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The 3D'omics Concept


Understanding the interplay between animals and microorganisms associated with them has been recognised as an essential topic by the European Commission for improving and optimising animal health, welfare, and production worldwide. To understand the truly relevant biomolecular interactions that impact food production processes, researchers are implementing novel strategies based on the analysis of animal genomes, the metagenomes of the associated microorganisms, and the different omic layers interconnecting them — the so-called holo’omic framework.

However, current methods provide us information analogous to what would be learned from studying the functioning of the Amazon rainforest through mixing all living organisms in the jungle in a big pot and quantifying their relative abundances without acknowledging, for instance, which bird nests or which fungi are associated with which tree.

Now, we are finally capable of breaking these barriers and boosting animal-microbiota research: The 3D-omics project will develop a framework to generate and analyse 3D’omic data that aims at unveiling microbe-microbe and animal-microbe interactions that have so far remained undetected due to technical limitations. Critically, 3D’omics builds on the holo-omic framework, but proposes a novel groundbreaking twist that aspires to achieve a several-fold resolution gain compared to conventional multi-omic approaches.

The need for the 3D’omics solution
Reconstructing intestinal microbial landscapes in 3D is not a whim or a personal defiance of restless researchers, but a well-meditated strategic decision resulting from the realisation that current methods to analyse the microbiome are not enabling us to capture essential information to understand biological interactions between microbes and animals. Acknowledging such interactions is essential to develop microbiota-modulation solutions and microbiota-aware animal breeds that will enable us to increase sustainability of livestock production, improving animal health and welfare. 

Development of a novel methodological framework
In 3D’omics, we will develop an integrated methodological framework to generate and analyse 3D’omic data along with information derived from fluorescence-based imaging of bacteria and labelled feed compounds, and complementary health, nutrition, and performance analyses. The 3D’omics technology builds on the recent advancements in the fields of multi-omics, structural genomics as well as spatial transcriptomics and metabolomics. We will coherently implement multiple state-of-the-art molecular techniques coupled with cutting edge animal phenotyping techniques, to advance animal-microbiota research to a new frontier.

3D'omics in a nutshell

Elucidation of the three-dimensional (3D) conformation of biomolecules in cells and tissues is an essential element for understanding biomolecular interactions. The EU-funded "3D'omics" project aims to develop, optimise and implement knowledge of biomolecular interactions in application to animal production. The goal is to generate 3D omics landscapes, achieving reconstructions of intestinal host microbiota ecosystems. Using poultry and swine production systems, the project will analyse the effects of different factors, including animal development, diet, exposure to pathogens, and management practices on the 3D omics landscapes. The innovative research will pave the way to improved animal breeding practices, development of microbiota- and host-tailored feeds, and animal health treatments, increasing production efficiency and animal welfare.

3D omics analysis of host-microbiota interactions to advance animal production.
Acronym: 3D'omics

Understanding the interplay between animals and microorganisms associated with them has been recognised as an essential step for improving animal health, welfare and production. To understand the biomolecular interactions that impact production processes, researchers are implementing novel analytical strategies based on studying host genomes, their microbial metagenomes as well as the different ‘omic layers interconnecting them. However, such information, derived from conventional DNA/RNA sequencing and mass spectrometry, does not provide any information about how the different biological elements are spatially distributed in the ecosystem. In consequence, many microbe-microbe and animal-microbe interactions remain hidden due to the lack of resolution of the employed techniques. Acknowledging the three-dimensional (3D) conformation of biomolecules, cells and tissues is now considered a key element for advancing the understanding of biomolecular interactions. In 3D’omics we will develop, optimise and, for the first time, implement this technology in animal production to generate the so-called 3D’omic landscapes, the most accurate reconstructions of intestinal host-microbiota ecosystems ever achieved. Using two terrestrial production systems, namely poultry and swine, we will analyse the effect of a myriad of factors, including animal development, diet, exposure to pathogens and management practices, in the shaping of 3D’omic landscapes. Through coupling our new technology with cutting edge analyses of animal health and performance, we will advance phenotypic variability and genetic evaluations of production animals to a new frontier. We foresee our solution will open new research avenues to improve animal breeding practices, develop microbiota- and host-tailored feeds and animal health treatments, as well as to design new management practices that will enable increasing production efficiency and animal welfare while decreasing the environmental impact.

