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 met...

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Detalles Bibliográficos
Autores: Carlino, Niccolò, Blanco-Míguez, Aitor, Punčochář, Michal, Mengoni, Claudia, Pinto, Federica, Tatti, Alessia, Manghi, Paolo, Armanini, Federica, Avagliano, Michele, Barcenilla, Coral, Breselge, Samuel, Cabrera-Rubio, Raúl, Calvete-Torre, Inés, Coakley, Mairéad, Cobo-Díaz, José F., De Filippis, Francesca, Dey, Hrituraj, Leech, John, Klaassens, Eline S, Knobloch, Stephen, O'Neil, Dominic, Quijada, Narciso M., Sabater, Carlos, Skírnisdóttir, Sigurlaug, Valentino, Vincenzo, Walsh, Liam, Alvarez-Ordóñez, Avelino, Asnicar, Francesco, Fackelmann, Gloria, Heidrich, Vitor, Margolles Barros, Abelardo, Marteinsson, Viggó Thór, Rota Stabelli, Omar, Wagner, Martin, Ercolini, Danilo, Cotter, Paul D, Segata, Nicola, Pasolli, Edoardo
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/373917
Acceso en línea:http://hdl.handle.net/10261/373917
https://api.elsevier.com/content/abstract/scopus_id/85204442573
Access Level:acceso abierto
Palabra clave:Food
Food microbiome
Human microbiome
Large-scale microbiome analysis
Metagenomic assembly
Metagenomics
Strain-level genomics
Unexplored microbial diversity
Descripción
Sumario: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.

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