{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T06:56:19Z","timestamp":1790751379722,"version":"4.1.0"},"reference-count":47,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Inroduction<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>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).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:italic>Pseudomonas<\/jats:italic>\n                      and the\n                      <jats:italic>Escherichia-Shigella<\/jats:italic>\n                      group. The high relative abundance of\n                      <jats:italic>Pseudomonas<\/jats:italic>\n                      spp., a psychrotrophic spoilage-associated genus, suggests potential metabolic activity and a possible contribution to quality deterioration at low temperatures, while the\n                      <jats:italic>Escherichia-Shigella<\/jats:italic>\n                      group is commonly used as an indicator of possible fecal contamination and hygiene deficiencies.\n                      <jats:italic>Eperythrozoon (Mycoplasma)<\/jats:italic>\n                      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\n                      <jats:italic>Eperythrozoon (Mycoplasma)<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1946469","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T06:06:00Z","timestamp":1790748360000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["RNA-based characterization of ribosomally active microbial communities during beef slaughtering"],"prefix":"10.3389","volume":"17","author":[{"given":"Muhammad Sharjeel","family":"Chaughtai","sequence":"first","affiliation":[{"name":"Centre for Food Science, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna","place":["Vienna, Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franz-Ferdinand","family":"Roch","sequence":"additional","affiliation":[{"name":"Centre for Veterinary Public Health and One Health, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna","place":["Vienna, Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Thalguter","sequence":"additional","affiliation":[{"name":"Clinical Centre for Population Medicine in Fish, Pig and Poultry, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna","place":["Vienna, Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tea","family":"Movsesijan","sequence":"additional","affiliation":[{"name":"Centre for Food Science, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna","place":["Vienna, Austria"]},{"name":"Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH","place":["Tulln, Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beate","family":"Conrady","sequence":"additional","affiliation":[{"name":"Department of Veterinary and Animal Sciences, University of Copenhagen","place":["Copenhagen, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monika","family":"Dzieciol","sequence":"additional","affiliation":[{"name":"Centre for Food Science, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna","place":["Vienna, Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Wagner","sequence":"additional","affiliation":[{"name":"Centre for Food Science, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna","place":["Vienna, Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelyne","family":"Selberherr","sequence":"additional","affiliation":[{"name":"Centre for Food Science, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine Vienna","place":["Vienna, Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-018-0470-z","article-title":"Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2\u2019s q2-feature-classifier plugin","volume":"6","author":"Bokulich","year":"2018","journal-title":"Microbiome"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. 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