Skip to main content
European Commission logo print header

Understanding microbiomes of the ruminant holobiont

Project description

The role of the microbiome in ruminant health and production

Ruminant livestock species, such as cattle, sheep and goats, depend on their body-associated microbes for critical functions and for interacting with the environment. The host ruminant-microbiome association, the holobiont, is the biological unit influencing the development, growth, health and environmental hoofprint of ruminants. The key objective of the EU-funded HoloRuminant project is to study the role of the microbiome on animal health and production efficiency. Researchers will undertake a multi-omics approach to analyse the microbiome and the host, as well as the impact of their interaction at key stages during ruminant life. The ultimate goal is to characterise and identify ruminant-associated microbiomes associated with improved production efficiency, health and welfare.


Sustainability of ruminant production is of concern to society because of its implications for the environment, the economy and food security. Microbiomes associated with the host play a key role in health, welfare and environmental efficiency in ruminant production systems. However, despite the information already available, we lack the insights to precisely link the causes and mechanisms of microbial influence on ruminant phenotypes. This is because the interconnection and communication between the animal and its different microbiomes have never been studied in a deep, integrated way.
The goal of the project is to elucidate the role of ruminant-associated microbiomes and their interplay with the host in early life and throughout fundamental life events. HoloRuminant will use a holistic multi-omics approach to characterise the acquisition and evolution of microbiomes from different body sites, their inheritability and their influence on the host’s resistance to disease and environmental efficiency of production. Specifically we will: determine microbiomes’ functions by combining multi-level information for microbes, host and their interaction; define microbiomes’ roles during challenging life periods such as perinatal, weaning, and after exposure to pathogens; and evaluate the effect of ruminant microbiomes on critical phenotypes for sustainable production, health and welfare. This will allow the identification of novel microbial markers for monitoring, predicting and selecting phenotypes of interest. By engaging actors from the livestock value chain, we will evaluate the socio-economic impact and acceptability of the innovations proposed among stakeholders and the public.
HoloRuminant will provide highly innovative, standardized methodologies that will radically advance our understanding of the ruminant holobiont. This knowledge and the tools created will allow the use of microbiome-based diagnostics and solutions for improving ruminant sustainabilty.

Call for proposal


See other projects for this call

Sub call



Net EU contribution
€ 1 240 470,00
75007 Paris

See on map

Ile-de-France Ile-de-France Paris
Activity type
Research Organisations
Total cost
€ 1 240 470,00

Participants (24)