168529 20260209162330.0 doi 10.1016/j.fbio.2026.108356 sideral 147942 ART-2026-147942 eng Merino, Natalia Universidad de Zaragoza (orcid)0000-0003-4774-0973 Deciphering poultry microbial ecosystems by classical and modern tools 2026 Food 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. Access copy available to the general public Unrestricted info:eu-repo/grantAgreement/ES/DGA/A06-23R info:eu-repo/grantAgreement/ES/MCIU/PID2021-123404NB-I00 info:eu-repo/grantAgreement/ES/MICIU/PID2024-156601NA-I00 info:eu-repo/semantics/openAccess by-nc https://creativecommons.org/licenses/by-nc/4.0/deed.es info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Espina, Laura (orcid)0000-0002-3170-9755 Berdejo, Daniel Universidad de Zaragoza (orcid)0000-0001-5053-8309 Pagán, Rafael Universidad de Zaragoza (orcid)0000-0002-0238-6328 García-Gonzalo, Diego Universidad de Zaragoza (orcid)0000-0002-7629-8101 2008 640 Universidad de Zaragoza Dpto. Produc.Animal Cienc.Ali. Área Nutrición Bromatología 2008 780 Universidad de Zaragoza Dpto. Produc.Animal Cienc.Ali. Área Tecnología de Alimentos 77 (2026), 108356 [19 pp.] Food biosci. Food bioscience 2212-4292 1609525 http://zaguan.unizar.es/record/168529/files/texto_completo.pdf Versión publicada 2559989 http://zaguan.unizar.es/record/168529/files/texto_completo.jpg?subformat=icon icon Versión publicada oai:zaguan.unizar.es:168529 articulos driver 2026-02-09-14:42:48 ARTICLE