000169232 001__ 169232
000169232 005__ 20260223164759.0
000169232 0247_ $$2doi$$a10.1186/s40168-025-02288-3
000169232 0248_ $$2sideral$$a148290
000169232 037__ $$aART-2026-148290
000169232 041__ $$aeng
000169232 100__ $$aFernández-Trapote, Elena
000169232 245__ $$aMicrobiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life
000169232 260__ $$c2026
000169232 5060_ $$aAccess copy available to the general public$$fUnrestricted
000169232 5203_ $$aBackground Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing. Results The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found. Conclusions Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life.
000169232 536__ $$9info:eu-repo/grantAgreement/ES/MICINN/AEI/CNS2022-136066$$9info:eu-repo/grantAgreement/ES/MICINN/PID2020-118813GB-I00$$9info:eu-repo/grantAgreement/ES/MICINN PRE2021-098910
000169232 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc-nd$$uhttps://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
000169232 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion
000169232 700__ $$aCobo-Díaz, José F.
000169232 700__ $$aOliveira, Márcia
000169232 700__ $$aPuente, Alba
000169232 700__ $$0(orcid)0000-0001-5053-8309$$aBerdejo, Daniel$$uUniversidad de Zaragoza
000169232 700__ $$aPuente, Héctor
000169232 700__ $$aCordero-García, Rebeca
000169232 700__ $$aLópez, Mercedes
000169232 700__ $$aPrieto, Miguel
000169232 700__ $$aArgüello, Héctor
000169232 700__ $$aAlvarez-Ordóñez, Avelino
000169232 7102_ $$12008$$2640$$aUniversidad de Zaragoza$$bDpto. Produc.Animal Cienc.Ali.$$cÁrea Nutrición Bromatología
000169232 773__ $$g14, 1 (2026), [20 pp.]$$pMicrobiome$$tMicrobiome$$x2049-2618
000169232 8564_ $$s3735146$$uhttps://zaguan.unizar.es/record/169232/files/texto_completo.pdf$$yVersión publicada
000169232 8564_ $$s2268373$$uhttps://zaguan.unizar.es/record/169232/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada
000169232 909CO $$ooai:zaguan.unizar.es:169232$$particulos$$pdriver
000169232 951__ $$a2026-02-23-14:55:00
000169232 980__ $$aARTICLE