https://phaidra.vetmeduni.ac.at/o:3737 Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome Carlino, Niccolò Niccolò Carlino Blanco-Míguez, Aitor Aitor Blanco-Míguez Punčochář, Michal Michal Punčochář Mengoni, Claudia Claudia Mengoni Pinto, Federica Federica Pinto Tatti, Alessia Alessia Tatti Manghi, Paolo Paolo Manghi Armanini, Federica Federica Armanini Avagliano, Michele Michele Avagliano Barcenilla, Coral Coral Barcenilla Breselge, Samuel Samuel Breselge Cabrera-Rubio, Raul Raul Cabrera-Rubio Calvete-Torre, Inés Inés Calvete-Torre Coakley, Mairéad Mairéad Coakley Cobo-Díaz, José F. José F. Cobo-Díaz De Filippis, Francesca Francesca De Filippis Dey, Hrituraj Hrituraj Dey Leech, John John Leech Klaassens, Eline S. Eline S. Klaassens Knobloch, Stephen Stephen Knobloch O'Neil, Dominic Dominic O'Neil Quijada, Narciso M. Narciso M. Quijada 0000-0002-1956-7205 Sabater, Carlos Carlos Sabater Skírnisdóttir, Sigurlaug Sigurlaug Skírnisdóttir Valentino, Vincenzo Vincenzo Valentino Walsh, Liam Liam Walsh Master EU Consortium Alvarez-Ordóñez, Avelino Avelino Alvarez-Ordóñez Asnicar, Francesco Francesco Asnicar Fackelmann, Gloria Gloria Fackelmann Heidrich, Vitor Vitor Heidrich Margolles, Abelardo Abelardo Margolles Marteinsson, Viggó Thór Viggó Thór Marteinsson Rota Stabelli, Omar Omar Rota Stabelli Wagner, Martin Martin Wagner 0000-0001-8032-9858 Ercolini, Danilo Danilo Ercolini Cotter, Paul D. Paul D. Cotter Segata, Nicola Nicola Segata Pasolli, Edoardo Edoardo Pasolli Cell Press journal article open access eng 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. Food Microbiome Human Microbiome Food Strain-Level Genomics Metagenomics Metagenomic Assembly Large-Scale Microbiome Analysis Unexplored Microbial Diversity http://creativecommons.org/licenses/by-nc-nd/4.0/ https://phaidra.vetmeduni.ac.at/api/object/o:3737/download 10.1016/j.cell.2024.07.039 https://phaidra.vetmeduni.ac.at/o:605 application/pdf Cell issn:1097-4172 VoR Cell 187 20 13.29 MB 2024