New version (FoodMicrobionet v 4.1.2).

FoodMicrobionet v 4.1.2 is here!

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 8467 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. Further major changes include:

  • I have switched to SILVA 138.1 for taxonomic assignment and fixed former genus Lactobacillus; revision of taxonomic assignment of studies 34 to 170 completed; revision of taxonomic assignment of studies 1 to 33 in progress, scheduled to be completed by June 2022;
  • added fields for geoloc, primers and sequence organization (paired end, overlapping) to studies (multiple values separated by comma possible) to studies and geoloc_name_countries,  geoloc_name_countries_continent and lat_lon to samples

If you want to get more facts and figures on this version of FoodMicrobionet have a look here.

As usual, this version will be made publicly available when a new manuscript is published. There will be two versions available:

  • FMBN for ShinyFMBN 2.3: this version is designed to be compatible with the ShinyFMBN app, v2.3 but lacks fields on primers and geographic location
  • FMBN_plus: the complete database, available as a R list, will be distributed only in the framework of scientific collaboration agreements. Upon request phyloseq objects for studies 26 to 180 can be made available. This allows access to ASVs for each study.

New data and workflow.

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…

Bacterial interactions in cheese

Using 34 studies in the last version of DairyFMBN I have inferred microbial association networks (at the genus level) using NetCoMi, with four different methods (SparCC, CCREPE, SPRING, SpiecEasi). I then calculated how often an association was detected (by any method in any study) and which was the average stability (i.e. the mean of the number of times a given association was detected by the 4 methods within a study). here are the results for the top 25 copresence and mutual exclusion associations.

New paper

Here’s a new paper. Zotta, T., Ricciardi, A., Condelli, N., Parente, E., 2021. Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture. Critical Reviews in Food Science and Nutrition. doi:10.1080/10408398.2020.1870927Most of the figures have been generated by extracting data from DairyFMBN. 50 free e-reprints are available here: https://www.tandfonline.com/eprint/3C6T6Y8Y7X5MTGPYTUAV/full?target=10.1080/10408398.2020.1870927