RNA-based characterization of ribosomally active microbial communities during beef slaughtering
4 affiliations
- 1Centre for Food Science, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna , ,
- 2Centre for Veterinary Public Health and One Health, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna , ,
- 3Clinical Centre for Population Medicine in Fish, Pig and Poultry, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna , ,
- 4Department of Veterinary and Animal Sciences, University of Copenhagen , ,
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.
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BibTeX
@article{chaughtai2026rnabased,
title = {{RNA-based characterization of ribosomally active microbial communities during beef slaughtering}},
author = {Muhammad Sharjeel Chaughtai and Franz-Ferdinand Roch and Sarah Thalguter and Tea Movsesijan and Beate Conrady and Monika Dzieciol and Martin Wagner and Evelyne Selberherr},
journal = {Frontiers in microbiology},
year = {2026},
month = sep,
doi = {10.3389/fmicb.2026.1946469},
url = {https://europepmc.org/article/PMC/PMC13662132},
note = {CC BY},
}
RIS
TY - JOUR
TI - RNA-based characterization of ribosomally active microbial communities during beef slaughtering
AU - Muhammad Sharjeel Chaughtai
AU - Franz-Ferdinand Roch
AU - Sarah Thalguter
AU - Tea Movsesijan
AU - Beate Conrady
AU - Monika Dzieciol
AU - Martin Wagner
AU - Evelyne Selberherr
PY - 2026
DA - 2026/09/30
JO - Frontiers in microbiology
DO - 10.3389/fmicb.2026.1946469
UR - https://europepmc.org/article/PMC/PMC13662132
AB - 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.
SN - 1664-302X
ER -