Research Article: Ground beef microbiome changes with antimicrobial decontamination interventions and product storage

Date Published: June 5, 2019

Publisher: Public Library of Science

Author(s): Margaret D. Weinroth, Brianna C. Britton, Kathryn R. McCullough, Jennifer N. Martin, Ifigenia Geornaras, Rob Knight, Keith E. Belk, Jessica L. Metcalf, Joy Scaria.


Ground beef makes up more than half of the beef consumed in the U.S. market. Although numerous studies have been conducted on microbial safety and shelf life of ground beef limited work has been done using a culture-independent approach. While past studies have allowed for the evaluation of a few organisms of interest, there is limited work on the microbial community associated with fresh ground beef. In order to have a more complete picture of the microbial ecology of the product, a culture-independent approach utilizing 16S rRNA gene amplicon sequencing was used. The objectives of this study were to characterize the fresh ground beef microbiome and the effect that antimicrobial interventions and antioxidants, applied to beef trim before grinding, and product storage have on community composition using 16S rRNA gene amplicon sequencing. Beef trimmings were treated with antimicrobials and an antioxidant. Samples were ground, loafed, and overwrapped before being packaged in modified-atmosphere packaging. Samples were in dark storage for 21 days followed by five days in retail display. Periodically during storage, samples were collected for microbiological analysis and DNA isolation. Due to low microbial biomass, only 52 of 210 samples were included in the final analysis. These samples represented two antimicrobial treatments (peroxyacetic acid, and a sulfuric acid and sodium sulfate blend) and a control, from day-15 of dark storage and day-5 of retail display. As sample age increased, so did the number of raw reads (P < 0.001) and aerobic plate counts (P < 0.001), which were correlated (r = 0.94, P = 0.017). Across all samples, lactic acid bacteria were most abundant followed by Enterobacteriaceae; several rare taxa were also identified (namely Geobacillus, Thermus, and Sporosarcina). Antimicrobial treatment altered the bacterial alpha (P < 0.001) and beta (P = 0.001) diversity, while storage day altered alpha (P = 0.001) diversity. Enterobacteriaceae relative abundance differed (P < 0.05) among treatments and was highest in control samples. In addition to confirming previously described dominant microbial differences in culture-dependent results, these data identified genera not typically associated with ground beef and allowed for study of shifts in the entire microbiome and not just a subset of indicator organisms.

Partial Text

Beef is a widely consumed protein in the U.S. market, with an estimated per capita consumption of 54.4 lbs in 2017 [1]. Of this, an estimated 62% of all beef sold is ground [2]. The marketing of ground beef relies on a safe product that has an acceptable shelf life. In terms of safety, Escherichia coli O157:H7, non-O157 Shiga toxin-producing E. coli (STEC), and Salmonella spp. are pathogens that have been associated with ground beef [3–5]. In conjunction with safety concerns, the quality of ground beef over time has also been extensively studied. While spoilage bacteria (such as Lactobacillus spp., Leuconostoc spp., and Pseudomonas spp. [6]) are not a threat to consumer health, their growth during product storage can decrease shelf life and increase off flavor and odors. Factors such as storage temperature, food safety interventions, packaging type, and length of distribution and retail display all have an effect on the shelf life of the product.