This is a new script for converting *_agg.RDS or *_physeq.Rdata files created using the ShinyFMBN app (v1.1 or later) in OTU, taxonomy and sample metadata tables suitable for use with the Marker Data Profiling analysis pipeline of Microbiome Analyst ( Click here to download. Please beware: I am too old to be willing to write foolproof scripts and try to predict the vagaries of lazy users. If you are a fool (and/or don’t read/follow the instructions provided as comments in the script) the script will not work. Period.


Dr. Sandrine Guillou has kindly invited me to give a talk at IAFP’s European Symposium on Food Safety in Nantes. Il will be speaking in symposium S4 (Network Analysis to Better Decipher Functions and Dynamics of Food Microbial Ecosystems) and the title of my talk is: “Shining Light on Networks in Food Microbiomes: FoodMicrobionet and the ShinyFMBN App“. You can download the presentation here. While we wait for the review of the manuscript I have submitted, you can cite FMBN 3.1 using this talk: Parente, E., Ricciardi, A., Zotta, T. 2019. Shining Light on Networks in Food Microbiomes: FoodMicrobionet and the ShinyFMBN App. Proceedings of IAFP’s European Symposium on Food Safety, Nantes, April 24-26, 2019.

Structure of association networks in food bacterial communities

A new article on FoodMicrobionet is on line at:

You have free access (until the end of February) using this link:

Here we skilfully explore the properties of microbial association networks in selected foods and compare them with association networks in the human micro biome and in soil microbial communities. Enjoy!

PS why not doing he same? The new Shiny FoodMicrobionet app will provide an easy access to FoodMicrobionet data and will conveniently generate files suitable for analysis with Conet, Cytoscape, Gephi and more. You can download the beta here.

New version posted

I have included material on a new version of FMBN (2.0.3) in the versions page. I will start now collecting material for a new version. If you are interested to contribute contact me. You can download instructions and templates for submission here.

Why should you contribute?

Contributors receive new versions of FoodMicrobionet and R scripts as soon as they are ready and are entitled to assistance in the use of the software for data extraction and analysis. In general, I am more inclined to use data received from authors of published papers (and include the data in FoodMicrobionet in a way that matches what has been published). However, we are also including material obtained by directly processing projects deposited in SRA and ENA with a standardised pipeline. The whole issue about FMBN is to make data (which in most cases are already deposited in public repositories) freely available in an easy(ish) to use format. So, why bother contributing if you can get data and scripts anyway? Well, as a contributor you get the data and scripts 6-9 months before they are made public and you can freely use them for your metastudies and reviews. The only thing we require is that you cite the source and the relevant published papers.

Long time, no see

A few updates. We are apparently on

Feel free to review our web site.

Plus, with Danilo Ercolini, Francesca De Filippis and Teresa Zotta we have submitted a couple of manuscripts. One has a few useful scripts attached, I will make them available with the data as soon as the manuscript is accepted (however, if you are shrewd enough you can find them yourself). The other is on microbial association networks (guest star Karoline Faust, whom I thank).

Version 1.0.3 has just been published

After a long and difficult reviewing process the first paper on FoodMicrobionet has just been published: Parente E., Cocolin L., De Filippis F., Zotta T., Ferrocino I., O’Sullivan O.,  Neviani E., De Angelis M., Cotter P. D., Ercolini D. 2015. 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.

We would very much appreciate your opinion on this.