A Comparison of 16S rRNA Profiles Through Slaughter in Australian Export Beef Abattoirs

Microbial contamination of beef cattle carcases and subsequent cross-contamination during processing is inevitable and virtually impossible to prevent. The understanding of microbial contamination in the beef industry is currently limited to hypotheses based on traditional microbiological tools. Additionally, the complex structural and functional responses of beef cattle microbial communities to the fragmentation in the supply chain remains unknown. This study used 16S rRNA metagenomics in combination with traditional microbiology to monitor and compare changes in the microbiota throughout slaughter in an integrated (abattoir A) and a fragmented (abattoir B) beef abattoir in Australia. The composition in the bacterial communities varied between the abattoirs, though the presence of the most predominant bacterial species within the microbiota at each abattoir was similar. Lactobacillales and Pseudomonadales most notably dominated hides, carcases and the environment in abattoir B. In abattoir A, Bacteroidales, Lactobacillales and Pseudomonadales fluctuated but generally shared the dominance over the rest. Combined results of total viable count (TVC) and 16S rRNA gene profiling revealed that an upward hide pulling system adopted by abattoir B led to increased transmission of hide contaminants to post-hide pull carcases. The findings from this study indicate that common beef-associated microbiota exist in varying composition in Australian abattoirs and 16S rRNA metagenomics is a powerful tool to understand in-depth movement of microbial contaminants.