Deciphering poultry microbial ecosystems by classical and modern tools

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. Culture-dependent 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.