Tools

FoodMicrobionet has been developed with one main purpose: to facilitate the access to data on the structure of food bacterial communities generated by amplicon targeted high throughput sequencing to facilitate the process of writing original articles and reviews and of visually exploring microbial food communities. Therefore, FoodMicrobionet is first of all, a database. The data tables, when imported in network analysis software can be used to generate output in a variety of formats. A flow chart for the development of FoodMicrobionet is shown below:

FMBNflowchartFoodMicrobionet contributors provide OTU tables, sample description tables and project tables, ideally from published studies. Although differences in the experimental setup and in bioinformatic analysis pipelines may introduce a bias and may make comaparisons difficult, edge, nodes and project tables include several fields which allow the users to extract the information they need.

The raw tables are transformed into raw edges, nodes and project tables, which are imported in an existing version of FoodMicrobionet. The specifications for nodes and edges tables can be found here. Edges store the information on abundance of a given Operational Taxonomic Unit (OTU) in a given sample. FoodMicrobionet is a bipartite network and two types of nodes are generated: OTU nodes and sample nodes. Node tables are used to add a variety of metadata to nodes to allow selection and filtering.

Network analysis software is used to generate FoodMicrobionet and perform filtering, visualisation and analysis operations. The network is created in Gephi, but a Cytoscape version is released to contributors when a version is developed. It can be used by experienced user to perform all operations needed for visualisation and analysis (filtering, application of styles and layouts, calculations of statistics).

Web visualisations are currently generated using the SigmaJS exporter plugin for Gephi. The web visualisation offers limited filtering and exploration options compared to the network files, but can be used even by unexperienced users without any need to install software. Visit the versions page to access the visualisations for public versions of FoodMicrobionet. Nodes and edges tables are publicly released as supplementary material whenever a FoodMicrobionet version is published in a journal.