Dr. Fernando’s lab, who took me in as one of their own, I thank you for all the time and struggles of finishing my genomic work. I would like to thank my parents and my family back home, who have supported me throughout this journey, even when they ask about my studies knowing my explanation will confuse them. I know how much work it takes to provide for a family, and I will be forever grateful for all the opportunities I was awarded thanks to my parents’ efforts. Most important of all, I would like to thank my wife, Jesse, for being my rock throughout this journey and in life. Having your support has been vital to my time in graduate school, and coming home to you and our children make even the most v frustrating days worth it. Everything I have done and will do in this life is for you and our kids, and I cannot wait to continue our future and watch Paisley and Lane grow. vi TABLE OF CONTENTS Acknowledgements ................................................................................................... iv Introduction ............................................................................................................... 1 Review of Literature ................................................................................................... 4 1. Introduction ...................................................................................................................4 2. The Microbiota of Meat ..................................................................................................5 3. Factors Affecting Meat Spoilage ......................................................................................7 3.1 Temperature .................................................................................................................................... 8 3.2 Moisture and Water Activity ............................................................................................................ 9 3.3 Atmospheric Gas ............................................................................................................................ 10 3.4 pH ................................................................................................................................................... 12 3.5 Metabolic Substrates ..................................................................................................................... 13 4. Microbial Interventions to Increase Shelf-life ................................................................ 14 4.1 Cooking .......................................................................................................................................... 15 4.2 Smoking ......................................................................................................................................... 17 4.3 Fermentation ................................................................................................................................. 18 4.4 Drying ............................................................................................................................................. 20 4.5 Packaging ....................................................................................................................................... 21 4.6 Antimicrobials ................................................................................................................................ 22 4.7 Bioprotective Cultures ................................................................................................................... 26 5. Quality of Processed Meats .......................................................................................... 27 5.1 Salt ................................................................................................................................................. 28 5.2 Nitrite ............................................................................................................................................. 31 5.3 Organic Acids ................................................................................................................................. 32 vii 6. Techniques for Evaluating Microbial Ecology ................................................................. 33 7. Data Analyses for Microbial Ecology ............................................................................. 35 8. Conclusion ................................................................................................................... 37 Detailed Materials & Methods .................................................................................
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