Antimicrobial resistance in livestock is a public health threat due to the risk of zoonotic transmission to humans and its negative consequences on animal health and welfare when diseases cannot be treated. AVANT is a multi-actor inter-sectorial project aimed at developing alternatives to antimicrobials for the management of bacterial infections in pigs, especially diarrhoea during the weaning period, as the major indication for antimicrobial use in livestock in Europe. Antimicrobial treatment options for pigs are increasingly limited because of planned restrictions in the use of colistin and zinc, two current choices for treatment of post-weaning diarrhoea. The AVANT portfolio comprises a variety of alternatives for treatment or prevention of diarrhoea and/or respiratory infections, namely (i) gut-stabilizing interventions based on a symbiotic (pre- and probiotic) product and faecal microbiota transplantation; (ii) novel veterinary medicinal products containing bacteriophages and polymers for targeted treatment of enterotoxigenic E.coli infections; (iii) immuno-stimulating injectable and feed additive products, and (iv) alternative feeding strategies targeting sows and piglets. During pre-clinical studies, efficacy, toxicity, and mode of action of these interventions is tested, and their dosage and formulation optimized. The results and a survey for veterinarian-, farmer- and consumers perception of antimicrobial alternatives, will be used together with legal and economic considerations to select three interventions for large-scale farm trials, assessing clinical efficacy and impact on antimicrobial use. All steps are supported by regulatory advice for quick market entry post-project. Generated and existing data on antimicrobial use, pig demographics and projected consumption of pork, will be used in mathematical modelling to estimate the reduction in antimicrobial use that could be achieved by 2030 if the AVANT alternatives were widely adopted in pig production.

MyToolBox mobilises a multi-actor partnership (academia, farmers, technology SMEs, food industry and policy stakeholders) to develop novel interventions aimed at achieving a 20-90% reduction in crop losses due to fungal and mycotoxin contamination. MyToolBox will not only pursue a field-to-fork approach but will also consider safe use options of contaminated batches, such as the efficient production of biofuels. A major component of MyToolBox, which also distinguishes this proposal from previous efforts in the area mycotoxin reduction, is to provide the recommended measures to the end users along the food and feed chain in a web-based Toolbox. Cutting edge research will result in new interventions, which will be integrated together with existing measures in the Toolbox that will guide the end user as to the most effective measure(s) to be taken to reduce crop losses. We will focus on small grain cereals, maize, peanuts and dried figs, applicable to agricultural conditions in EU and China. Crop losses using existing practices will be compared with crop losses after novel pre-harvest interventions including investigation of genetic resistance to fungal infection, cultural control, the use of novel biopesticides (organic-farming compliant), competitive biocontrol treatment and development of forecasting models to predict mycotoxin contamination. Research into post-harvest measures including real-time monitoring during storage, innovative sorting of crops using vision-technology and novel milling technology will enable cereals with higher mycotoxin levels to be processed without breaching regulatory limits in finished products. Research into the effects of baking on mycotoxin levels will provide better understanding of process factors used in mycotoxin risk assessment. Involvement of leading institutions from China are aimed at establishing a sustainable cooperation in mycotoxin research between the EU and China.

An important gap in continued sustainability of fish farming is the lack of a proper understanding on digestive function and aquafeeds utilization. The WiseFeed project will focus on this gap using an integrative approach and considering selected key fish species in culture, the feed composition and feeding protocols. The approach in WiseFeed is based on a collaborative effort for advancing both the fundamental physiological knowledge and practical applicability. WiseFeed will build an integrated network of research groups from the academia and partners in SME and large enterprises where the overall aim is to improve performance and sustainability of aquafeeds for fish production. WiseFeed has the following specific objectives: - Develop model that quantifies digestion, absorption and retention efficiency of selected macro nutrients in key cultured fish species - Develop software package to optimize feeding strategies - Elucidate the role and effects of specific amino acids and dietary supplements for enhancing metabolism, growth and N-retention including effects of elevated temperatures due to climate changes. The research that forms the basis for WifeFeed is funded by on-going national R&D projects that constitute the scientific and technical pillars of the current proposal. The secondments will bring external expertise to each of these R&D projects and coordinate efforts among similar and related activities. The secondments also build the competence of each of the participating researchers The practical benefits of WiseFeed will be improved production yield, reduced feeding cost and reduced N-waste from fish farms. The expected added value will be a faster advance in common objectives by facilitating progress and fulfilment of the R&D objectives for each participant. Furthermore, it is also the aim of WiseFish to establish a consolidated network beyond the framework of this proposal to give response to new challenges of the aquafeed industry.

Understanding the interplay between animals and microorganisms associated with them has been recognised as an essential step for improving animal health, welfare and production. To understand the biomolecular interactions that impact production processes, researchers are implementing novel analytical strategies based on studying host genomes, their microbial metagenomes as well as the different ‘omic layers interconnecting them. However, such information, derived from conventional DNA/RNA sequencing and mass spectrometry, does not provide any information about how the different biological elements are spatially distributed in the ecosystem. In consequence, many microbe-microbe and animal-microbe interactions remain hidden due to the lack of resolution of the employed techniques. Acknowledging the three-dimensional (3D) conformation of biomolecules, cells and tissues is now considered a key element for advancing the understanding of biomolecular interactions. In 3D’omics we will develop, optimise and, for the first time, implement this technology in animal production to generate the so-called 3D’omic landscapes, the most accurate reconstructions of intestinal host-microbiota ecosystems ever achieved. Using two terrestrial production systems, namely poultry and swine, we will analyse the effect of a myriad of factors, including animal development, diet, exposure to pathogens and management practices, in the shaping of 3D’omic landscapes. Through coupling our new technology with cutting edge analyses of animal health and performance, we will advance phenotypic variability and genetic evaluations of production animals to a new frontier. We foresee our solution will open new research avenues to improve animal breeding practices, develop microbiota- and host-tailored feeds and animal health treatments, as well as to design new management practices that will enable increasing production efficiency and animal welfare while decreasing the environmental impact.

There is a massive and urgent need to ensure security and safety of the food supply of the growing world population. The ongoing war in Ukraine as well as the energy crisis emphasized this even further. However, agriculture and food industries continue to be vulnerable to problems of contamination with biotoxins produced by plants, algae and particularly by fungi. Global warming and extreme weather events make the occurrence of these toxic metabolites even less predictable. Alarmingly, the EU currently faces a lack of food safety specialists, as recognised by the European Commission. These challenges lay the foundation for BIOTOXDoc – Safe food in a world of changing climate: The doctoral training programme to develop novel control, mitigation and risk assessment methods for biotoxins. The objective of BIOTOXDoc is to train doctoral students (PhDs) in a broad range of skills and complementary competencies - necessary to innovate various scientific fields and approaches, so urgently needed to control and mitigate biotoxins - by taking advantage of a multidisciplinary, multi-sectoral team of world-class experts. The training and research will include development of early warning systems and on‑site testing by portable mass spectrometry. PhDs will develop novel detoxification strategies of biotoxins and will assess the combined toxicity of co‑occurring biotoxins. Moreover, PhDs will develop much-needed rapid as well as confirmatory tests for biotoxins and aim to close major gaps in our current knowledge of biotoxins. The major common link between all PhDs, working on a wide range of biotoxins at different points along the food and feed chain, is the influence of climate change on biotoxin occurrence and the resulting demand of revised strategies to mitigate its impact on the European population.