European dairy industry is an important agri-food sector; it represents more than 300,000 jobs and 10 billion € positive trade balance. Five out of the ten top global dairy companies are European and more than 80% of European companies are SMEs. More than 300 cheeses and dairy products are sold all over the world and are protected as geographical indications or traditional specialties. Mastering cheese-ripening processes to avoid sanitary risk and waste, and produce typical cheeses with organoleptic properties valued by the consumers is of economic and social significance. E-MUSE aims to develop innovative modelling methodologies to improve knowledge about complex biological systems and to control and/or predict their evolution by combining artificial intelligence and systems biology. This multidisciplinary strategy integrating genome-scale metabolic models, dynamic modelling methodologies, together with the design of efficient statistical and machine learning tools, will allow analysing of multi-omics data and linking the results to macro-scale properties related to cheese ripening and consumer preference. Bioinformatics has addressed this issue by data mining; however, a gap still exists between the molecular scale information and the macroscopic properties that E-MUSE will contribute to fill. Moreover, in the context of sustainable development, more and more consumers are diversifying their diet and consume plant-based food. Introduction of plant-based proteins in the cheese process brings issues such as bitterness or safety. Modelling strategies from the E-MUSE project will help to target and solve these issues. Finally, E-MUSE will train researchers with multidisciplinary skills in mathematics, bioinformatics and/or biology to design and use innovative multiscale modelling methodologies, with the ultimate outcome of a dynamic modelling software giving researchers a harmonised language to address future research questions about complex biological systems.

The application of enzymes in industrial processes is increasingly important to achieve the EU’s sustainability goals and strengthen the bioeconomy, replacing oil-based chemistry. However, enzymes still find hurdles for their industrial application: low success rates of discovery and engineering; tedious and expensive methods to explore diversity; and limited activity/stability in the final application. RADICALZ assembles an interdisciplinary and intersectoral consortium to deliver faster, more versatile and more affordable tools for enzyme discovery and engineering, enabling the development of novel enzymes, new formulations and ingredients for more environment-friendly and healthier consumer products. This project will: i) develop new droplet microfluidic tools to find suitable enzymes for consumer products; ii) develop user-friendly software solutions based on machine learning (ML) for faster and more accurate enzyme engineering; iii) develop novel enzymes and bio-based, bio-catalytically synthesized ingredients for consumer products (glycosides, wash-enhancing enzymes, bio-based thickeners, natural antioxidants and fragrances); iv) develop bio-based, condition-responsive capsules for the protection and triggered release of enzymes and ingredients in the formulation of consumer products. RADICALZ will reduce the average time for enzyme discovery and evolution to <4 weeks, access 10 bio-based ingredients to replace oil-based chemistry, reducing the environmental impact –supported in depth in ≥3 cases– across 3 different types of consumer products. RADICALZ assembles 6 leading European companies and 6 pioneer academic teams expert in enzyme discovery and evolution, biocatalysis, chemical engineering, microbiology, soft-matter physics and microfluidics. The planned activities span 48 months and 7 work packages. The project is estimated at ca. 6 M€ (42% allocated to industrial partners and 64% of the total dedicated to creating highly-qualified jobs).

Ruminant animals, including cattle, sheep and goats, rely on microbial activity in their digestive tract to digest grass and other forages that they consume. A balanced, stable digestion (fermentation) is essential for good growth or milk production. Most livestock producers require productivity higher than that which can be sustained by forage feeding alone, and include some grain in the diet to increase production rates. Gut microbes produce acids more rapidly from the starch in grain than the cellulose in forages, leading to lower pH values prevailing in grain-fed animals. This has adverse effects on the microbes, which require near-neutral pH to perform optimally. This sub-acute ruminal acidosis (SARA) is a major economic and health issue in ruminant livestock production. Animals suffering SARA are less productive, and they suffer from necrosis of the rumen wall, liver abscesses and laminitis. SARA is often difficult for the farmer to detect - it is 'sub-acute' and can only be detected easily at slaughter. SARA is an under-researched condition, such that only a small number of papers have addressed the dietary and microbiological causes of SARA and its underlying pathology, particularly concerning the role of the large intestine. This project aims to understand why SARA is prevalent on some farms but not others, an observation that is common knowledge but not well documented. Farm management conditions and nutrition will be monitored in these farms, and the animals will be followed to slaughter, when the extent of pathological damage will be assessed. Samples of ruminal digesta and wall tissue will be taken for analysis and tissue necrosis, abscesses and laminitis will be scored. SARA also affects some animals but not others within a herd. Remote motion-sensing technology will be used to externally monitor movements, such as rumination activity, that may alert livestock producers to problematic animals. Post mortem analysis will also be carried out on these animals. The root cause of SARA lies in altered gut microbiology. Digesta samples will be taken forward to describe the microbes that are present in the rumen and intestine in susceptible and non-susceptible animals, with the idea that some microbial species may be particularly important in causing the disease while others may be protective. Candidate 'probiotic' bacteria isolated from non-susceptible animals will be investigated with a view to developing them as feed additives. The role of soluble lipopolysaccharide (LPS) in the inflammation will be investigated. LPS is released when bacteria lyse - it is known as 'endotoxin' in human medicine. Materials that may bind soluble LPS to prevent inflammation will also be investigated as potential feed additives. The overall aims are to explain the underlying mechanism of pathogenesis of SARA, to investigate if microbiome analysis can predict the severity of SARA, and to develop simple, non-invasive methods for monitoring animal behaviour relating to SARA and preventing the condition. Three academic partners, three complementary companies, Quality Meat Scotland and DairyCo are involved in the project. The industrial partners will ensure that relevance to the livestock industry is maintained throughout the project and that the pathway to impact will be short and rapid.

Although microorganisms dominate almost every ecological niche in our planet, it has only been during the past 10-15 years that we have begun to gain insights into the composition and function of microbial communities (microbiomes) as a consequence of major advances in High Throughput DNA sequencing (HTS) technologies. These approaches have allowed a comprehensive analysis of microbiomes for the first time. Following initial curiosity-driven investigations of microbiomes using HTS technologies, the field has evolved to harness the insights provided, leading to the development of a new multi-billion euro industry focused on characterisation and modulation of microbiomes. The vast majority of this investment has been in the clinical space. In contrast, far less is known about microbiomes across complex food chains, making it difficult to harness food-chain microbiome data for the development of more sustainable food systems and to yield innovative products and applications. This is despite the evident importance of microbes throughout the food chain. MASTER will take a global approach to the development of concrete microbiome products, foods/feeds, services or processes with high commercial potential, which will benefit society through improving the quantity, quality and safety of food, across multiple food chains, to include marine, plant, soil, rumen, meat, brewing, vegetable waste, and fermented foods. This will be achieved through mining microbiome data relating to the food chain, developing big data management tools to identify inter-relations between microbiomes across food chains, and generating applications which promote sustainability, circularity and contribute to waste management and climate change mitigation. We will harness microbiome knowledge to significantly enhance the health and resilience of fish, plants, soil, animals and humans, improve professional skills and competencies, and support the creation of new jobs in the food sector and bioeconomy.