- 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.
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.
FMBN2.0.2. Minor 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.
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.
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 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 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.
FMBN v 1.0.2 is the first public version. It includes data from 17 published and unpublished studies on dairy foods, meat, sourdoughs and fermented vegetable products (olives). The network includes 552 sample and 964 OTU nodes, with 18,115 OTU-sample interactions, and is by far the largest repository of data on bacterial communities in foods. Click here to access the web visualisation. This version will be presented as oral communication at the 3rd International Conference on Microbial Diversity (Perugia, Italy, October 27-29, 2015). Cite this version as: Parente E., Cocolin L., De Filippis, F., Zotta T., Ferrocino I., Neviani E., De Angelis M., Di Cagno R., Cotter P. D., Ercolini D. 2015. FoodMicrobionet: a tool for the visualisation and analysis of the structure of bacterial food microbial communities. 3rd International Conference on Microbial Diversity, Perugia, October 27-29, 2015.
FMBN v 0.6.2 is the first proof of concept version. It includes data from 9 published and unpublished studies on dairy products and dairy starter cultures. The network includes 879 nodes (262 sample nodes and 617 OTU nodes) with 6,015 edges (OTU-sample connections). Click here to access the web visualisation. This version is unpublished.
There are 44 studies and 2233 samples in this version of FoodMicrobionet. The samples belong to 9 major food groups and 76 different foods. There are 148 different combinations of food, nature, process, fermentation/spoilage. 3411 taxa have been identified at different taxonomic levels. This makes it by far the largest set of data on bacterial communities in foods (as of January 2019).
The ShinyFMBN app was also updated and provides better integration with external resources. The app is currently under embargo (pending revision of a manuscript). You will be able to access it on Mendeley data.
The app (version 1.2, which is compatible with R3.6 and the new installation procedure of Bioconductor packages), the database and a few other things are available at Mendeley data, and are connected to an article in IJFM-
You can cite this version as: 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.