Food surveillance programs have traditionally relied on culture-dependent tools for the detection and enumer-ation of microbial groups along the food chain.While essential,these approaches provide a limited view of co...Food surveillance programs have traditionally relied on culture-dependent tools for the detection and enumer-ation 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 complemen-tary insights into microbial diversity and function.Given the global consumption of poultry meat and its sig-nificance 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 ap-proaches reveal microbial diversity and functional genes related to antimicrobial resistance,virulence,and ge-netic 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.展开更多
基金supported by Projects PID2021-123404NB-I00 and PID2024-156601NA-I00 funded by MICIU/AEI/10.13039/501100011033 and by“ERDF A way of making Europe”and by the Government of Aragón(Grant Grupo AESA A06_23 R)Department of Science,Technology,and University Education of the Government of Aragón(Spain)provided N.Merino with a Grant Odón de Buen to carry out this research.
文摘Food surveillance programs have traditionally relied on culture-dependent tools for the detection and enumer-ation 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 complemen-tary insights into microbial diversity and function.Given the global consumption of poultry meat and its sig-nificance 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 ap-proaches reveal microbial diversity and functional genes related to antimicrobial resistance,virulence,and ge-netic 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.
