Curated Food Metagenomic Data

curatedFoodMetagenomicData (cFMD)

Within Domino, University of Trento is working on the implementation of the curatedFoodMetagenomicData (cFMD) resource.

The cFMD is a curated, open resource that compiles:

• • High quality curated metadata on food samples

• • Taxonomic profiles, showing which microbes are present

• • Functional profiles, showing what microbes are capable to do

• • Reconstructed microbial genomes

This allows researchers to explore the microbial diversity present in foods and study how these microbes may affect food quality, safety, fermentation, and even potential links with the human microbiome.

Last release (June 2026)

• cFMDv1.3.2: available at the website: https://github.com/SegataLab/cFMD

Main highlights of the release:

• Addition of new 681 metagenomes in the cFMD database from 22 publicly available studies.
• These newly added metagenomes represent 16 countries, with Morocco being a new addition to the list.
• New metagenomes are taxonomically profiled with MetaPhlAn 4 (marker genes database vJan25) and functionally profiled with HUMAnN v3.6 (v30_CHOCOPhlAn_201901).
• Integration of 3,071 prokaryotic genomes and 205 eukaryotic genomes assembled from the new datasets.

Improvements compared to the previous release:

• 20% increase in the no. of food metagenomes.
• Almost 30% increase (28.9%) in the total no. of reconstructed microbial genomes.
• Inclusion of novel food products such as korean rice vinegar and yucha along with expanding food types from broader categories such as fruits, vegetables and meats.

Therefore, now “cFMD encompasses 18,180 reconstructed microbial genomes spanning 1,153 prokaryotic SGBs and 110 eukaryotic SGBs comprehending 4,125 metagenomes that are consistently profiled. These metagnomes are linked with 109 food-related studies and represent 54 countries.”

The cFMD continues to be a cornerstone resource for anyone studying the microbial landscape of the foods we eat.

Definitions:

1. Metagenome refers to the genetic content of any group of microorganisms.
2. Eukaryotic genomes refer to the complete set of genes or genetic material present a eukaryotic cell (in this context present in food).
3. Prokaryotic genomes refer to the complete set of genes and genetic material present in a prokaryotic cell.
4. SGB (species level genome bins) refer to a genome-based definition of a microbial species.

Access and further reading

🔗Explore the FMD database

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

🔗 Check out the cFMD workshop held for DOMINO partners

🔗 Read more about University of Trento and his involvement in Domino.