The EU Horizon 2020 project “ Understanding microbiomes of the ruminant holobiont” (HoloRuminant) gathers 25 public and private partners with cross-cutting complementary skills from 12 European countries (Belgium, Denmark, Finland, France, Germany, Ireland, Italy, Lithuania, Netherlands, Norway, Spain, and United-Kingdom), one associated country (Israel) and four other countries (Australia, Canada, New-Zealand, and USA). Among them, 10 are research institutions and 11 universities.
The partners are European and international leaders in their domains and have a strong experience in collaborative research at national, European and International scale including partnership with the livestock breeding, health and nutrition industry. The coordinator of the project is INRAE (Institut national de recherche pour l’agriculture, l’alimentation et l’environnement), represented by Dr. Diego Morgavi, who is Director of Research at INRAE. This five-year project will run from October 2021 till September 2026.
Project Description
The ruminant host and its associated microbiomes are central in this project, rooted within the holobiont concept which means that they are considered as a single functional unit. To study the multiple interactions, within the HoloRuminant project, a holistic multi-omics approach is used to characterise the establishment and dynamics of microbiomes.
The goal of HoloRuminant is to elucidate the role of ruminant-associated microbiomes and their interplay with the host animal in early life and throughout fundamental life events (e.g. weaning, feed transitions and lactation) that are known to affect health, welfare and environmental efficiency in ruminant production systems. In this way, HoloRuminant will determine the connectivity between microbiomes from different body sites, their heritability and their influence on the host’s key performance indices of efficiency of production, growth, resistance to disease, methane emissions, carbon footprint and phenotypic resilience to changing environmental conditions.
Objectives
These are the objectives of HoloRuminant
Characterise ruminant-associated microbiomes: through established and novel, harmonized procedures through a multi-omics approach (metagenomics, metatranscriptomics, metaproteomics and metabolomics), referred to in this project as a holo-omics approach.
Define microbiome establishment and maintenance: define the establishment of the holobiont through the transfer of microbes from the dam (vertical) and farm environment (horizontal) and within the microbiomes at different body sites of the same individual as well as during challenging life periods such as perinatal, weaning, and following exposure to pathogens.
Evaluate the effect of ruminant microbiomes on animal production, health and welfare: establishment of the nature of interconnection dependencies of microbiomes and critical phenotypes and develop novel microbial markers based on this knowledge.
Facilitate the adoption by end-users of the proposed innovations through intensive interaction with stakeholders on different platforms.
Role of Ghent University
At Ghent University, we are specifically targeting the transition period around calving of dairy cows. In two long-term experiments, each lasting about 2 years, 2 groups of 100-120 cows are monitored at the experimental farms of ILVO and the Hooibeekhoeve. In these experiments, performed within the frame of a VLAIO-LA trajectory coordinated by Ghent University, the resilience of these transition cows has been characterized based on their metabolic, oxidative and inflammatory status. Furthermore, in 25% of these cows rumen pH has been monitored continuously. Additionally, rumen, saliva and faeces samples have been taken to assess the microbial fingerprint of these animals. Moreover, several candidate key mechanisms are investigated to better understand the host-microbiome interaction.
