The 3D'omics Consortium

The 3D'omics project is a multidisciplinary project that aims to reconstruct the animal-microbiota multi-omic interplay in 3D to better understand how animal genomes and microbial metagenomes interact. To achieve this ambitious goal, the consortium is composed of 13 partners across 11 countries - including 6 universities, 2 research centres, and 5 companies.

University of Copenhagen, Denmark

Four different departments of Copenhagen University (UCPH) are part of this project: the GLOBE Institute, the Section of Microbiology at the Department of Biology, the Department of Veterinary and Animal Sciences, and Department of Food and Resource economics.

Role in the project
UCPH will be the Coordinating institution and it will lead the management (WP1) and the dissemination, exploitation and communication (WP2) work packages. UCPH will also lead the development of the sample preparation technology (WP3), and will further participate in several tasks in the other work packages.

University of Veterinary Medicine, Austria

The Vetmeduni Vienna (UVM) is the only academic institution in Austria to carry out teaching and research in veterinary medicine. It is dedicated to foster animal health, preventive veterinary medicine, public health and food safety. 

Role in the project
UVM, led by Prof. Michael Hess, will lead WP6, aimed at addressing multiple disease challenges in poultry production through deconstructing pathogen-microbiota-animal interactions through 3D’omics. UVM will carry out animal trials with different poultry species, and will also perform animal phenotyping and KPI analyses. UVM will also be in charge of ethics management.

KU Leuven, Belgium

Role in the project
KU Leuven, led by Associate Professor Karoline Faust, will contribute to data analysis and visualisation (WP5), the poultry health challenge (WP6), and the swine nutrition challenge (WP7).

ETH Zurich, Switzerland

Role in the project
ETH, led by Senior Assistant Dr. Annelies Geirnaert, will conduct the sampling in in vitro animal microbiota experiments for setting up the 3D’omics technology and investigating synbiotic-pathogen-microbiota interactions in detail prior to animal trials.

Ben Gurion University of the Negev, Israel

Role in the project
BGU will contribute to in vitro model development (WP3), the swine nutrition challenge analysis (WP7), 3D’omics-based microbiota manipulation (WP8), and the international interaction networking (WP2).

Norwegian University of Life Sciences, Norway

Role in the project
NMBU will lead the swine nutrition challenges (WP7), which will include feed formulations trials, prebiotic trials, and phenotyping / KPI profiling of animals. In addition, NMBU will play a key role in conventional multi-omic profiling and the technical comparison between conventional multi-omics and 3D’omics (WP9).

Centre for Genomic Regulation, Spain

Role in the project
CNAG, through Prof. Marc A. Marti-Renom, will lead the data analysis and visualisation (WP5), aimed at developing informatic and mathematical procedures to reconstruct and analyse the intestinal 3D multi-omic landscapes.

Max Delbrück Center for Molecular Medicine, Germany

Role in the project
MDC, led by Prof. Ana Pombo, will develop 3D’omics technology to reconstruct 3D multi-omic intestinal landscapes from micro-scale genomic and transcriptomic data (WP4), towards a detailed characterisation of the micro-scale microbial ecosystems of poultry and swine with unprecedented resolution.

Afekta Technologies Ltd., Finland

Role in the project
In 3D’omics Afekta will be responsible for the development of the metabolomics methods across different work packages, as well as conducting the actual metabolomics measurements using both the newly developed and existing methods. Afekta will also participate in the development of data-analytical methods involving the data fusion with the other omics methods in the data analysis
work package (WP5).

Aviagen Inc., UK

Role in the project
Aviagen will provide industry support for the tasks focused on poultry trials (WP6) along with subsequent analyses and interpretation of data. Aviagen will also be involved with implementation (WP8) and impact assessment (WP9) of the technologies developed in the project.

Novogene, Netherlands

Role in the project
Novogene will contribute to the overall sequencing tasks, adapting the existing whole genome amplification method to new tissue types (WP4). Novogene will also perform the sequencing of both 3D’omic and conventional multi-omics libraries (WP6, WP7).

Biomin Holding GmbH, Austria

Role in the project
Biomin will be involved in the poultry challenge trials (WP5) and the knowledge transfer of 3D’omics technology to the feed industry (WP8, WP9). Biomin will also provide all PoultryStar® formulations for the in vivo trials.

Norsvin SA, Norway

Role in the project
Norsvin will link the results of the 3D'omics technology to existing knowledge of the role of the microbiome in feed efficiency in pigs. Specifically, Norsvin will participate in the swine nutrition challenges (WP6), and the
impact assessment (WP9).

Advisory Board Members

Thomas Bosch

Kiel University, Germany

Yolanda Sanz

National Research Council, Spain

Angela Sessitsch

Austrian Institute of Technology, Austria 

Geoff Simm

University of Edinburgh, UK