Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

, 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 KlaassensStephen Knobloch, Dominic O'Neil, Narciso M Quijada, Carlos Sabater, Sigurlaug Skírnisdóttir, Vincenzo Valentino, Liam Walsh, 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, Angela Sessitsch, Tanja Kostic, Johanna Maria Ley, Milica Pastar, Livio Antonielli

Publikation: Beitrag in FachzeitschriftArtikelBegutachtung

Abstract

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.

OriginalspracheEnglisch
Seitenumfang37
FachzeitschriftCell
Volume187
Issue20
DOIs
PublikationsstatusElektronische Veröffentlichung vor Drucklegung - 16 Aug. 2024

Research Field

  • Exploration of Biological Resources

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