The objective of the PAS-AGRO-PAS project is to increase productivity, adaptiveness, sustainability and profitability of Mediterranean agro-pastoral production systems, by exploiting every dimension of their multifunctionality through a novel systemic approach that will identify stressors currently impacting on agro-pastoral systems’ viability, with views to implementing tailored strategies that redirect agro-pastoralism from subsistence-oriented fragile production systems towards commercially-oriented resilient systems. To achieve this objective, PAS-AGRO-PAS will explore a representation of 10 agro-pastoral production systems from Portugal, Spain, France, Italy, Cyprus, Morocco, Egypt and Tunisia, covering a wide range of environmental, agro-ecological, economic, socio-cultural and institutional traits and challenges; and will apply a systemic approach from farm to global scale, interlinking three systems: (i) “agro-ecosystem”, with interventions on the productivity and diversification of crops, pasture and livestock resources (such as better utilisation of crop residues, new grazing surfaces, use of biodiverse pasture seeds, including forage legumes into rotations with crops, alley cropping with barley, drought-tolerant forage and crop varieties, effective treatment of manure, matching livestock production cycle to feed resources, multi-nutrient blocks to enhance digestibility, etc.) that will be implemented, in order to ensure low input, maintenance/increase of biodiversity, enhanced soil fertility and custody for local adapted breeds – in the short term, and the rehabilitation of rangelands and the reduction of vulnerabilities to climate change – in the long term; (ii) “socioeconomic system”, with interventions towards the valorisation of agro-pastoral products (through assurance of quality, safety and typicity, and creation of notebooks of product standards for origin/quality certification), the leveraging of the marketable “healthy” trait of food produced with environmentally friendly systems, the efficient integration into markets, and the rising of the “commercialisation mentality” of agro-pastoralists, in order to ensure economic benefits and generational renewal; and (iii) “information system”, whereby, within a multi-actor co-creation process, the agro-pastoralists’ traditional knowledge will be sourced and steadily integrated with the outputs of this project, taking advantage of the networked and cooperative digitalisation of Agriculture 4.0, in order to efficiently manage information resources and access to decision-making support e-tools. Furthermore, the successful implementation of PAS-AGRO-PAS with the expected impacts at the farm, at the regional and at the global scale will be sustained by two important pillars: (i) “capacity building activities” for agro-pastoralists on effective strategies, climate change mitigation and adaptation, quality of their products, pricing and economic profitability, commercialisation and entrepreneurship, inclusive development, with special focus on women, the youth and newcomers; and “divulgation activities” with key stakeholders and policy-makers for providing policy guidelines for more enabling structural, economic and institutional settings; and (ii) the development of the PAS-AGRO-PAS Mediterranean e-platform, which through systematised data, reports, models and web applications for resource allocation, ration formulation and feed management, optimum slaughter weight prediction, and e-commerce, will better inform evidence-based decisions for both agro-pastoralists and policy-makers.

The future challenge in animal production will be to provide food to a growing human population by respecting a balance between quality products, consumer acceptance and safety, as well as animal welfare. In a perspective of safe and sustainable food systems, reducing the use of antibiotics in livestock is a major concern. In fact, antibiotic resistance is one of the major medical challenges of the 21st century. The transfer of genes conferring resistance through the environment and the food chain, the potential for development of resistant bacteria and the appearance of therapeutic failures in human medicine, notably due to zoonotic bacteria, constitute major health issues for livestock farming sectors. In the pig breeding industry, the weaning period is often accompanied by a decreased growth rate caused by disparate food intake and diarrhoea due to digestive disorders that might be associated with bacterial population disequilibrium (i.e. dysbiosis) and/or opportunistic intestinal infections. Alarmingly, during this transition period the prophylactic use of antibiotics is still very frequent in order to limit piglet morbidity and mortality. Thus, reducing the prophylactic use of antibiotics in weaning pigs is a main issue and there is a strong need for alternatives. In this context, we have built a public-private partnership that gathers INRA scientists and industries from economic sectors of both animal feeding and pig breeding. PigletBiota is a precompetitive project that will study the physiological and genetic bases of the piglet sensitivity at weaning, as a prerequisite to identify innovative actions to adapt animals and pig production systems to a reduction of antibiotic use. The global aim of the PIGLETBIOTA project is to develop research that will contribute to adapt pig production systems to a reduction of antibiotics. The project proposes an integrative biology approach to determine the main factors influencing the variability of the individual’s robustness at weaning. We will monitor piglets for health, immune, stress and zootechnical traits and will characterize the intestinal microbiota diversity and composition as well as the contribution of host’s genotypes. The experimental design will combine various environments, including experimental and commercial farms, and ages at weaning and all animals will be fed without antibiotics. Animals (n~1000) will be clinically surveyed, measured for various traits related to production, immunity and stress, and genotyped with high-density SNP chips. The genetic parameters of the sensitivity at weaning will be estimated and genetic association studies performed. Faecal samples before and after the weaning date will be collected for characterizing the dynamics of the gut microbiota and studying its influence on the individual sensitivity at weaning. Animal and microbiota data will be vertically integrated in order to better understand the interplay between the these two levels of this biological system, and to develop robust indicators of weaning sensitivity. Finally, a functional screening using INRA platforms dedicated to human studies will be performed in order to detect active molecules to be tested in vivo and by using an axenic pigs model. The PigletBiota public-private consortium will favor translational research and innovation.

