FoodBioSystems - Development of effective rapid detection techniques to assess Fusarium spp. and T-2 and HT-2 mycotoxin level throughout the UK oats food chain PhD

Updated: 15 days ago
Location: Cranfield, ENGLAND

This PhD project aim to develop effective and easy-to-use methods to monitor Fusarium species and T-2+HT-2 mycotoxin level in oat and oat-based products throughout the oat food chain. FoodBioSystems is a UK Biotechnology and Biological Sciences Research Council (BBSRC) funded doctoral training partnership (DTP) which brings together six UK universities internationally recognised for their expertise in agriculture, food and nutrition, as well as fundamental bioscience disciplines. The DTP is led by the University of Reading in collaboration with Cranfield University, Queen’s University Belfast, Aberystwyth University, Surrey University and Brunel University London. Read moreRead less


Oats consumption is in constant increase due to its many benefits including being a rich source of fibre, essential amino acids, antioxidants, vitamins and its health benefits including reduction of coronary heart diseases. Oats-based products are also a great source of alternative for gluten-free products. In 2019, oat production was 1.1 million tonnes in the UK for an equivalent value of £145M; of these 522 thousand tonnes went to UK Millers. The latter transform oats into flakes, flour and other cuts from which exportation to the EU represents a £22M market. As such the UK oat milling industry needs to comply with EU Food Safety regulations to avoid rejection at the EU borders and drastic food and income losses. Among the regulations, the most tricky to comply with are the ones linked with mycotoxins – secondary metabolites produced by fungi.

Good agriculture practices have already been established for known mycotoxins such as deoxynivalenol and zearalenone produced by Fusarium graminearum, a pathogenic fungus which produces characteristic Fusarium Head Blight symptoms. However, lesser is known for other mycotoxins including T-2+HT-2. These are mainly produced by F. langsethiae, which produces no visual symptoms on oats making it very challenging to detect.

The EU is now looking at the implementation of regulatory limits which would result in at least 13% of the UK oats being not compliant. Thus, there is a need to help the oat food industry to develop strategies to detect, monitor and prevent the risk of T-2+HT-2 in oats. 

Studies at Cranfield University (CU) in collaboration with Richardson Milling (Ltd) UK have previously shown a lack of easy-to-use and reliable testing kits for Fusarium species and T-2+HT-2 detection in oats. The following objectives have been developed to tackle this challenge.

The objectives are:

1. At CU, development of a colorimetric (destructive) and spectroscopy (non-destructive) technique to monitor different Fusarium spp. in oat samples,

2. At Queens University (QUB), development of new biosensor techniques to detect T-2+HT-2 in oat and oat-based products (6 months placement in 2023/2024),

3. Evaluate the performance of the developed techniques on samples taken at different stages of the oat food chain,

4. Apply the techniques in a 3-year survey for selected farmers.

To successfully meet these objectives, the student will have the opportunity to apply state-of-the-art techniques in molecular biology (Loop-mediated isothermal amplification), analytical chemistry (LC-MS/MS qTRAP), microbiology, and biosensor development (aptamer). The student will be able to characterize the efficiency of the techniques developed and will be able to apply them on samples from the oat food industry.

The student will be regularly interacting with farmers, merchants, and oat millers and will undergo a 3-month placement in the industry (nearby Cranfield) to fully understand the food chain. 

This project is a wonderful opportunity to minimize food losses by developing innovative techniques to support decision-making throughout the food chain.

Training opportunities:

The student will receive an outstanding range of specific opportunities. At Cranfield, the Applied Mycology Group has expertise in fungal ecology, ecophysiology, analytical chemistry, and molecular biology which will help the student in significantly enhancing their fundamental and applied research expertise. The student will be able to attend MSc course modules in our Food Systems and Management and Future Food Sustainability courses which will provide an excellent background knowledge on raw material quality assurance, food diagnostics, food mycology and the food security agenda. In addition, Cranfield provides through the Doctoral Researchers’ Core Development (DRCD) programme training in project and time management, scientific writing skills, statistics and data management, and presentation skills.

The student will spend 6 months (Year 2) at the diagnostics lab (QUB) with excellent facilities, especially related to diagnostics of mycotoxins detection. The diagnostics lab has developed a range of biosensor platforms in collaboration with industrial partners (e.g. Biacore AB, Neogen Lateral flow device) and the PhD student will be trained on these techniques through the placement at QUB.

The student will also have a 3 months placement with farmers, merchant and Richardson milling (UK) Ltd to develop their understanding of the industrial settings.


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