New version (FoodMicrobionet v 4.2)

This version is a small improvement over FoodMicrobionet 4.1.2 and includes 211 studies, 12,748 samples, 9,640 taxa and 1,019,872 taxon-sample relationships. The main improvements are:

  • A versions table was added to facilitate tracking changes
  • ASV tables for all studies processed with DADA2 are now accessible (via accession number)
  • former links to Florilege now point to Omnicrobe.

As usual, the database will be publicly available (on GitHub and Mendeley data) when the first paper describing it is published.

Stay tuned for version 4.2

I am about to release version 4.2. With more than 12,000 samples, more than 210 studies and almost 1,000,000 sample-taxa relationships this is by far the largest database of metataxonomic studies on the composition of bacterial communities of food and food environments. Further improvements include:a. I have reprocessed almost all studies from version 0.6, 1 and 2. b. the integration with sequence data is greatly improved: it is now possible to access ASVs using the study accession number. The R lists containing the phyloseqs with the ASVs will be available on Zenodo from September 1st, 2022.

New review

After some effort we have managed to publish a new review on Microbial association network in cheese:

Parente, E., Zotta, T., Ricciardi, A., n.d. A review of methods for the inference and experimental confirmation of microbial association networks in cheese. Int J Food Microbiol 368, 109618.

You can get free reprints (until April 29, 2022) using this link.

New data and workflow.

A new version of DairyFMBN has been added to Mendeley data ( and quarantine will expire at the end of July. This is connected to an astounding ( 😉 )workflow for inference of microbial association networks, which is available on GitHub ( Both are related to a review on microbial association networks in cheese which is about to be published as a preprint…