New version (FoodMicrobionet v 4.1.2).

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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.

New version (3.2.6)

I have made major changes to the taxonomic table of the database, which is now compatible with SILVA taxonomy. Although SILVA taxonomy does not match the taxonomy in the List of Prokaryotic names with Standing in Nomenclature the change was necessary because new studies in FoodMicrobionet are processed using SILVA v138 and this was causing inconsistencies in the higher level taxonomy of taxa (i.e. the same genus might potentially have a different lineage depending on when it was added to the database) and this, in turn, would prevent correct aggregation at levels higher than genus. In case you want to know, I did compare taxonomic assignments done with SILVA v132 and v138 for five studies using different 16S RNA gene regions as a target. The same sequence was assigned to a different “taxon” in as many as 70% of the cases. However, when doing comparisons at the genus level, >96% of the sequences were assigned to the same genus using either version of the database. Mismatches were mostly due to sequences (actually Amplicon Sequence Variants) which, when tested with Seqmatch had consistently a Sab<0.80 with the best match. Again, the best way to compare studies is to reprocess data based on the same target using exactly the same pipeline, but this is time consuming. Doing comparisons at the genus level is still a reasonable alternative: Article A comparison of bioinformatic approaches for 16S rRNA gene p…
The update version of the last public version of FoodMicrobionet should be shortly available here.

As usual, we are open to collaborations and if you are interested in obtaining data from FoodMicrobionet 3.2.6 contact me.

DairyFMBN

A shiny app for accessing 42 studies on milk, fermented milks and dairy products extracted from FoodMicrobionet 3.2.3 is available on Mendeley data. The app is just a variation of ShinyFMBN v2, so there is no need for a new manual. The app is cited in:

Parente, E., Ricciardi, A., Zotta, T. 2020. The microbiota of dairy milk: a review. International Dairy Journal, in press, doi:10.1016/j.idairyj.2020.104714

Note that this app has been tested with R 3.6.3 and Bioconductor 3.10 but not with later versions.

FMBN 3.2.3 version details

  • FoodMicrobionet now includes 104 studies and 5335 samples
  • minor changes to lineages for some taxa
  • corrected a few inconsistencies in the study table
  • added food codes to study description for version 3.1
  • added surname and email field for the corresponding author of studies
  • corrected a mismatch in row numbers and sample ids for the sample table (and corrected edges). This was probably due to deletion of a sample from a previous version and was causing errors in selection with the Shiny app after sample with id 1572.

FMBN includes an impressive variety of food types, with data on both foods and food environments:

  • Animal and vegetable fats and oils and primary derivatives thereof 53
  • Composite dishes 115
  • Eggs and egg products 21
  • Fish, seafood, amphibians, reptiles and invertebrates 362
  • Fruit and fruit products 252
  • Grains and grain-based products 149
  • Major isolated ingredients, additives, flavours, baking and processing aids 72
  • Meat and meat products 1086
  • Milk and dairy products 2516
  • Vegetables and vegetable products 537
  • Sugar and similar, confectionery and water-based sweet desserts 42
  • Alcoholic beverages 30
  • Starchy roots or tubers and products thereof, sugar plants 17
  • Legumes, nuts, oilseeds and spices 65
  • Seasoning, sauces and condiments 18

This version will be not made public (but parts of it will be released as supplementary material for review articles). We are however willing to discuss collaboration opportunities with other research groups.

Note that this app has been tested with R 3.6.3 and Bioconductor 3.10 but not with later versions.

FMBN 2.0.3 version details

FMBN2.0.3. Minor changes: Changed FoodId for study 11 (A01QX->A049Q). Added number of reads for some samples. Removed a few duplicates in lineages. Expanded the definition for llabel. Table specifications are here. Project table is here. Edge and nodes tables are here. Accessibility is now much improved, using R scripts: With very little effort you can extract files for analysis from the edge and node tables using this R script and produce graphical and statistical analyses using this one. Read the instructions carefully. You can cite this version and the scripts using this paper.

FMBN 2.0.2 version details

FMBN2.0.2Minor changes: Fixed problems with inconsistent lineages for a few OTU nodes. Major changes: Revised specification for node and edges tables: now you can use Custom1 to 3 fields for more efficient filtering and application of styles. A web visualisation of the filtered network (weighted degree >17) is available here. This version will allow a better integration with the Bipartite package of R and with the CoNet app of Cytoscape. A .pdf version (187 Mb) of the filtered network (weighted degree>17) is available here. A .pdf version (10.9 Mb) of the “robust” network (identification at the genus level or above, edges with abundance <0.1% removed) is available here.

FMBN 2.0 version details

FMBN2.0 is a significantly improved version. It includes 33 studies, 29 of which have been published or are about to be published. With 3929 nodes (2204 OTU nodes, 1413 Food samples, from 59 food types, 312 Food environment nodes) and 87197 connections between OTU and Sample/Environment nodes, FMBN is by far the largest repository of data on the bacterial microbiota of foods. Most data were obtained with similar sequencing platforms, gene targets and bioinformatic pipelines, and were either provided directly by the participating groups or obtained by analysing publicly available bioprojects. Refer to the projects table and edge and node specifications for more details. Minor changes: Corrected mismatches for some samples and bioprojects. Fixed outlinks for sequences deposited in NCBI BioProject database. Corrected a few inconsistencies in lineages and in fields for food classification. Major changes. Revised specification for node and edges tables. Added 672 samples from 8 studies. Added Nreads, Shannon and Chao1 whenever available, otherwise Nreads set to 2999. 

FMBN 1.1 version details

FMBN1.1 is an intermediate version which has been presented as a poster at FoodMicro 2016, in Dublin. Minor changes: Corrected an error in weights for BioProject SRP052240 (weights were twice their real value). Checked and corrected all weights for minor rounding errors. Solved a problem related to OTU node merging in Gephi. Corrected wrong labels for some OTUs. Major changes: Added 493 samples from 8 studies. Revised specification for node tables. Introduced “Environment” nodes. Cite this version as: Parente E., De Filippis F., Zotta T., Cotter P., O’Sullivan O., Puglisi E., Ercolini D. 2016. FoodMicrobionet 1.1.6: a network analysis tool for the exploration of food bacterial communities. Food Micro 2016 Abstract Book, Dublin, IRL, July 19-22, 2016. PO2-FS-080. Click here to access the web visualisation.

FMBN 1.0.3g version details

FMBN v 1.0.3g is a “robust” version of v 1.0.3. In this version the nodes for OTUs identified as belonging to the same genus were merged and low abundance (<0.1%) OTUs were removed from each sample. This might alleviate the problems related to comparison of studies in which different bioinformatics platfors were used. Click here to access the web visualisation (it might be necessary to reduce the zoom level to visualise the network). Cite this version as: Parente E., Cocolin L., De Filippis F., Zotta T., Ferrocino I., O’Sullivan O.,  Neviani E., De Angelis M., Cotter P. D., Ercolini D. 2016. 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.

FMBN 1.0.3 version details

FMBN v 1.0.3 includes minor updates to the previous version (including updates to references for published studies. Click here to access the web visualisation. Cite this version as: Parente E., Cocolin L., De Filippis F., Zotta T., Ferrocino I., O’Sullivan O.,  Neviani E., De Angelis M., Cotter P. D., Ercolini D. 2016. 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.