A new article on FoodMicrobionet is on line at: http://www.sciencedirect.com/science/article/pii/S0740002017306305
You have free access (until the end of February) using this link: https://authors.elsevier.com/a/1WNd22eGSbN~R1
Here we skilfully explore the properties of microbial association networks in selected foods and compare them with association networks in the human micro biome and in soil microbial communities. Enjoy!
PS why not doing he same? The new Shiny FoodMicrobionet app will provide an easy access to FoodMicrobionet data and will conveniently generate files suitable for analysis with Conet, Cytoscape, Gephi and more. You can download the beta here.
A manuscript related to FoodMicrobionet has just been published.
De Filippis, F., Parente, E., Zotta, T., Ercolini, D. 2018. A comparison of bioinformatic approaches for 16S rRNA gene profiling of food bacterial microbiota. International Journal of Food Microbiology. 265:9-17 https://doi.org/10.1016/j.ijfoodmicro.2017.10.028
Look here. Free downloads (until Dec. 24th, 2017) here.
ShinyFMBN, a Shiny app for exploring, filtering and extracting data from FoodMicrobionet v 3.0 is here…
With this app you will be able to:
- explore studies in FoodMicrobionet;
- filter samples to extract a subset of the database;
- (optionally) aggregate taxa or samples;
- export data (OTU abundance tables) and metadata in a variety of formats:
- .RDS files for further analysis
- a phyloseq class object for use with Shiny-phyloseq
- a .gml file for use in Gephi and Cytoscape
- OTU and sample tables ready for import in the CoNet app of Cytoscape
You can download the first version of the manual here. You can download the beta here. Unfortunately I did not have the time for extensive testing so, if you notice something strange let me know. In the message please provide your name, affiliation, current position, and drop a few lines on why you are interested in the app.
I am working on a major revision of the database and scripts (eventually access and analysis will be through Shiny apps). If there is any major feature you would like to see in the new version let me know.
The EBI metagenomics portal has plenty of data on food metagenomes, including amplicon (16S RNA gene/16S RNA) targeted studies. Have a look: their analysis pipeline provides taxonomic assignment tables for individual runs and for the whole study in .tsv format.
I have included material on a new version of FMBN (2.0.3) in the versions page. I will start now collecting material for a new version. If you are interested to contribute contact me. You can download instructions and templates for submission here.
Why should you contribute?
Contributors receive new versions of FoodMicrobionet and R scripts as soon as they are ready and are entitled to assistance in the use of the software for data extraction and analysis. In general, I am more inclined to use data received from authors of published papers (and include the data in FoodMicrobionet in a way that matches what has been published). However, we are also including material obtained by directly processing projects deposited in SRA and ENA with a standardised pipeline. The whole issue about FMBN is to make data (which in most cases are already deposited in public repositories) freely available in an easy(ish) to use format. So, why bother contributing if you can get data and scripts anyway? Well, as a contributor you get the data and scripts 6-9 months before they are made public and you can freely use them for your metastudies and reviews. The only thing we require is that you cite the source and the relevant published papers.
A few updates. We are apparently on omics.com https://omictools.com/foodmicrobionet-tool
Feel free to review our web site.
Plus, with Danilo Ercolini, Francesca De Filippis and Teresa Zotta we have submitted a couple of manuscripts. One has a few useful scripts attached, I will make them available with the data as soon as the manuscript is accepted (however, if you are shrewd enough you can find them yourself). The other is on microbial association networks (guest star Karoline Faust, whom I thank).
Two posters related to FoodMicrobionet will be on display at FoodMicro 2016, Dublin. I am afraid that the quality of the images on the posters is not the best (but they fold nicely in a suitcase). You can see the images at higher resolution in the .pdf versions.
- PO2-FS-080 – FOODMICROBIONET 1.1.6: A NETWORK ANALYSIS TOOL FOR THE EXPLORATION OF FOOD BACTERIAL COMMUNITIES. Eugenio Parente*, Francesca De Filippis , Teresa Zotta, Paul Cotter , Orla O’Sullivan, Edoardo Puglisi, Danilo Ercolini.
- PO2-FS-109 – A COMPARISON OF BIOINFORMATICS PIPELINES FOR THE ANALYSIS OF 16S METAGENOMICS DATA OF FOOD MICROBIAL COMMUNITIES, Francesca De Filippis, Danilo Ercolini, Eugenio Parente.
See you in Dublin!
Collection of data for FoodMicrobionet 2.0 is complete and statistical analysis is under way. Details will be published in this post and in the Versions page.
A web visualisation of the filtered web (weighted degree>17) is available here.
I have just published a new script to transform an edge table in an OTU abundance table. Using this you can (if you so wish) transform the whole FoodMicrobionet dataset (or part of it) in a very large abundance table. A newer version of the script, which comes handy when using FMBN 2.0 edge tables and allows to generate files which can be used with the package Bipartite of R (more on this later) is available here. Be careful with this script, however, it must be run in pieces.