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Browsing Theses and Dissertations by Subject "16S amplicon sequencing"

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    Ground beef degradation: evolution of chemical and microbial properties and sensory characteristics during shelf-life
    (Colorado State University. Libraries, 2019) Levey, Jennifer R., author; Martin, Jennifer N., advisor; Belk, Keith E., committee member; Woerner, Dale R., committee member; Prenni, Jessica E., committee member
    Two separate experiments were conducted on the same lots of ground beef. The first experiment aimed to examine changes in culture-dependent microbes and the changes in sensory characteristics and chemical properties in aerobically stored ground beef after 16/17d and 23/24d dark storage periods in anaerobic chub packaging. Three lots of ground beef one lot from the West (n=30) and two lots from the Midwest (n=100)) were treated as three separate replications. The three lots were stored in 4.54kg chub packages for 16 or 17 days and 23 or 24 days dark storage prior to regrinding and packaging into PVC overwrapped trays. The overwrapped trays were placed into a retail case under fluorescent lights for 5d. Subjective odor score (off-odor intensity; 1 = no off-odor to 5 = extreme off-odor), traditional culture bacterial counts (Pseudomonas spp., Enterobacteriacae, Lactic Acid Bacteria, and psychrotrophic plate counts), and lipid oxidation indicators were analyzed as a split-plot design, whereas subjective (1= Very bright red to 6= Very dark red or brown) and objective color (Hunter CIE L*, a*, and b* values) were analyzed as a repeated measures design. All bacterial counts increased (P≤0.05) during retail case display following both dark storage periods. Overall, off-odor intensity increased (P≤0.05) over both retail case display periods; however, the off-odor intensity score after 16/17d dark storage was lesser than the off-odor intensity score after 23/24d dark storage. Subjective color panel scores for ground beef redness decreased (P≤0.05) over both retail case display periods; however, a more rapid decrease (P≤0.05) in ground beef color during the retail case display period was observed after 23/24d dark storage comparative to 16/17 day dark storage. Similarly, the redness (a* value) decreased (P≤0.05) more rapidly following 23/24d dark storage comparative to after 16/17d dark storage. An increase (P≤0.05) in TBARS values was observed for both retail case display periods. For the second experiment, instead of using culture-dependent microbiological methods, culture-independent methods of investigating microbial diversity were employed in conjunction with a GC/MS analysis of the volatile organic acids (VOCs) produced during storage. 16S rRNA amplicon sequencing was utilized to analyze the diversity and microbial constituents of the microbial community during the retail case display period after both 16/17d and 23/24d dark storage, and a targeted analysis utilizing GC/MS was used to evaluate the changes of VOCs production. The relative peak areas of the VOCs were analyzed as a split-plot design, where replication was the main plot, dark storage period was the sub-plot, and retail case storage day was the sub-subplot. Differences (P≤0.05) in Faith Phenotypic Diversity Index were observed during retail case display; however, the range of diversity was (1.02 to 1.28) was not large enough to be biologically relevant. The taxonomic analysis resulted in bacteria previously identified to contribute to beef spoilage. Lactobacillales, Enterobacteriales, and Pseudomonadales were in the top ten bacteria orders present across all samples throughout retail case display. Eighteen different VOCs were identified through the targeted analysis. The compounds identified via targeted analysis included aldehydes, ketones, volatile fatty acids, sulfones, and alcohols. Hexanal, an indicator of spoilage, increased (P≤0.05) during both retail case display periods. Moreover, acetoin and acetic acid also increased (P≤0.05) during both retail case display periods.