The paper describing FoodMicrobionet v 3.1 is now available:
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.
Check it out, there are several important novelties. Don’t forget to read the supplementary material and to access the datasets and scripts on Mendeley datasets.
You can download it for free at https://authors.elsevier.com/a/1ZDuwcF3i1Aey until August 3 2019.
I am working on version 3.2 of FoodMicrobionet (which will include 70+ studies and 3500+ samples) and version 2 of the Shiny app. However, these versions will not be made public anytime soon and will only be shared with partners with whom I have research collaborations. If you are interested in collaborating in the development of FoodMicrobionet or in the submissions of research projects related to FoodMicrobionet contact me.
New data and scripts, including version 1.2 of the ShinyFMBN app are available at Mendeley data.
This is a new script for converting *_agg.RDS or *_physeq.Rdata files created using the ShinyFMBN app (v1.1 or later) in OTU, taxonomy and sample metadata tables suitable for use with the Marker Data Profiling analysis pipeline of Microbiome Analyst (https://www.microbiomeanalyst.ca). Click here to download. Please beware: I am too old to be willing to write foolproof scripts and try to predict the vagaries of lazy users. If you are a fool (and/or don’t read/follow the instructions provided as comments in the script) the script will not work. Period.
Dr. Sandrine Guillou has kindly invited me to give a talk at IAFP’s European Symposium on Food Safety in Nantes. Il will be speaking in symposium S4 (Network Analysis to Better Decipher Functions and Dynamics of Food Microbial Ecosystems) and the title of my talk is: “Shining Light on Networks in Food Microbiomes: FoodMicrobionet and the ShinyFMBN App“. You can download the presentation here. While we wait for the review of the manuscript I have submitted, you can cite FMBN 3.1 using this talk: Parente, E., Ricciardi, A., Zotta, T. 2019. Shining Light on Networks in Food Microbiomes: FoodMicrobionet and the ShinyFMBN App. Proceedings of IAFP’s European Symposium on Food Safety, Nantes, April 24-26, 2019.
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.