A new version is in development

I am working on version 3.2 of FoodMicrobionet (which will include 70+ studies and 3500+ samples) and version 2 of the Shiny app. However, these versions will not be made public anytime soon and will only be shared with partners with whom I have research collaborations. If you are interested in collaborating in the development of FoodMicrobionet or in the submissions of research projects related to FoodMicrobionet contact me.

New paper

The paper describing FoodMicrobionet v 3.1 is now available:

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.

Check it out, there are several important novelties. Don’t forget to read the supplementary material and to access the datasets and scripts on Mendeley datasets.

You can download it for free at https://authors.elsevier.com/a/1ZDuwcF3i1Aey until August 3 2019.


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 (https://www.microbiomeanalyst.ca). 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.