Structure of association networks in food bacterial communities

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.

Comparison of bioinformatic approaches

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 FoodMicrobionet v 3.0

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:

  1. explore studies in FoodMicrobionet;
  2. filter samples to extract a subset of the database;
  3. (optionally) aggregate taxa or samples;
  4. export data (OTU abundance tables) and metadata in a variety of formats:
    1. .RDS files for further analysis
    2. a phyloseq class object for use with Shiny-phyloseq
    3. a .gml file for use in Gephi and Cytoscape
    4. 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.

Continue reading

New version posted

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.

Long time, no see

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).

FMBN@FM2016

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!