Ground Beef Microbiome Changes with Antimicrobial Decontamination Interventions and Product Storage

Numerous studies have been conducted on microbial safety and shelf life of ground beef, though limited work has been done using a culture-independent approach. The objective of this study was to characterize the fresh ground beef microbiome and the effect that antimicrobial interventions, 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. These data confirm previously described microbial differences in culture-dependent results while identifying genera not typically associated with ground beef.