The overall objective of 3D’omics is to develop, implement and assess the impact (technological, economical, and societal) of a new innovative framework to generate and analyse 3D’omic landscapes, with which to decipher the characteristics and functions of the livestock microbial ecosystems and understand how they influence production, health and welfare of animals.

Measurable operational objectives of the project:

O1) Develop the 3D’omics technology to reconstruct 3D multi-omic intestinal landscapes from micro-scale genomic, transcriptomic, metabolomic, and imaging data.

O2) Showcase the 3D’omics technology in two monogastric animal systems: poultry and swine.

O3) Incorporate 3D’omics data in the models used by the breeding and feeding industries to analyse phenotypic variability, to perform genetic evaluations and to modulate microbial ecosystems.

O4) Acknowledge the technical, economic and societal impact of 3D’omics technology and outline a roadmap for its industrial implementation.

O5) Establish strong collaborations and knowledge transfer activities with related microbiome initiatives.

Expected impacts of the project:

I1. Enable inclusion of data on microbial ecosystems in the models used to analyse
phenotypic variability and to perform genetic evaluations

I2. Improve resource use and environmental impact of terrestrial livestock production

I3. Improve robustness and health of terrestrial livestock, in relation to productive functions

I4. Reinforce collaborations with initiatives in related domains to promote coherence and
applicability of research on microbial ecosystems

Ultimately, we foresee that our new framework will open new research avenues to improve the generation of animal breeds with enhanced microbiota-related genetic features, probiotics, microbiota - and host-tailored feeds, animal health treatments, and management practices that will enable increasing production efficiency while decreasing environmental impact and improving animal welfare. 

Project Partners

1 KOBENHAVNS UNIVERSITET (UCPH) - Denmark
2 FUNDACIO CENTRE DE REGULACIO GENOMICA (CRG) - Spain
3 VETERINAERMEDIZINISCHE UNIVERSITAET WIEN (UVM) - Austria
4 MAX DELBRUECK CENTRUM FUER MOLEKULARE MEDIZIN (MDC) - Germany
5 KATHOLIEKE UNIVERSITEIT LEUVEN (KUL) - Belgium
6 EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH (ETH) - Switzerland
7 BEN-GURION UNIVERSITY OF THE NEGEV (BGU) - Israel
8 NORGES MILJO-OG BIOVITENSKAPLIGE UNIVERSITET (NMBU) - Norway
9 AFEKTA TECHNOLOGIES LTD (ATL) - Finland
10 AVIAGEN LIMITED (AVI) - United Kingdom
11 NOVOGENE NETHERLANDS BV (NGE) - Netherlands
12 BIOMIN HOLDING GMBH (BIO) - Austria
13 NORSVIN SA (NORSVIN) - Norway

For more details about the partners, have a look at our consortium page.

Advisory Board Members

Angela Sessitsch - Austrian Institute of Technology (AIT), Austria
Geoff Simm - University of Edinburgh, UK
Thomas Bosch - University of Kiel (CAU), Germany
Yolanda Sanz - Spanish National Research Council at the Institute of Agrochemistry and Food Technology (CSIC-IATA), Spain

Start date: 1 September 2021
End date: 31 August 2025

9 work packages

13 partner institutions from 11 countries

Coordinated by Kobenhavns Universitet (UCPH) Denmark
Project coordination: Antton Alberdi

Overall budget € 10 073 540,00
EU contribution € 9 994 415,00

3D'omics receives funding from the European Commission.

The project has received funding from the European Union’s Horizon 2020 Research
and Innovation Action (RIA) programme under grant agreement number No. 101000309.

Overall budget € 10 073 540,00
EU contribution € 9 994 415,00

Funded under the topic: SOCIETAL CHALLENGES
Food security, sustainable agriculture and forestry, marine, maritime and inland water research, and the bioeconomy.

This project has received funding from the European Union’s Horizon 2020 Research
and Innovation programme under grant agreement number No. 101000309.
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Coordinator: Antton Alberdi (UCPH)
     Data and privacy policy    Contact: 3d-omics@sund.ku.dk