You are what you eat?

Well, maybe your microbiome is about 3% exactly what you ate, at least.

ABSTRACT

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

AUTHORS: Niccolò Carlino, Aitor Blanco-Míguez, Michal Punčochář, Paul D. Cotter, Nicola Segata1, Edoardo Pasolli and many more...

DOI: doi: 10.1016/j.cell.2024.07.039

Published online in Cell, 2024/09/03

Highlights

With curated Food Metagenomic Data (FMD), we integrated and analyzed >2,500 food metagenomes.

Over 10,000 prokaryotic and eukaryotic MAGs uncover substantial food microbial diversity.

Food microbes account for up to an average of 3% of the adult gut microbiome.

Strain-level analysis highlights potential instances of food-to-gut microbe transmission.

Summary

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.