New version (FoodMicrobionet v 4.1.2).

Featured

FoodMicrobionet v 4.1.2 is here! If you want to cite it and get links to GitHub and Mendeley data (were you can download files and scripts) have look at this preprint or at the published paper (Parente, E., Zotta, T., Ricciardi, A., 2022. FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities. International Journal of Food Microbiology, 372, https://doi.org/10.1016/j.ijfoodmicro.2022.109696). The paper is free to download at https://authors.elsevier.com/a/1f0z4cF3iBTqK until June 24th, 2022.

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 8,467 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.

Since the manuscript describing it has now been accepted for publication in IJFM (Hallelujah), this version is publicly available on GitHub and on Mendeley Data. There are 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.

In addition, if you are really into it, you can inquire for a collaboration and get the phyloseq objects for almost all studies in FoodMicrobionet.

Stay tuned for version 4.2

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

New review

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.