Investigation of the anaerobic microbiota of beef carcass and rump steak cuts from five meat plants using 16S rRNA high- throughput sequencing

Vacuum packaging of beef extends shelf-life by preventing the growth of aerobic bacteria. However, anaerobic bacteria can still cause spoilage. The presence of anaerobic microflora on fresh beef carcass and rump steaks, which may contribute to meat spoilage, was explored. A total of 120 carcass and 120 rump steak swabs were collected in five meat plants. Swab samples were anaerobically enriched and incubated at 4°C for 3 weeks. This was followed by DNA extraction and 16S rRNA amplicon sequencing using the Illumina MiSeqTM, with subsequent bioinformatics analysis. The enriched microbiota of the samples was classified and grouped into 149 operational taxonomic units (OTUs). Both sample types consisted mainly of Carnobacterium, with an average relative abundance of 28.4% and 32.8% in beef carcasses and beef rump steaks, respectively. This was followed by Streptococcus, Serratia, Lactococcus, Enterococcus, Escherichia-Shigella, Raoultella and Aeromonas ranging from 1.5-20% and 0.1-29.8% in enriched carcasses and rump steak swabs, respectively. Trichococcus, Bacteroides, Dysgomonas, Providencia, Paraclostridium and Proteus were also present ranging from 0-0.8% on carcass and 0-1.8% on rump steak swabs, respectively. Alpha and Beta diversity measurements showed limited diversity between the two sample types, but some differences between samples from the beef plants investigated were evident. Keywords: beef carcass, rump steak, 16S rRNA sequencing, spoilage bacteria