Why spatial context matters
Understanding the interplay between animals and the microorganisms associated with them was essential for improving animal health, welfare and production. To identify the biomolecular interactions that shaped food production processes, researchers examined animal genomes, microbial metagenomes and the omic layers that interconnected them: the holo’omic framework.
Conventional methods, however, provided information analogous to studying the Amazon rainforest by mixing every organism in the jungle in one pot and measuring their relative abundances—without showing which birds nested in which trees, or which fungi lived alongside them.
3D’omics overcame this barrier by generating and analysing 3D’omic data, making previously hidden microbe–microbe and animal–microbe interactions visible.
The 3D’omics solution
Reconstructing intestinal microbial landscapes in 3D was a strategic response to the limits of conventional microbiome methods, which could not capture essential information about biological interactions between microbes and animals. The work supported the development of microbiota-modulation solutions and microbiota-aware animal breeds to improve the sustainability, health and welfare of livestock.
Development of a novel methodological framework
3D’omics developed an integrated framework to generate and analyse 3D’omic data alongside fluorescence-based imaging of bacteria and labelled feed compounds, plus complementary health, nutrition and performance analyses. The technology built on advances in multi-omics, structural genomics, spatial transcriptomics and metabolomics, coupled with cutting-edge animal phenotyping techniques.
Project overview
Acronym: 3D’omics
3D omics analysis of host–microbiota interactions to advance animal production.
Elucidating the three-dimensional conformation of biomolecules in cells and tissues was essential for understanding biomolecular interactions. The EU-funded 3D’omics project developed, optimised and implemented this knowledge for animal production, generating 3D omics landscapes and reconstructing intestinal host–microbiota ecosystems.
Using poultry and swine production systems, the project analysed how animal development, diet, pathogen exposure and management practices shaped these landscapes. The resulting framework opened new research avenues for animal breeding, tailored feeds, animal-health treatments and management practices that increased production efficiency and welfare while decreasing environmental impact.
Objectives and impact
The overall objective was to develop, implement and assess the technological, economic and societal impact of a framework for generating and analysing 3D’omic landscapes. This framework helped decipher the characteristics and functions of livestock microbial ecosystems, and how they influenced production, health and welfare.
Operational objectives
- Developed the 3D’omics technology to reconstruct 3D multi-omic intestinal landscapes from micro-scale genomic, transcriptomic, metabolomic and imaging data.
- Demonstrated the technology in two monogastric animal systems: poultry and swine.
- Incorporated 3D’omics data into breeding and feeding models used to analyse phenotypic variability, perform genetic evaluations and modulate microbial ecosystems.
- Assessed the technical, economic and societal impact of 3D’omics technology, and outlined a roadmap for industrial implementation.
- Established strong collaborations and knowledge-transfer activities with related microbiome initiatives.
Project impact
- Enabled microbial-ecosystem data to be included in models for phenotypic variability and genetic evaluation.
- Improved resource use and reduced the environmental impact of terrestrial livestock production.
- Improved the robustness and health of terrestrial livestock in relation to productive functions.
- Reinforced collaborations with related initiatives to promote coherent, applicable microbial-ecosystem research.
3D’omics in numbers
- Project period
- 1 September 2021 – 31 December 2025
- Work packages
- 9
- Partner institutions
- 13 institutions from 11 countries
- Coordinator
- Københavns Universitet (UCPH), Denmark
- Project coordination
- Antton Alberdi
- Overall budget
- €10,073,540.00
- EU contribution
- €9,994,415.00
Project partners
- Københavns Universitet (UCPH), Denmark
- Fundació Centre de Regulació Genòmica (CRG), Spain — ended in 2024; taken over by CNAG
- Veterinärmedizinische Universität Wien (UVM), Austria
- Max Delbrück Centrum für Molekulare Medizin (MDC), Germany
- Katholieke Universiteit Leuven (KUL), Belgium
- Eidgenössische Technische Hochschule Zürich (ETH), Switzerland
- Ben-Gurion University of the Negev (BGU), Israel
- Norges Miljø- og Biovitenskaplige Universitet (NMBU), Norway
- Afekta Technologies Ltd (ATL), Finland
- Aviagen Limited (AVI), United Kingdom
- Novogene Netherlands BV (NGE), Netherlands
- Biomin Holding GmbH (BIO), Austria
- Norsvin SA (NORSVIN), Norway
- Center for Genomic Analysis (CNAG), Spain — joined in 2024, taking over from CRG
Read more about the organisations on the consortium page.
Advisory Board
- Angela Sessitsch — Austrian Institute of Technology (AIT), Austria
- Geoff Simm — University of Edinburgh, United Kingdom
- Thomas Bosch — University of Kiel (CAU), Germany
- Yolanda Sanz — Spanish National Research Council at the Institute of Agrochemistry and Food Technology (CSIC-IATA), Spain
Funding
3D’omics received funding from the European Commission through the European Union’s Horizon 2020 Research and Innovation Action (RIA) programme, under grant agreement No. 101000309.
The project was funded under the topic Societal Challenges: food security, sustainable agriculture and forestry, marine, maritime and inland water research, and the bioeconomy.
