Healthy terrestrial livestock microbial ecosystems for sustainable production

Activities shall address relevant microbial ecosystems of terrestrial livestock, and their effects on the production, health and welfare of animals. They should look in a balanced way at the characterisation of microbial ecosystems (including microbial communities and microbe-derived metabolites), assessing variability within and between breeds in relation to variability of production systems and diet; at microbial behaviour (e.g. interactions between microbiota, evolution with age of animals, transmission); at microbial functions and interactions with host, environment and management practices, including feeding where relevant; and at possible ways in which those ecosystems can be managed, including socio-economic aspects, in order to reduce environmental impact, improve production and its quality, and/or health in particular during challenging periods such as early life, weaning or after disturbances. Activities will include the incorporation of data on microbial ecosystems in the models used to analyse phenotypic variability and to perform genetic evaluations. The activities shall address either ruminants, or monogastrics. Gut microbiome of pigs or poultry can be addressed only in so far as the activities are complementary to those in related projects selected under LC-SFS-03-2018. Proposals may cover one or more species and one or more microbial ecosystem.

Research on anti-microbial resistance can be included as long as it is not the main objective of the project (see topic SFS-12-2018/2019). Research on single animal pathogens is not the focus of the topic. The projects are encouraged to interact as appropriate with relevant collaborative projects in Europe as appropriate and with international initiatives such as the rumen microbial genomics network of the Global Research Alliance on agricultural greenhouse gases[[https://globalresearchalliance.org/research/livestock/networks/rumen-microbial-genomics-network/]].

The Commission considers that proposals requesting a contribution from the EU of up to EUR 10 million would allow this specific challenge to be addressed appropriately. Nonetheless, this does not preclude submission and selection of proposals requesting other amounts. Funding will allow support for at least one project relating to ruminants and one to monogastrics.

Research is increasingly paying attention to the importance of interactions between the animal host and microbiota and their effects on the production efficiency, and the health and welfare of animals. These interactions are highly dynamic and influenced not only by genetics, but also by external factors such as environment, nutrition/feeding and management. Recent developments in omics science and technologies have opened new avenues for understanding not only the biology and genetics of animals, but also the ecosystems in which they function and those which they harbour, i.e. microbiomes. This is particularly relevant for micro-organisms that are currently non-culturable. Research on the interplay between the animals and their microbial ecosystems is needed to contribute to the improvement of sustainable livestock production.

Funded activities will contribute to deciphering the characteristics and functions of the livestock microbial ecosystems and understand the ways in which they influence production, health and/or welfare of animals. They will provide standardised methodologies for further application in livestock production to the greatest extent possible, including socio-economic aspects.

In the short- to medium term, the application of the knowledge and solutions developed will, as appropriate:

• enable inclusion of data on microbial ecosystems in the models used to analyse phenotypic variability and to perform genetic evaluations;
• improve resource use and environmental impact of terrestrial livestock production;
• improve robustness and health of terrestrial livestock, in relation to productive functions;
• reinforce collaborations with initiatives in related domains to promote coherence and applicability of research on microbial ecosystems.

In the longer term, the funded activities will contribute to more resilient production systems.