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

Abstract

Inroduction: 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.

Methods: 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).

Results: 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).

Discussion: 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.