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 included 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 was the data visualisation platform that displays 3D multi-omic results in a user-friendly way, while providing access to raw data stored in public databases such as ENA and Metabolights. Our platform is user-friendly and easily navigable, giving an intuitive overview of our findings. 

Work Package 5 ran for the whole duration of the project, 52 months, and was concluded in December 2025.

Milestone 4 of the project has been achieved: "Informatic and mathematical procedures for analysing 3D’omics data are ready". 

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