The livestock sector is highly concerned by the global food system, both by an expected increase in the demand for animal products such as milk, and by the ecological footprint of animal production, which must be minimized. Increasing feed efficiency (FE) in dairy cows would reduce some of the direct emissions (methane and ammonia) from livestock production but would also have a substantial positive impact on the induced emissions associated with crop production, due to the better feed conversion. Genetic improvement of FE is a particularly attractive strategy because it would impact most of the dairy farms for a limited cost. The decreased use of feed inputs implied by such an efficiency gain would give a competitive advantage to dairy production, but will also contribute to reducing environmental impacts. Thus, this project is expected to provide the essential elements needed for genetic selection strategies to improve FE in dairy cows. It fits with the fifth of the major societal challenges of ANR and the first research theme of the APIS-GENE consortium on FE and limitation of N pollution and methane emission by ruminants to improve the overall efficiency of ruminants. Selecting for FE is not as straight forwards as it might first seem, there is evidence to suggest that robustness and adaptive capacity, especially for reproductive females, can be adversely affected by short-sighted strategies to improve efficiency. Thus, the choice of indicators used to assess FE is of great important, and it is essential to verify and validate the anticipated benefits of any such strategies to improve efficiency for their long-term consequences. Another key issue is to be able to better exploit new possibilities to target specific characteristics that contribute in part to FE. Such characters have rarely been studied because they have been very difficult to phenotype. The project will use new phenotyping technologies and the newly available information from them to develop selection for efficient use of body reserves whilst limiting the risks of undesirable trade-offs with other life functions that have been associated with high levels of production in dairy cows. DeffiLait aims to elucidate ways by which to improve the FE of dairy cows without decreasing their robustness, to build strategies for doing this, and models to predict the future increases in FE attainable by selection programs, and directly on farm. The project will first involve developing new tools for large-scale phenotyping of the major biological characteristics that are directly involved in FE. The project will produce new tools to better estimate body condition, morphology, and digestive efficiency in large scale studies. These phenotypic measures will also impact on our capabilities for on-farm advising, and monitoring in livestock, which are also levers for improving efficiency at farm level. Then, to study the major determinants of FE, the project will also build an original database of dairy cow lactations with a large set of phenotypes to describe the main sources of energy transformation, thus explaining the observed between-animal variability in FE. This dataset will then be used to quantify the contribution of the different mechanisms to the variability in FE, and to test different indicators and strategies to improve FE. A specific focus will be made on body reserves mobilization in early lactation to assess its genetic components and correlation with other traits with a larger dataset involving commercial farms. The project will then develop simulation tools to predict the short- and long-term consequences of different selection strategies in different environments. The expected results will contribute to the definition of strategies of selection to combine efficiency and robustness. The project will provide a coherent framework to undertake a balanced genetic selection on these traits, and thereby make a significant - and lasting – contribution to improving FE.

The objective of ADAPT-HERD is to develop management simulation tools to implement innovative strategies for resilience and efficiency (R&E) in small ruminants herds, based on harnessing animal adaptive capacities. These tools will address a wide range of current feed resource constraints in the Mediterranean area (Egypt, France, Spain and Tunisia) and the future perturbations induced by climate change. The locally tailored management solutions will improve the ability of livestock systems to adapt to climate change by: i) managing early-life nutrition to safeguard adult adaptive capacities; ii) managing reproduction to find the best match between feed supply and herd demand; iii) tailoring group feeding strategies depending on animals’ adaptive capacities and iv) managing herd demography with replacement and culling to adjust feed demand. To achieve this, ADAPT-HERD brings together information from animal and herd levels with: i) a fine-grained experimental approach (adaptive mechanisms and trade-offs); ii) field phenotyping of local breeds (adaptation to local conditions) and iii) local production environment characterization. These multi-level information will be used to develop computer models and test scenarios. Interfacing and disseminating project’s deliverables as a user-friendly toolbox will be achieved with a participatory modelling framework. The toolbox will help to adapt agricultural practices to change in resource availability by proposing different technical solutions of herd management aimed at facing feed resource perturbations induced by climate change. The challenge is not to find an optimal strategy for R&E, but to explore how management strategies impact the relationship between R&E. These strategies will be grounded in a deep understanding of how local breeds adapt to feed resource constraints. They will be complementary to on-going projects that focus on genetic selection and breeding solutions to improve R&E in small ruminants.

Reducing methane (CH4) emissions from ruminants is a major challenge for the livestock sector. An optimal CH4 mitigation strategy should also induce co-benefits such as enhanced animal productivity and health. CH4 is produced during the fermentation of feeds in the rumen. This process is carried out by a complex microbial community (rumen microbiota) and mediated by hydrogen (H2) in the rumen ecosystem. Our knowledge on the drivers that shape H2 flows is still incomplete. H2Rumen aims to generate fundamental knowledge on H2 flows in the rumen ecosystem and to translate this knowledge into predictive mathematical models of rumen fermentation. Our scientific outputs will be of high value for the optimal design of CH4 mitigation strategies with co-benefit for the animal. Our hypothesis is that thermodynamics and microbial interactions jointly control hydrogen transactions in the rumen ecosystem. H2Rumen addresses the following fundamental scientific question: Where does H2 go? We will answer this question with an integrative approach that combines in vitro experiments, in silico modelling and omics approaches. For that, H2Rumen brings together an interdisciplinary team with expertise on rumen fermentation, rumen microbiology and metabolic modelling. In addition to the impact on ruminant livestock, our methods might be applicable to other ecosystems such as the human gut, engineering bioreactors and fermented food ecosystems.