University of Veterinary Medicine Vienna Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities The resident microbiome in food industries may impact on food quality and safety. In particular, microbes residing on surfaces in dairy industries may actively participate in cheese fermentation and ripening and contribute to the typical flavor and texture. In this work, we carried out an extensive microbiome mapping in 73 cheese-making industries producing different types of cheeses (fresh, medium and long ripened) and located in 4 European countries. We sequenced and analyzed metagenomes from cheese samples, raw materials and environmental swabs collected from both food contact and non-food contact surfaces, as well as operators' hands and aprons. Dairy plants were shown to harbor a very complex microbiome, characterized by high prevalence of genes potentially involved in flavor development, probiotic activities, and resistance to gastro-intestinal transit, suggesting that these microbes may potentially be transferred to the human gut microbiome. More than 6100 high-quality Metagenome Assembled Genomes (MAGs) were reconstructed, including MAGs from several Lactic Acid Bacteria species and putative new species. Although microbial pathogens were not prevalent, we found several MAGs harboring genes related to antibiotic resistance, highlighting that dairy industry surfaces represent a potential hotspot for antimicrobial resistance (AR) spreading along the food chain. Finally, we identified facility-specific strains that can represent clear microbial signatures of different cheesemaking facilities, suggesting an interesting potential of microbiome tracking for the traceability of cheese origin. en TEXT article Probiotics; Cheese microbiology; Metagenome; Food Microbiology; Microbiota; Humans; Dairying methods; Europe; Metagenomics methods; Bacteria genetics classification isolation & purification 2024 2024 De Filippis, Francesca (University of Naples Federico II) Ercolini, Danilo (University of Naples Federico II) Ruas-Madiedo, Patricia (Instituto de Productos Lácteos de Asturias / Instituto de Investigación Sanitaria del Principado de Asturias) Calvete-Torre, Inés (Instituto de Productos Lácteos de Asturias / Instituto de Investigación Sanitaria del Principado de Asturias) Quijada, Narciso Martín (University of Veterinary Medicine Vienna / Austrian Competence Centre for Feed and Food Quality, Safety and Innovation) Cobo-Díaz, José F (Universidad de León) Carlino, Niccolò (University of Trento) Barcenilla, Coral (Universidad de León) Cabrera-Rubio, Raul (Teagasc - The Irish Agriculture and Food Development Authority / Instituto de Agroquímica y Tecnología de Alimentos) Valentino, Vincenzo (University of Naples Federico II) Yap, Min (Teagasc - The Irish Agriculture and Food Development Authority) Cotter, Paul D. (Teagasc - The Irish Agriculture and Food Development Authority / University College Cork) Álvarez-Ordóñez, Avelino (Universidad de León) Segata, Nicola (University of Trento) Margolles, Abelardo (Instituto de Productos Lácteos de Asturias / Instituto de Investigación Sanitaria del Principado de Asturias) Wagner, Martin (University of Veterinary Medicine Vienna / Austrian Competence Centre for Feed and Food Quality, Safety and Innovation) Pasolli, Edoardo (University of Naples Federico II) Sequino, Giuseppina (University of Naples Federico II) Sabater, Carlos (Instituto de Productos Lácteos de Asturias / Instituto de Investigación Sanitaria del Principado de Asturias) Nature Portfolio