University of Veterinary Medicine Vienna Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication. en TEXT journal article Wissenschaftlicher Artikel Text Wissenschaftlicher Artikel Text journal article Food Microbiome Human Microbiome Food Strain-Level Genomics Metagenomics Metagenomic Assembly Large-Scale Microbiome Analysis Unexplored Microbial Diversity 2024 2024 Niccolò Carlino Aitor Blanco-Míguez Michal Punčochář Claudia Mengoni Federica Pinto Alessia Tatti Paolo Manghi Federica Armanini Michele Avagliano Coral Barcenilla Samuel Breselge Raul Cabrera-Rubio Inés Calvete-Torre Mairéad Coakley José F. Cobo-Díaz Francesca De Filippis Hrituraj Dey John Leech Eline S. Klaassens Stephen Knobloch Dominic O'Neil Narciso M. Quijada Carlos Sabater Sigurlaug Skírnisdóttir Vincenzo Valentino Liam Walsh Master EU Consortium Avelino Alvarez-Ordóñez Francesco Asnicar Gloria Fackelmann Vitor Heidrich Abelardo Margolles Viggó Thór Marteinsson Omar Rota Stabelli Martin Wagner Danilo Ercolini Paul D. Cotter Nicola Segata Edoardo Pasolli Cell Press