o:3530 Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities en 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. Probiotics; Cheese microbiology; Metagenome; Food Microbiology; Microbiota; Humans; Dairying methods; Europe; Metagenomics methods; Bacteria genetics classification isolation & purification 1552099 10.1038/s41522-024-00541-5 2024-10-04T10:06:18.400Z 44 yes 46 Francesca De Filippis University of Naples Federico II 0000-0002-3474-2884 Vincenzo Valentino University of Naples Federico II person 0000-0002-6055-4721 Min Yap Teagasc - The Irish Agriculture and Food Development Authority person Raul Cabrera-Rubio Teagasc - The Irish Agriculture and Food Development Authority / Instituto de Agroquímica y Tecnología de Alimentos person Coral Barcenilla Universidad de León person 0000-0002-3956-3914 Niccolò Carlino University of Trento person 0009-0004-7409-449X José F Cobo-Díaz Universidad de León person 0000-0002-0898-2358 Narciso Martín Quijada University of Veterinary Medicine Vienna / Austrian Competence Centre for Feed and Food Quality, Safety and Innovation person 0000-0002-1956-7205 Inés Calvete-Torre Instituto de Productos Lácteos de Asturias / Instituto de Investigación Sanitaria del Principado de Asturias person Patricia Ruas-Madiedo Instituto de Productos Lácteos de Asturias / Instituto de Investigación Sanitaria del Principado de Asturias person Carlos Sabater Instituto de Productos Lácteos de Asturias / Instituto de Investigación Sanitaria del Principado de Asturias person Giuseppina Sequino University of Naples Federico II person Edoardo Pasolli University of Naples Federico II person Martin Wagner University of Veterinary Medicine Vienna / Austrian Competence Centre for Feed and Food Quality, Safety and Innovation person 0000-0001-8032-9858 Abelardo Margolles Instituto de Productos Lácteos de Asturias / Instituto de Investigación Sanitaria del Principado de Asturias person Nicola Segata University of Trento person 0000-0002-1583-5794 Avelino Álvarez-Ordóñez Universidad de León person 0000-0002-9951-4786 Paul D. Cotter Teagasc - The Irish Agriculture and Food Development Authority / University College Cork person 0000-0002-5465-9068 Danilo Ercolini University of Naples Federico II person 0000-0003-3061-9560 application/pdf 5388996 https://phaidra.vetmeduni.ac.at/o:3530 no yes 16 70 1552253 NPJ Biofilms and Microbiomes 16 10 1 Nature Portfolio 2024