18 June 2021

European project to improve animal production: Unraveling the animal-microbe interplay at the microscale


In the new European research project 3D’omics, researchers aim to address major challenges in animal production by creating and optimising a technology to analyse animal-microbiota interactions at the microscale. The developed technology will be implemented in two production systems, namely poultry and swine. The project involves both university and industry partners and has received €10 million over the next four years from EU Horizon 2020.

Foto: Colourbox.

Billions of farm animals provide food to humans worldwide. However, large-scale animal production also faces major challenges: Production of considerable amounts of waste, usage of antibiotics and harvest of enormous amounts of crops.

3D’omics, a new European project supported by EU Horizon 2020, aims to minimize the impact of those challenges by understanding the interactions between animals and microorganisms. The project is led by the University of Copenhagen, and the consortium includes scientists from eight European universities and research institutions, as well as five different companies from the private sector.

Project coordinator at the University of Copenhagen Antton Alberdi explains that identifying microbial communities that interact optimally with animals can contribute to preventing development of diseases by boosting immunity of animals, using less medical drugs, improving digestive capacity of organisms, and thus producing less waste.

“Gut microorganisms have a systemic impact on many biological processes of farm animals. Because of this, understanding animal-microbiota interactions is recognised as one of the key steps to advance towards more efficient animal production, more sustainable procedures and to improve the welfare of animals,” says Antton Alberdi, Assistant Professor at the Center for Evolutionary Hologenomics, Globe Institute.

Discovering the host-microbe interactions in a 3D environment

The project aims to develop a brand new technology, which functions as a framework to analyse the data at the microscale. The resulting technology will allow researchers “to see”, in 3D, the interactions between microbes and other microbes as well as with the host, hence the project’s name, 3D’omics.

And scientists are in need of a new methodology to progress in the understanding of the intricate interactions on micro scale, explains Antton Alberdi.

“An analogy of the current procedures used for analysing intestinal microbial communities would be to collect trees and birds in the Amazon rainforest, mix them all in a giant blender, extract DNA from the mixture to reconstruct their genomes, and finally try to determine which bird nests on which tree. Clearly, the approach can be improved,” he says.

By generating high-quality imaging and molecular data, the scientists will be able to reconstruct the interactions among bacteria as well as between bacteria and animal hosts while accounting for their three-dimensional spatial features.

The technology will combine different types of biological data, including fluorescence imaging, bacterial genome sequencing, gene expression data and metabolomics, to reconstruct the biomolecular interactions of bacteria and animal intestinal cells in three dimensions.

“3D’omics is structured in three stages,” explains Antton Alberdi.

“In the first stage, the consortium will develop and optimise the 3D’omics technology, from the field to data analysis, through the interdisciplinary collaboration of multiple partners with very different expertise,” he says.

In the second stage, the developed technology will be implemented in two production systems, namely poultry and swine, aiming at addressing specific production challenges. In poultry, for example, the goal is to understand the specific mechanisms of action of a feed additive in chickens.

“We will also study the interactions between a deadly pathogenicity of turkeys and the gut microbiota that it requires to develop its pathogenity. In swine, we will study how fibres engineered for boosting the growth of specific microorganisms modify microbial aggregations, and how this affects digestibility of nutrients,” Antton Alberdi explains.

In the third stage, the impact of the 3D’omics technology and its implementability in current industrial set-ups will be assessed.

The methodological framework will be made applicable to a variety of scientific disciplines including animal and life sciences, as well as basic ecology and evolution.


Project coordinator Antton Alberdi
+45 53 84 01 19 (DK)
+45 34 667 498 730 (ES)