000168529 001__ 168529 000168529 005__ 20260209162330.0 000168529 0247_ $$2doi$$a10.1016/j.fbio.2026.108356 000168529 0248_ $$2sideral$$a147942 000168529 037__ $$aART-2026-147942 000168529 041__ $$aeng 000168529 100__ $$0(orcid)0000-0003-4774-0973$$aMerino, Natalia$$uUniversidad de Zaragoza 000168529 245__ $$aDeciphering poultry microbial ecosystems by classical and modern tools 000168529 260__ $$c2026 000168529 5060_ $$aAccess copy available to the general public$$fUnrestricted 000168529 5203_ $$aFood surveillance programs have traditionally relied on culture-dependent tools for the detection and enumeration of microbial groups along the food chain. While essential, these approaches provide a limited view of complex microbial ecosystems, often underestimating fastidious and viable but non-culturable microorganisms. In recent years, culture-independent tools, including sequencing and omics-based strategies, offer complementary insights into microbial diversity and function. Given the global consumption of poultry meat and its significance for food safety, spoilage, and antimicrobial resistance dissemination, a comprehensive characterization of poultry-associated microbial communities is essential. This review critically examines culture-dependent and culture-independent approaches to study the microbiome, resistome, virulome, and mobilome across the poultry production chain, comparing the type of information generated, their advantages and limitations. Culturedependent methods enable quantification and isolation of viable strains, while culture-independent approaches reveal microbial diversity and functional genes related to antimicrobial resistance, virulence, and genetic mobility. Integrating both strategies strengthens surveillance, improves risk assessment, and supports targeted interventions throughout the poultry sector. This review also highlights key priorities for future research, including greater attention to post-slaughter processing environments, a more systematic investigation of the mobilome and virulome, and the integration of multi-omics, culturomics, and quasi-metagenomics to better link microbial diversity with functional activity and viability. 000168529 536__ $$9info:eu-repo/grantAgreement/ES/DGA/A06-23R$$9info:eu-repo/grantAgreement/ES/MCIU/PID2021-123404NB-I00$$9info:eu-repo/grantAgreement/ES/MICIU/PID2024-156601NA-I00 000168529 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc$$uhttps://creativecommons.org/licenses/by-nc/4.0/deed.es 000168529 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion 000168529 700__ $$0(orcid)0000-0002-3170-9755$$aEspina, Laura 000168529 700__ $$0(orcid)0000-0001-5053-8309$$aBerdejo, Daniel$$uUniversidad de Zaragoza 000168529 700__ $$0(orcid)0000-0002-0238-6328$$aPagán, Rafael$$uUniversidad de Zaragoza 000168529 700__ $$0(orcid)0000-0002-7629-8101$$aGarcía-Gonzalo, Diego$$uUniversidad de Zaragoza 000168529 7102_ $$12008$$2640$$aUniversidad de Zaragoza$$bDpto. Produc.Animal Cienc.Ali.$$cÁrea Nutrición Bromatología 000168529 7102_ $$12008$$2780$$aUniversidad de Zaragoza$$bDpto. Produc.Animal Cienc.Ali.$$cÁrea Tecnología de Alimentos 000168529 773__ $$g77 (2026), 108356 [19 pp.]$$pFood biosci.$$tFood bioscience$$x2212-4292 000168529 8564_ $$s1609525$$uhttps://zaguan.unizar.es/record/168529/files/texto_completo.pdf$$yVersión publicada 000168529 8564_ $$s2559989$$uhttps://zaguan.unizar.es/record/168529/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada 000168529 909CO $$ooai:zaguan.unizar.es:168529$$particulos$$pdriver 000168529 951__ $$a2026-02-09-14:42:48 000168529 980__ $$aARTICLE