Versions

FoodMicrobionet is an ongoing initiative and the original plan was to publish new versions at 6 months intervals. From version 0.6 to 2 FMBN versions were made publicly available as interactive visualisations as they were published in scientific journals or presented at scientific meetings. Companion files were made available to members of the FoodMicrobionet consortium (web visualisation, Gephi and Cytoscape network files, nodes and edge tables) as they became available and to the scientific community (web visualisation, nodes and edge tables) upon publication of an update in a scientific journal. Visit this page to learn more on the FoodMicrobionet tools. From version 3.0 our new policy is to distribute FoodMicrobionet as a Shiny app and, if at all possible, to make it available on data repositories (Mendeley data). See below for further details. Gephi web visualisations are not released any more, but you can build them yourself in Gephi using the .gml file which can be exported using the app.

  • FMBN v 0.6.2 is the first proof of concept version. It includes data from 9 published and unpublished studies on dairy products and dairy starter cultures. Click here for details.
  • FMBN v 1.0.2 is the first public version. It includes data from 17 published and unpublished studies on dairy foods, meat, sourdoughs and fermented vegetable products (olives). Click here for details.
  • FMBN v 1.0.3 includes minor updates to the previous version (including updates to references for published studies. Click here for details. 
  • FMBN v 1.0.3g is a “robust” version of v 1.0.3. In this version the nodes for OTUs identified as belonging to the same genus were merged and low abundance (<0.1%) OTUs were removed from each sample. This might alleviate the problems related to comparison of studies in which different bioinformatics platfors were used. Click here for details.
  • FMBN1.1 is an intermediate version which has been presented as a poster at FoodMicro 2016, in Dublin. Click here for details.
  • FMBN2.0 is a significantly improved version. It includes 33 studies, 29 of which have been published or are about to be published. With 3929 nodes (2204 OTU nodes, 1413 Food samples, from 59 food types, 312 Food environment nodes) and 87197 connections between OTU and Sample/Environment nodes, Click here for details.

  • FMBN2.0.2. A minor update. Click here for details.

  • FMBN2.0.3. Minor changes. Improved accessibility using R scripts. Click here for details.
  • FMBN3.0. Major changes in tables structures and improved accessibility using a Shiny app. Click here for details.
  • FMBN3.1. Major changes: structure of tables revised, app improved.  Click here for details. Published as: Parente, E., De Filippis, F., Ercolini, D., Ricciardi, A., Zotta, T., 2019. Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database. International Journal of Food Microbiology, 305 (September 2019): 108249 DOI: 10.1016/j.ijfoodmicro.2019.108249.
  • FMBN3.2.3. Click here for details (December 2019).
  • FMBN3.2.6. Click here for details (June 11, 2020).
  • FMBN4.1.2. Click here for details (December 15, 2021).