v1.3.2

New data:

• Addition of 681 metagenomes from 22 publicly available food studies.

• 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 MAGs and 205 eukaryotic MAGs generated from the new datasets.

Script update:

• The script for downloading MAGs from Zenodo now warns the user and skips when attempting to download MAGs from datasets for which no MAGs were generated.

v1.3.1

New

• Syncronization with MetaCheeseDB

  • Incorporation of two new cheese metagenomic datasets (YasirM_2023 and UNINA_SM_2025), for a total of 134 new samples and 839 new MAGs

  • Inclusion of additional metadata for cheese metagenomic datasets (see https://magliulo.github.io/metacheesedb/jekyll/2025-12-03-metadata.html)

Fix

• Removal of metadata columns from MetaPhlAn 4 taxonomic profiles, enabling more effective integrative analysis across multiple datasets

v1.3.0

New

• Improved SGB/taxonomic assignment of prokaryotic and eukaryotic MAGs newly included in v1.2.1
  • Instead of providing BUSCO-derived taxonomy, eukaryotic MAGs from v1.2.1 are now assigned with the same approach used in Carlino et al, 2024
  • Prokaryotic MAGs that were unassigned in v1.2.1 due to being far (genomic distance > 0.05) from all SGBs in MetaRefSGB vMar22 have now been included in MetaRefSGB vJan25, allowing definition of novel SGBs from the datasets included in v1.2.1
• Updated MetaPhlAn 4 taxonomic profiles with the ChocoPhlAn vJan25 database (previously, vMar22)

Fix

• Inclusion of eukaryotic MAGs in the Zenodo links accessed by the MAG downloader script. These were wrongly missing in the previous version

v1.2.1_patch

This patch release removes 58 metagenomes (and their associated files) from the CM_UNINA_FFOOD dataset that were redundant with metagenomes from the SequinoG_2024_b dataset.

v1.2.1

New data

Inclusion of 835 new food metagenomes and their associated data (metadata, taxonomic profiles, functional profiles, and metagenome-assembled genomes) spanning 26 new publicly available food metagenomic datasets. The new microbiome data was generated using the same tools and databases described in Carlino et al (2024, https://doi.org/10.1016/j.cell.2024.07.039)

New structure

This release also involves a deep re-structuring of the database, which now provides dataset-specific files accessible through dataset-specific folders. Check the repository description for details.

v1.2.0

Addition of HUMAnN functional profiles for the metagenomes analyzed in Carlino et al., "Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome", Cell, 2024 (https://doi.org/10.1016/j.cell.2024.07.039)

v1.1.0

cFMD containing data released and analyzed in the publication: Carlino et al., "Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome", Cell, 2024 (https://doi.org/10.1016/j.cell.2024.07.039)

v1.0.1

cFMD containing data released and analysed in the publication under revision.

v1.0.0

Release relative to the data included and analysed in the paper under revision

Full Changelog: https://github.com/SegataLab/cFMD/commits/v1.0.0