Evaluation of the fresh beef bacterial community through processing retail display conditions using 16S rRNA gene amplification sequencing



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Microorganisms are ubiquitous and provide challenges in the food production system. Beyond monitoring for pathogens or food safety hazards, there is a need for understanding and controlling spoilage organisms, and indicators of potential spoilage especially with products that have a more limited shelf-life, such as fresh meat. Arguably, just as important, yet less widely studied is the presence and behavior of the natural product microbial community.

This project was composed of two phases, one with whole muscle steaks, and another with ground beef. Both employed 16S rRNA sequencing to better understand the bacterial community in fresh beef. The overall objective was to characterize the microbial community in fresh beef from the U.S. and understand how packaging environment and retail display influence changes or shifts in the community. The first project evaluated the microbial community of beef steaks subjected to four different packaging environments widely used in the beef industry and to one of three different retail display conditions. The second project evaluated the bacterial community present in commercially ground beef that either had or had not been exposed to lactic acid as beef trim, after three chub storage aging periods and retail display. For the microbial community evaluation DNA extractions were performed prior to 16S rRNA sequencing on the V3-V4 region. Data processing and filtering were performed with the DADA2 package in R. Analysis was performed on relative abundance, alpha diversity, and beta diversity values.

Dominant phyla in both studies were Proteobacteria and Firmicutes. Commonly identified genera at end of retail display of fresh beef steaks included Carnobacterium, Pseudomonas, and Lactobacillus. At the phyla level, lighting and packaging type did not have a significant effect on relative abundance. There were, however, some indications that lighting had an effect on some of the genera. With retail steaks, this study provided some evidence that light exposure of packages may have an impact on the genera found on fresh beef steaks. Ground beef, from untreated trim, bacterial richness was found to decrease with retail display time. From this study it was determined that an antimicrobial dip, in combination with chub storage age and retail display, can influence the microbial community of ground beef.



Beef, Microbiome, Microbial community, Shelf-life, Fresh meat, 16S