Well, I don’t have the time and resources to maintain this site, so I am going to dismiss it. You can find stuff related to FoodMicrobionet
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. The main improvements are:
As usual, the database will be publicly available (on GitHub and Mendeley data) when the first paper describing it is published.
I am about to release version 4.2. With more than 12,000 samples, more than 210 studies and almost 1,000,000 sample-taxa relationships this is by far the largest database of metataxonomic studies on the composition of bacterial communities of food and food environments. Further improvements include:a. I have reprocessed almost all studies from version 0.6, 1 and 2. b. the integration with sequence data is greatly improved: it is now possible to access ASVs using the study accession number. The R lists containing the phyloseqs with the ASVs will be available on Zenodo from September 1st, 2022.
After some effort we have managed to publish a new review on Microbial association network in cheese:
Parente, E., Zotta, T., Ricciardi, A., n.d. 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
You can get free reprints (until April 29, 2022) using this link.
Please be aware that the most recent public version of FoodMicrobionet will always made available on GitHub. Versions on Mendeley data are released when a new paper is released (and this is not very often).
The manual for ShinyFMBN 2.3 is now available in .html format.
With new annotation on geographic location you can now find how many samples are available for each country or continent in FoodMicrobionet.
We have just posted a metastudy on BioRxiv
A new version of DairyFMBN has been added to Mendeley data (https://data.mendeley.com/datasets/3cwf729p34/5) and quarantine will expire at the end of July. This is connected to an astounding ( 😉 )workflow for inference of microbial association networks, which is available on GitHub (https://github.com/ep142/MAN_in_cheese). Both are related to a review on microbial association networks in cheese which is about to be published as a preprint…
An updated version of DairyFoodMicrobionet is available on Mendeley data
Meanwhile, the development version of FoodMicrobionet (3.2.8) includes >167 studies and >9700 samples. Whoever is interested to use it for research purposes can contact me for details.