In this WP, we used the proof-of-principle data generated in WP3 and WP4 to develop the baseline procedures for reconstructing the 3D multi-omic models and analysing them, which are currently being used (and further refined) for analysing the data generated in WP6 and WP7.

These methods include the development of conventional multi-omics pipelines, such as pre-processing strategies (i.e., quality-filtering, clonality removal, host read removal), metagenomic (i.e. assembly, binning, annotation), metatranscriptomic (i.e. mapping, de-novo assembly) and host transcriptomic (i.e. mapping) modules for generating multiple omic profiles from the bulk intestinal samples.

One of the main outcomes of 3D'omics will be a data visualisation platform that will display 3D multi-omic results in a user-friendly way, while providing access to raw data stored in public databases such as ENA and Metabolights. We are currently working heavily to make this platform user-friendly and easily navigable. Our aim is to display microbial community composition directly next to the sampling location of the micro-samples, giving an intuitive overview of our findings. 

Work Package 5 runs for the whole duration of the project, so 52 months, and will be concluded in December 2025.

Milestone 4 of the project has not yet been fully achieved --> MS4 "Informatic and mathematical procedures for analysing 3D’omics data are ready". 

The outcome of this Work Package will be 2 bioinformatic processing pipelines (which were already shared confidentially within the consortium and with the EC), 1 public 3D'omics visualisation platform (currently under construction), and 1 public report of 3D'omics data and metadata standards (in prep.).