In recent years, there has been a rapid development of techniques that, separately, have enabled the generation of multiple omics data, including both microbial and host components, processing very small amounts of biological material, generating 3D reconstructions of biological elements, and analysing complex microbial communities. Hence, the technology required for 3D multi-omics are finally in place and we will use it to develop, implement, and assess a new methodological framework that will revolutionise animal-microbiota research in animal science and beyond. 

The 3D’omics project is structured in 4 sections encompassing 9 work packages (WP), meticulously designed to achieve its objectives. The project consists of two structural WPs (Section 1) that will be active throughout the entire duration of the project, and seven more WPs clustered in three clearly defined sections: technology development (Section 2), technology showcasing (Section 3), and implementation and assessment (Section 4).

WP1: Project Management
Lead: UCPH

Management of the overall progress of the project through efficient scientific, administrative, financial, ethical, and data management. Guarantees that internal and EU reporting is performed adequately, makes certain that the project complies with ethical legislation, and ensures tasks and objectives are fulfilled efficiently within budget and on time.

WP2: Dissemination, Exploitation, and Communication (DEC)
Lead: UCPH

Communication of 3D’omics to relevant stakeholders and the general public, and promotion of new collaborative interactions with international projects to maximise the impact of 3D’omics technology.

WP3: Sample Preparation
Lead: UCPH

Development of optimal procedures for sampling, fixating, slicing, and micro-dissecting intestinal sections containing epithelial tissue and microbial communities. Generation of biological samples for the in vitro work in WP6/7, and creation of preliminary evidence for improving designs of trials in WP6/7.

WP4: Data Generation
Lead: MDC

Development of laboratory protocols and workflows to generate multi-omic data from intestinal microsections from different sample types.

WP5: Data Analysis and Visualisation
Lead: CRG

Development of the analytical procedures required to generate and visualise the 3D reconstruction models from 3D’omic data, and develop mechanistic and deep learning approaches to understand omic interactions between microbes and animals and predict phenotypic/performance outcomes.

WP6: Poultry Health Challenges
Lead: UVM

Showcasing the 3D’omics technology in addressing production challenges associated with diverse types of pathogens in poultry.

WP7: Swine Nutritional Challenges
Lead: NMBU

Showcasing the 3D’omics technology in addressing production challenges associated with nutrition in swine.

WP8: Incorporation into Models
Lead: BGU

Providing guidelines and expectations to implement 3D’omics data in genetic evaluation and phenotypic assessment procedures in industrial breeding and feeding programmes.

WP9: Technology Impact Assessment
Lead: NMBU

Assessment of the technical, social, and economic impact of the 3D’omics technology.


Management structure

The management structure for the 3D’omics project has been devised based on models successfully used in prior large-scale public-private collaborative projects funded by the European Commission. Overall, the management structure ensures that there are clear and frequent lines of communication between the Project Coordinator and all the 3D’omics partners, and between the 3D’omics consortium and the Research Executive Agency (REA).