RNA-based characterization of ribosomally active microbial communities during beef slaughtering

Abstract

Microbiological contamination on beef carcasses shortens shelf-life and poses substantial food-safety risks. The application of RNA-based analysis nowadays enables insights into the potentially active fraction of microbial communities by targeting ribosomal RNA rather than DNA. Here, we profiled the rRNA-derived microbiota present at three critical stages of cattle slaughter, skinning, splitting, and chilling, in an Austrian slaughterhouse, using 16S rRNA cDNA sequencing (Illumina MiSeq). While microbial alpha diversity was similar across the three processing stations, PERMANOVA revealed a statistically significant effect of the processing step on microbial community composition. Carcasses at skinning and chilling harbored high relative abundances of rRNA-derived Pseudomonas and the Escherichia-Shigella group. The high relative abundance of Pseudomonas spp., a psychrotrophic spoilage-associated genus, suggests potential metabolic activity and a possible contribution to quality deterioration at low temperatures, while the Escherichia-Shigella group is commonly used as an indicator of possible fecal contamination and hygiene deficiencies. Eperythrozoon (Mycoplasma) was more abundant at the splitting stage and, to a lesser extent, at the chilling stage, suggesting that some cattle may enter the slaughter already colonized and facilitating cross-contamination during carcass manipulation. The subsequent decline during chilling aligns with the cold sensitivity and limited environmental persistence of Eperythrozoon (Mycoplasma) . These findings demonstrate the value of RNA-based approaches for delineating the active fraction of carcass-associated microbiota, with potential to inform interventions that enhance meat hygiene and safety.