Metagenomic Studies of the Microbiota of Fermented Cacao Beans – Application for the Chocolate Industry

An opportunity for a fully-funded PhD studentship is currently being offered by the Faculty of Health and Applied Sciences at UWE Bristol.

The closing date for applications is Monday 27 February 2017.

About the studentship

Cocoa and chocolate products can vary hugely in flavour according to their geographical provenance. Several factors are likely to influence the development of flavour including the fermentation process of the cacao beans. Preliminary studies at UWE Bristol have shown that all specific microbial species involved in the fermentation process can be characterised from DNA extracted from fermented cocoa beans, roasted beans and finished chocolate products. This will enable us to evaluate how the microbiota involved in the fermentation process lead to specific chocolate flavour. This in turn could help in the development of fermentation “spiking” or targeted inoculations to produce specific flavoured chocolate, or to make the large number of small-scale fermentations more reproducible.

Furthermore, the chocolate industry has changed to a much higher demand for certified cacao (Rainforest Alliance, UTZ, FairTrade). Companies like Mars have stated that by 2020, all their cacao will be certified sustainable. There is, therefore, a need for methodologies to be developed enabling the characterisation and geographical tracking of certified cocoa products. While DNA markers can be utilised to identify the crop itself, such an approach is likely to be ineffective in West Africa (today’s main world cacao producer) where the level of crop diversity is minimal. Identifying farm-specific DNA markers characterising the microbiota on the surface of fermented cacao beans will resolve this issue.

This project will embed stakeholders in the project design with a view to facilitating research uptake and exploring best practice in knowledge exchange. It is anticipated that the student will also undertake a range of public engagement and knowledge exchange activities throughout the project lifecycle.

 Aims of PhD project:

  1. Further developing chloroplast-based marker screening approaches of chocolate-derived material to identify location of small cooperative producers.
  2. Identifying farm-specific DNA markers characterising the microbiota on the surface of fermented cacao beans from chocolate samples via Next Generation Sequencing.
  3. Developing molecular specific assay for diagnostic SNPs of specific cocoa origin,
  4. liaising with the chocolate industry to assess the potential of these molecular screening methods for tracing sustainably certified cacao products.

Supervision team and research environment

This PhD will be based at UWE Bristol.

The supervisory team will comprise Dr Joel Allainguillaume (Director of Studies), Professor Dawn Arnold and Dr Emma Weitkamp. The student will have weekly face-to-face meetings with the Director of Studies and input from other members of the team in response to the specific needs of the student and the research.

  • Dr Joel Allainguillaume, Senior Lecturer in Molecular Genetics (UWE Bristol). Works on the application of molecular and genomics approaches to address problems of agronomic, ecological and conservational importance including the use of Next Generation Sequencing (NGS).
  • Dawn Arnold is a Professor in Molecular Plant Pathology (UWE Bristol) and leads the Molecular Genetics research group investigating the molecular biology of plant-pathogen interactions.
  • Dr Emma Weitkamp is an Associate Professor in Science and Communication. Current research projects investigate the way we communicate 'distant' risks, considering the role of narrative in this process.

The PhD student will join The Centre for Research in Biosciences (CRIB) which brings together world-class multidisciplinary, collaborative research with focus on the following themes: biomedicine, bio-sensing and analytical, agri-food, plant science and environmental science. CRIB address both, fundamental and applied aspects of research. Close links with national and international academic partners, health organisations and industry ensure that our research has real social and economic impact.

The PhD student will be a member of the Faculty of Health and Applied Sciences, which provides a programme of training and support for PhD students. This includes access to any relevant UWE Bristol modules, or external university modules/courses to meet their specific training needs for 60 Master’s level credits. Additional short courses are available free of charge to all postgraduate research students through the Graduate School Researcher Development Programme, which is delivered by the UWE Bristol Graduate School.

Funding details

The studentship will start on 1 April 2017 or 1 May 2017 and consists of an annual tax-free stipend of £14,296 subject to satisfactory progress, for three years. In addition, full-time tuition fees will be covered for three years.

The studentship will only fully fund applicants who are eligible for Home/EU fees. Applicants who are normally required to cover overseas fees will have to cover the difference between the Home/EU and the overseas tuition fee rates.

Eligibility criteria

Applicants must have a good honours degree (2.1 or equivalent) in a relevant discipline together with experience in molecular biology, microbiology and next generation sequencing analysis. A Masters qualification is desirable, but not essential if the applicant has relevant research experience. A recognised English language qualification is required. 

How to apply

Download and complete the application form and send it directly to the UWE Bristol Graduate School. Please ensure you include the title of the research project you propose to undertake, and detail why you are interested in undertaking this PhD project and what relevant knowledge, experience and qualifications you would bring to the research. Please see the guidance notes for further information about how to complete the application form.

Please also complete the Equal Opportunities form and complete the first section of the Application reference sheet before sending to your nominated referees.

For an informal discussion about the studentship, please contact Dr Joel Allainguillaume

Closing date

The closing date for applications is Monday 27 February 2017.

Further information

Interviews will take place in the week commencing 13 March 2017. 

If you have not heard from us by 13 March 2017, we thank you for your application but do not wish to pursue it on this occasion.

The starting date of this PhD studentship is  1 April 2017 or 1 May 2017.

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