FMBN version history

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 It includes data from 9 published and unpublished studies on dairy products and dairy starter cultures. The network includes 879 nodes (262 sample nodes and 617 OTU nodes) with 6,015 edges (OTU-sample connections). This version is unpublished.
  • 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 It includes data from 17 published and unpublished studies on dairy foods, meat, sourdoughs and fermented vegetable products (olives). The network includes 552 sample and 964 OTU nodes, with 18,115 OTU-sample interactions, and is by far the largest repository of data on bacterial communities in foods. Click here to access the web visualisation. This version will be presented as oral communication at the 3rd International Conference on Microbial Diversity (Perugia, Italy, October 27-29, 2015). Cite this version as: Parente E., Cocolin L., De Filippis, F., Zotta T., Ferrocino I., Neviani E., De Angelis M., Di Cagno R., Cotter P. D., Ercolini D. 2015. FoodMicrobionet: a tool for the visualisation and analysis of the structure of bacterial food microbial communities. 3rd International Conference on Microbial Diversity, Perugia, October 27-29, 2015.
  • FMBN v 1.0.3 includes minor updates to the previous version (including updates to references for published studies.
  • 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. Cite this version as: Parente E., Cocolin L., De Filippis F., Zotta T., Ferrocino I., O’Sullivan O.,  Neviani E., De Angelis M., Cotter P. D., Ercolini D. 2016. FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis. International Journal of Food Microbiology, 219: 28-37 doi:10.1016/j.ijfoodmicro.2015.12.001. Click here to access the paper on ScienceDirect.
  • FMBN1.1 is an intermediate version which has been presented as a poster at FoodMicro 2016, in Dublin. Minor changes: Corrected an error in weights for BioProject SRP052240 (weights were twice their real value). Checked and corrected all weights for minor rounding errors. Solved a problem related to OTU node merging in Gephi. Corrected wrong labels for some OTUs. Major changes: Added 493 samples from 8 studies. Revised specification for node tables. Introduced “Environment” nodes. Cite this version as: Parente E., De Filippis F., Zotta T., Cotter P., O’Sullivan O., Puglisi E., Ercolini D. 2016. FoodMicrobionet 1.1.6: a network analysis tool for the exploration of food bacterial communities. Food Micro 2016 Abstract Book, Dublin, IRL, July 19-22, 2016. PO2-FS-080.
  • 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, It includes 33 studies, 29 of which have been published or are about to be published.  Minor changes: Corrected mismatches for some samples and bioprojects. Fixed outlinks for sequences deposited in NCBI BioProject database. Corrected a few inconsistencies in lineages and in fields for food classification. Major changes. Revised specification for node and edges tables. Added 672 samples from 8 studies. Added Nreads, Shannon and Chao1 whenever available, otherwise Nreads set to 2999.
  • FMBN2.0.2. A minor update.
  • 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.
  • FMBN3.1. Major changes: structure of tables revised, app improved. There are 44 studies and 2233 samples in this version of FoodMicrobionet. The samples belong to 9 major food groups and 76 different foods. There are 148 different combinations of food, nature, process, fermentation/spoilage. 3411 taxa have been identified at different taxonomic levels. This makes it by far the largest set of data on bacterial communities in foods (as of January 2019). The ShinyFMBN app was also updated and provides better integration with external resources. The app is currently under embargo (pending revision of a manuscript). You will be able to access it on Mendeley data. You can cite this version 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. 104 studies and 5335 samples (December 2019).
  • FMBN3.2.6. major changes to the taxonomic table of the database, which is now compatible with SILVA taxonomy. (June 11, 2020).
  • FMBN4.1.2. With 180 studies and 10,155 samples belonging to 8 major food groups this is arguably the largest and best annotated database on metataxonomic data for for bacterial communities. The database includes 1684 environmental samples and 8,467 food samples, belonging to 16 L1 categories and 196 L6 categories of the FoodEx2 classification. Taking into account further annotation on sample nature, heat treatment and spoilage fermentation, samples in FoodMicrobionet belong to 316 different combinations. The details for the structure of the database are here.  Cite as: Parente, E., Zotta, T., Ricciardi, A., 2022. FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities. International Journal of Food Microbiology, 372, https://doi.org/10.1016/j.ijfoodmicro.2022.109696).
  • FMBN4.2. 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. As usual, the database is publicly available (on GitHub and Mendeley data) when the first paper describing it is published. Have a look at this preprint for links and further details. (September 2022).