3D'omics · EU research project

Reconstructing intestinal ecosystems in three dimensions.

3D'omics brought spatial and multi-omics approaches together to reveal where microbes, hosts and molecular activity meet in the intestine.

  • Host–microbiota interactions
  • Spatial multi-omics
  • Poultry and swine systems

From samples to a spatial ecosystem

Intestinal tissueCapture structure at the right scale
Multi-omics profilesConnect microbes, hosts and molecules
3D reconstructionMake hidden relationships visible

The research

A new view of the animal–microbiota relationship.

The intestinal ecosystem is shaped by interactions that are easy to miss when tissue is studied without its spatial context. 3D'omics combined sample preparation, multi-omics profiling and 3D analysis to explore those relationships in situ.

Using poultry and swine production systems, the project examined how development, diet, pathogen exposure and management practices shape these landscapes—supporting more sustainable animal health and production.

Diagram of the 3D'omics workflow, from animal trials and tissue sampling to multi-omics profiling and 3D reconstruction
3D'omics connects experimental systems, spatial sampling, molecular profiling and reconstruction.
A key project resource

Start with the 3D'omics Data Portal.

Explore the project’s datasets and their accompanying information in one place. The portal is the fastest route to the data, methods and context behind 3D'omics research.

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Find the right datasetBrowse project data and associated details.
Understand the contextSee how samples, methods and results connect.
Build on the workUse project resources to guide the next question.

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Watch & learn

Get a quick introduction to 3D'omics.

Two short explainer videos introduce the project and the scientific challenge it addresses.