Understanding microbiomes of the ruminant holobiont

Summary: 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 microbiomebased diagnostics and solutions for improving ruminant sustainability.

HoloRuminant has the following objectives:

Characterize ruminant-associated microbiomes

• Consolidate and derive novel knowledge from existing ruminant microbiome data.
• Pioneer and advance functional information on the eukaryotic microbiomes, viruses and yet uncultured bacteria and archaea.
• Understand the functional capacity of microbiomes by combining multi-level information for microbes, hosts and their interaction (use of (meta)genomics, (meta)transcriptomics, (meta)proteomics, and metabolomics), a concept otherwise known as “holo-omics”.
• Establish the relationships (or lack of) between microbiomes across multiple body sites of the same individual.

Define microbiome establishment and maintenance

• Define 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.
• Characterize microbiome roles 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

• Establish the nature of interconnection dependencies that exist between the microbiomes and critical phenotypes for sustainable ruminant production.
• Identify novel microbial markers for monitoring and predicting phenotypes of interest.
• Integrate microbial markers and host genetics into statistical models for identifying phenotypic variance.
• Identify management and feeding practices related with beneficial microbiomes associated with health and KPIs.

Facilitate the adoption by end-users of the proposed innovations

• Consider stakeholders’ needs, expectations and the levers and brakes for adoption of novel practices.
• Evaluate the potential acceptability and socio-economic impact of the innovations proposed in the project.

Interact with influencer stakeholders for knowledge transfer.

The HoloRuminant project has received funding from European Union’s Horizon 2020 research and innovation program under Grant Agreement No 101000213. This publication reflects the views only of the author, and not the European Commission (EC). The EC is not liable for any use that may be made of them information contained herein.

PROJECT PARTNERS

• AARHUS UNIVERSITET (AU)
• AGRESEARCH LIMITED (AGR)
• AGRIFOOD AND BIOSCIENCES INSTITUTE (AFBI)
• THE AGRICULTURAL RESEARCH ORGANISATION OF ISRAEL – THE VOLCANI CENTRE (ARO)
• BEN-GURION UNIVERSITY OF THE NEGEV (BGU)
• AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS (CSIC)
• COMMONWEALTH SCIENTIFIC AND INDUSTRIAL RESEARCH ORGANISATION (CSIRO)
• FEDERAZIONE EUROPEA DI ZOOTECNICA (EAAP)
• EUROPEAN FORUM OF FARM ANIMAL BREEDERS (EFFAB)
• INSTITUT DE L’ELEVAGE (IDELE)
• INSTITUT DE RECERCA I TECNOLOGIA AGROALIMENTARIES (IRTA)
• INRAE TRANSFERT SAS (IT)
• LUONNONVARAKESKUS (LUKE)
• NORGES MILJO-OG BIOVITENSKAPLIGE UNIVERSITET (NMBU)
• NATIONAL UNIVERSITY OF IRELAND GALWAY (NUIG)
• THE QUEEN’S UNIVERSITY OF BELFAST (QUB)
• SRUC (SRUC)
• TEAGASC – AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY (TEAGASC)
• THE GOVERNORS OF THE UNIVERSITY OF ALBERTA (UAL)
• THE REGENTS OF THE UNIVERSITY OF CALIFORNIA (UCSB)
• UNIVERSITEIT GENT (UGent)
• UNIVERSITAET GREIFSWALD (UG)
• WAGENINGEN UNIVERSITY (WU)