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 remain unknown. This study used 16S rRNA gene sequencing 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. Briefly, the primary difference between an integrated and a fragmented abattoir is that fragmented abattoirs receive cattle from multiple sources, whereas integrated abattoirs typically receive cattle that has been produced using the same production system and from a limited number of sources. 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 (2.4-56.2%) and Pseudomonadales (2.4-59.4%) most notably dominated hides, carcases, and the environment in abattoir B. In abattoir A, Bacteroidales (3.9-43.8%), Lactobacillales (0.0-61.9%), and Pseudomonadales (0.5-72.1%) fluctuated but generally shared the dominance over the rest. Combined results of total viable count (TVC) and 16S rRNA gene profiling indicated that an upward hide pulling system adopted by abattoir B may lead to increased transmission of hide contaminants to post-hide pull carcases. Abattoir B had 3.2 log₁₀CFU/cm² reduction from hide to carcase, where abattoir A had 4.5 log₁₀CFU/cm² reduction. The findings from this study indicated that common beef-associated microbiota exist in varying composition in Australian abattoirs, and 16S rRNA amplicon sequencing is a powerful tool to understand in-depth movement of microbial contaminants.