Category Archives: Foodmicrobionet

Making the most of FoodMicrobionet – a webinar

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It is almost time for the webinar, which will take place on Tuesday, April 21st, 2026 15:00 CET (this is to allow people from the USA and Alberta to attend without having to wake up before sunrise…). A few things worth knowing:

  • you can find FoodMicrobionet and related scripts in my GitHub repository. You may want to check out how to clone a repository, and how to download a folder or a raw file.
  • you can find a downloadable version of the ShinyFMBN app on Mendeley data and on GitHub: you are strongly encouraged to download the app because running it locally is much faster
  • you can run the app on Shinyapps.io by clicking on this link
  • further resources (studies with ASVs) are available on Zenodo
  • I will make available more example scripts next week so check the GitHub repository just before the webinar for the most recent version of the scripts
  • the recording is available here and here (I forgot to record part of the meeting)

If you are one of the few people left in the world who still reads manuals:

  • Table specifications for FoodMicrobionet are here
  • Instruction manual for the ShinyFMBN app are here

Please note: I will be accepting people in the webinar (you should be logged in the browser with the address you have used for registering) in the first 15 minutes

The following scientific papers are related to FoodMicrobionet

  • Parente, E., Cocolin, L., Filippis, F.D., Zotta, T., Ferrocino, I., O’Sullivan, O., Neviani, E., Angelis, M.D., 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. https://doi.org/10.1016/j.ijfoodmicro.2015.12.001
  • Parente, E., Filippis, F.D., 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, 108249. https://doi.org/10.1016/j.ijfoodmicro.2019.108249
  • Parente, E., Ricciardi, A., Zotta, T., 2020. The microbiota of dairy milk: A review. Int Dairy J 107, 104714. https://doi.org/10.1016/j.idairyj.2020.104714
  • Parente, E., Zotta, T., Ricciardi, A., 2021. Microbial association networks in cheese: a meta-analysis. Biorxiv 2021.07.21.453196. https://doi.org/10.1101/2021.07.21.453196
  • Zotta, T., Ricciardi, A., Condelli, N., Parente, E., 2022. Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture. Crit Rev Food Sci 62, 3898–3912. https://doi.org/10.1080/10408398.2020.1870927
  • Parente, E., Zotta, T., Ricciardi, A., 2022. A review of methods for the inference and experimental confirmation of microbial association networks in cheese. Int J Food Microbiol 368, 109618. https://doi.org/10.1016/j.ijfoodmicro.2022.109618
  • Parente, E., Zotta, T., Ricciardi, A., 2022. FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities. Int. J. Food Microbiol. 372, 109696. https://doi.org/10.1016/j.ijfoodmicro.2022.109696
  • Parente, E., Zotta, T., Giavalisco, M., Ricciardi, A., 2023. Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments. Int J Food Microbiol 391, 110124. https://doi.org/10.1016/j.ijfoodmicro.2023.110124
  • Parente, E., Ricciardi, A., 2024. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 13, 1689. https://doi.org/10.3390/foods13111689
  • Ricciardi, A., López, F.N.A., Giavalisco, M., Pietrafesa, R., Parente, E., 2025. Determining the core bacterial and fungal genera in table olive fermentations. Int. J. Food Microbiol. 442, 111344. https://doi.org/10.1016/j.ijfoodmicro.2025.111344

New dataset on bacterial and fungal communities of table olives.

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A new dataset with a collection of published metataxonomic studies on bacterial communities of table olives has just been released. You can find it here:

https://github.com/ep142/Metaolive

You can use it with your own data and obtain quantitative comparisons of microbial communities of table olives and their environments in published studies. All new data produced in our METAolive project will end up here. The dataset is extracted from FoodMicrobionet v5.

If you want to see a use case checkout our poster presented at the Food Systems Microbiomes meeting, held in Turin from 14/5 to 17/5.

This project is co-funded by Ministero dell’Università e della Ricerca PRIN 2022, proposal 2022NN28ZZ, and received funding from the European Union Next-GenerationEU – PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR).

FoodMicrobionet 5 is now available!

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The new major version includes (finally) fungi. As usual, you can find everything you need:

This version is currently co-funded by Ministero dell’Università e della Ricerca PRIN 2022 PNRR, proposal P20229JMMH, Mining the biodiversity of non conventional yeasts as bioresources for innovative fermented beverages through a genomics, and received funding from the European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR)) CUP C53D23007560001

FoodMicrobionet 4.2.1 is now available

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I have just released a new version of FoodMicrobionet. Version 4.2.1 includes 233 studies and 13895 food and food environment samples. New tables have been added (Abstracts table) and metadata for studies (a study_type field now provides a classification in longitudinal cross-sectional or mixed for the study design) have been improved. You can access the new version:

  • on GitHub: data in the the_real_thing folder, plus a bunch of scripts
  • on Zenodo: here you can find the mindata files, with ASV sequences
  • on Mendeley data (the most recent version is in moderation, reserved DOI 10.17632/8fwwjpm79y.8)

Share (using the DOIs provided by Mendeley data and Zenodo) and enjoy. You can find the most recent publications on FMBN here.

New Foodmicrobionet publication

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Our last publication obtained using data in FoodMicrobionet is:
Parente, E., Zotta, T., Giavalisco, M., Ricciardi, A., 2023. Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments. Int J Food Microbiol 110124. https://doi.org/10.1016/j.ijfoodmicro.2023.110124
The code is pretty general and the work can be easily replicated for any other microbial group in FoodMicrobionet.
You can download a free .pdf (until 5/4/2023) here https://authors.elsevier.com/a/1gerCcF3iFHfL

Literature cited, project 2017J2RMTN

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