The project will produce knowledge on ruminant microbiomes and on their effect on the ruminant holobiont health, welfare and sustainable production. Making use of existing knowledge, and focusing on prevalent ruminant phenotypes, HoloRuminant will adopt an ambitious holo-omics approach to identify and functionally characterize beneficial microbiomes and keystone beneficial microbes that are associated with health and relevant KPIs. The collated ruminant microbiome data and standardized tools produced by HoloRuminant will be made available to the wider scientific community through the HoloR database and HoloR-tools repository of dedicated tools and pipelines. These expandable resources for the analysis and interpretation of ruminant microbiomes will be able to address future issues of ruminant production well beyond the duration of the project.
The collection of resources developed by the project will take into account ruminant associated microbiomes for improved animal health and welfare. The establishment and maintenance of microbial communities from key ruminant body sites from different breeds and species, management systems and environments will be studied and their effect on animal health, welfare and KPIs will be evaluated. Microbiomes prevalent in health and in ruminant phenotypes of diarrhoea, respiratory illness, acidosis and mastitis will be defined and used for addressing diagnostic needs. Beneficial microbial patterns and management solutions associated with KPIs and lower illness incidence will be identified. The knowledge and tools developed (and available to researchers and industry in HoloR and HoloR-tools) will be disseminated and promoted for inclusion in the existing models for phenotypic variability and for genetic evaluations allowing the selection of healthier animals ensuring a more sustainable production. In the medium term, the microbial data, where relevant, will be included in improved management practices, feeding systems and formulation of diets.
HoloRuminant will create insight and develop computational methods for the selection of more efficient and more sustainable animals. It will identify microbiomes associated with greater environmental efficiency (better feed utilization and reduced methane emission) in correlation with ruminant breeds and genotypes. This information will be available in HoloR and HoloR-tools to industry and breeders that will propose solutions to farmers and other upstream actors of the production chain. Breeders will include this information in their selection models, feed additive producers will develop products to favour beneficial microbes and developers of enteric methane mitigation solutions will use the information on the mechanism of action of additives to support products registration. Conscious consumers will be able to choose milk and meat produced using fewer resources and with reduced methane emissions. A more efficient and sustainable ruminant production will improve the image and business model of the food industry and farmers. Other effect of improved ruminant health mentioned in previous impacts is the decreased use of antibiotics, a recognized source of environmental pollution and a One Health issue.
The project will propose strategies to protect animals against diseases and nutritional disorders during challenging periods and enhance their robustness through microbiome modulation. HoloRuminant will identify management solutions such as improved feeding and transport practices for healthier animals; it will identify animals susceptible to acidosis and initiate the development of new microbiome-based profiling tools to predict mastitis and diagnose BRD. Industry will have access to the newly developed tools to test and improve specific solutions that will finally be transferred to farm advisers and farmers and reduce the incidence of diseases in the herd/flock.
The results of HoloRuminant will ultimately contribute to more efficient and sustainable production of ruminants using a streamlined process that will: (1) improve selection of animals with inherent beneficial microbiomes, (2) intelligently match diets with the microbiomes and genotype, the “hologenotype” of the farmed ruminant and (3) improve economic sustainability and general management practices. This will promote a higher resilience of production systems to seasonal instabilities, dietary changes, etc.