Niccolò Carlino Niccolò Carlino Aitor Blanco-Míguez Aitor Blanco-Míguez Michal Punčochář Michal Punčochář Claudia Mengoni Claudia Mengoni Federica Pinto Federica Pinto Alessia Tatti Alessia Tatti Paolo Manghi Paolo Manghi Federica Armanini Federica Armanini Michele Avagliano Michele Avagliano Coral Barcenilla Coral Barcenilla Samuel Breselge Samuel Breselge Raul Cabrera-Rubio Raul Cabrera-Rubio Inés Calvete-Torre Inés Calvete-Torre Mairéad Coakley Mairéad Coakley José F. Cobo-Díaz José F. Cobo-Díaz Francesca De Filippis Francesca De Filippis Hrituraj Dey Hrituraj Dey John Leech John Leech Eline S. Klaassens Eline S. Klaassens Stephen Knobloch Stephen Knobloch Dominic O'Neil Dominic O'Neil Narciso M. Quijada Narciso M. Quijada Carlos Sabater Carlos Sabater Sigurlaug Skírnisdóttir Sigurlaug Skírnisdóttir Vincenzo Valentino Vincenzo Valentino Liam Walsh Liam Walsh Master EU Consortium Avelino Alvarez-Ordóñez Avelino Alvarez-Ordóñez Francesco Asnicar Francesco Asnicar Gloria Fackelmann Gloria Fackelmann Vitor Heidrich Vitor Heidrich Abelardo Margolles Abelardo Margolles Viggó Thór Marteinsson Viggó Thór Marteinsson Omar Rota Stabelli Omar Rota Stabelli Martin Wagner Martin Wagner Danilo Ercolini Danilo Ercolini Paul D. Cotter Paul D. Cotter Nicola Segata Nicola Segata Edoardo Pasolli Edoardo Pasolli Cell Press 2024 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. PDFDocument eng 2024-12-09T10:40:31.554115Z 2024 Food Microbiome Human Microbiome Food Strain-Level Genomics Metagenomics Metagenomic Assembly Large-Scale Microbiome Analysis Unexplored Microbial Diversity 13934965 b application/pdf application/pdf http://creativecommons.org/licenses/by-nc-nd/4.0/