MSc By Research: Microbial fermentation of complex insoluble dietary fibre

The MSc by Research programme at the University of Aberdeen is for students interested in a research-intensive master's degree. It is designed specifically to enhance your skills for a PhD or research career. If you have your own ideas for a research project in this area, we would love to hear from you! Please reach out to one of the project supervisors above to discuss your ideas.

You can find further information about our academic requirements and programme structure here.

Dietary fibre is the fraction of food that cannot be broken down and absorbed in the upper intestinal tract and therefore passes through to the colon. It largely consists of carbohydrates from plant cell walls and storage compounds and is a major energy source for microbes resident in the colon, the microbiota. The microbiota ferments fibre to a range of compounds, including short-chain fatty acids, implicated in eliciting health-promoting effects on the human host. Most of the research to date on how the microbiota ferments fibre is based on single purified carbohydrates. Accordingly, current available nutritional fibre supplements aiming to aid gut health are largely based on such compounds, for example the prebiotic inulin. However, there is evidence that ingestion of large amounts of such refined fibre components at the expense of whole plants is not ideal for the maintenance of a healthy microbiota, as it promotes only a fraction of gut microbes. Fibre originating from whole food diets includes complex aggregates of different types of carbohydrates still bound together in insoluble cell wall fragments. Different microbes are needed to break this material down and there are extensive cross-feeding interactions within the microbial community, thus whole food fibre is likely superior at maintaining a diverse and balanced microbiota. Our understanding of microbial colonisation, biofilm formation and metabolism of complex insoluble fibre in the gut is limited. A better understanding of microbial complex fibre metabolism will lead to improved nutritional advice to the public and aid the food industry in developing healthier products.

Specific aims and objectives: We hypothesize that fibre particles with more open structure and large surface areas result in better access for microbes that can degrade them and consequently more efficient fermentation and metabolite formation by the microbiota. We have materials available from a range of different plants that have been ground to flours using techniques that lead to different surface structures. We will employ synthetic microbial communities, drawn from our extensive strain collection of anaerobic gut bacteria, to assess microbial fermentation of complex insoluble plant fibre.

Objective 1: Compare the efficiency of microbial fermentation of fibres with different surface characteristics by determining overall microbial growth, metabolite formation and biofilm characteristics by a model microbial community representing dominant gut bacteria that occupy different ecological niches in fibre breakdown.

Objective 2: Identify microbes with keystone functions and competitive/cooperative microbial relationships by assessing fibre breakdown and metabolite production of alternative synthetic microbial communities where specific microbes are in- or excluded.

Research methodology and training opportunities: The student will receive training in a wide range of methods, encompassing strictly anaerobic microbial culture, molecular community analysis (mostly PCR-based), metabolite analysis by various analytical techniques and a range of microscopy techniques, including scanning electron microscopy, confocal microscopy to visualise fluorescently labelled microbes on fibre surfaces and, depending on progress, assessment of spatial distribution of surface-attached bacteria and associated small molecules using a high resolution mass spectrometer interfaced with atmospheric pressure matrix assisted laser desorption ionisation (AP-MALDI).

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Applicants to this project should hold a minimum of a 2:1 UK Honours degree (or international equivalent) in a relevant subject.

We encourage applications from all backgrounds and communities, and are committed to having a diverse, inclusive team.

Informal enquiries are encouraged, please contact Dr Petra Louis (p.louis@abdn.ac.uk) for further information.

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APPLICATION PROCEDURE:

Please note: This is a self-funded opportunity.

• Prospective students should contact the lead supervisor (via the email address listed above) to discuss the research project and complete a proposal form prior to / or shortly after applying.
• Formal applications can be completed online: https://www.abdn.ac.uk/pgap/login.php
• You should apply for Medical Sciences (MSc) to ensure your application is passed to the correct team.
• Please clearly note the name of the supervisor and the project title on the application form. If this is not included, your application may not be considered for the project.
• Candidates should have (or expect to achieve) a minimum of a 2:1 UK Honours degree (or international equivalent) at undergraduate level.
• Your application must include: a personal statement, an up-to-date copy of your academic CV, and clear copies of your educational certificates and transcripts.
• If you are still undertaking your undergraduate degree, it is helpful to the selection panel if you could provide documentation showing your grades to date (this can be a screenshot from an online portal).
• Please note: Project supervisors will not respond to requests for funding assistance.
• If you require any additional assistance in submitting your application or have any queries about the application process, please don't hesitate to contact us at pgrs-admissions@abdn.ac.uk