The presence of undeclared allergens in food products poses a serious health risk to consumers and results in important economic losses for the food industry. The detection of allergens is typically performed using immunological methods. DNA-based methods complement immunoassays and provide higher specificity and sensitivity, especially in processed foods. DNA-based identification of allergens can currently only be performed using well equipped laboratories which can be difficult to implement in an industry settings where the identification should be fast and on-site. In SafeFood, I will develop a protocol to implement cutting-edge Nanopore sequencing technology for rapid, portable identification of allergenic plant ingredients in complex, multi-ingredient food products. DNA-based identification of allergenic plant species has been challenging due to the lack of variation of the traditional DNA barcodes. I will implement more robust species identification methods based on whole plastid genomes. First, I will compile a comprehensive open-access database of allergen species’ plastomes. Then, DNA extraction and library preparation will be optimized for an on-site protocol tailored to the constraints of the food industry. I will create artificial mixtures of complex food, with varying concentrations of allergens to test the method’s sensitivity, specificity and repeatability and compare the results to those of immunoassays. This innovative solution will solve an industry challenge by allowing on-site, fast and accurate allergen identification. By being hosted at a leading DNA service company, BaseClear, and with the collaboration of a specialised academic partner in EU food safety analyses, RIKILT, I will apply my expertise in plant genomics, develop skills in food chain analyses, in R&D and entrepreneurship. At the completion of this fellowship, I will be able to apply this knowledge and skill to further address societal challenges in the food industry.

Many of the nearly 400,000 species of plants provide food, feed, medicines, and construction materials. Besides these positive impacts, plants also affect us negatively through pollen allergies, poisonous species, as invasive species, and as adulterants in herbal medicines. Nevertheless, plants are the most promising biological resource for our future. Current extinction risks of global flora and vast decline in taxonomic expertise demand accurate and rapid identification approaches to understand and valorise botanical biodiversity. Advances in genomic data and DNA sequencing are revolutionizing plant systematics, and modern molecular identification methods make it possible to accurately determine plants in ways that were technically impossible only a decade ago. Recently, it has become possible to detect substitution in herbal pharmaceuticals, monitor invasive alien species, trace fragments such as pollen and spores, uncover illegal trade in endangered species, make rapid and accurate molecular biodiversity assessments, and study historical plant diversity through DNA in museum specimens. However, to efficiently harvest the potential of the opportunities provided by the new genomic techniques, society today is in urgent need of trained biosystematists experienced in both taxonomy and in handling enormous amounts of genomic data. Plant.ID will innovatively address these challenges by bringing together academic and non-academic partners including regulatory agencies, industry, SMEs and NGO stakeholders, with the aim of developing molecular identification of plants through tailored approaches to species delimitation, metabarcoding, gene capture, and genomic barcoding, in order to empower stakeholders with simplified molecular identification of plants. By bridging classical taxonomic expertise with cutting-edge genomic approaches, Plant.ID will train a new generation of ESRs who will have immediate relevance to harnessing the central role of plants in the modern world.

In PlantHUB will capture the academic, industrial and regulatory expertise from 5 world-class universities, 1 governmental organization, 7 enterprises including 4 SMEs to train 10 ESRs in skills and competencies necessary to apply responsible research and innovation (RRI) in the area of plant breeding and production. We wish to address the demand of RRI leadership in plant science related research and diffusion of innovation. The individual research projects are demand-driven, responding to the needs of companies - particular SMEs - to increase R&I capacities. The outcomes are new molecular tools for plant breeding, new forage, cereal and oil crop varieties, non-invasive imaging and phenotyping technologies, intelligent lighting systems for plant growth, new software and services for complex genomic analyses, and plant product quality. PlantHUB industrial doctoral programme is ground-breaking in a number of respects: (i) doctoral training is placed into an entrepreneurial environment of leading public and private organisations (ii) it combines practical hands-on R&D and technology transfer in plant breeding and production with RRI training and practise. On completion of the training, graduates will have deep interdisciplinary knowledge of plant breeding, crop improvement, high-throughput technologies, isotope and big data analysis. In combination with a portfolio of transferable skills they will be able to take a lead in stakeholder & public engagement, innovation management, technology transfer and entrepreneurship. Our programme will become a flagship example at the forefront of intersectoral research, underpinned with a carefully created training curriculum to foster awareness, know-how, expertise and competence in RRI.

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.