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. 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

doi:10.1016/j.cell.2024.07.039

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Title (eng)

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

Author

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

Abstract (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.

Keywords (eng)

Food MicrobiomeHuman MicrobiomeFoodStrain-Level GenomicsMetagenomicsMetagenomic AssemblyLarge-Scale Microbiome AnalysisUnexplored Microbial Diversity

Type (eng)

journal article

Language

[eng]

Persistent identifier

https://phaidra.vetmeduni.ac.at/o:3737

DOI

10.1016/j.cell.2024.07.039

Is in series

Title (eng)