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  MSc By Research: Matching genotype and phenotype: Comparing genome sequences of multiple gut anaerobic bacteria to identify key substrate degrading enzymes


   School of Medicine, Medical Sciences & Nutrition

  , , Dr Louie Van de Lagemaat  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

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.

The past two decades have shown huge advances in our understanding of how diet affects the composition of the gut microbiota, and how this in turn impacts the occurrence of many different diseases. Every individual has a different ‘microbial fingerprint’ and both the composition and functionality of this microbiota dictate how they degrade dietary components producing the bacterial metabolites that we now know are crucial to maintain health. Many studies have shown which specific bacteria seem to be important in different mammalian species, there is much less known about why they are important. Within the Rowett Gut Microbiology Group we have assembled a large culture collection of obligately anaerobic bacteria from a range of mammalian hosts, many of which have now been fully genome sequenced.

In this project the genome sequences of a diverse set of up to 20 bacteria, isolated from different hosts (deer, sheep, cattle, geese, panda, human), will be analysed in silico to identify different genes that uniquely adapt the bacterium to the environment from which it was isolated. A strong focus will be on carbohydrate active enzymes, to make the link between diet and the microbiome. The occurrence of specific genes will be followed up by phenotypic growth tests to establish whether the bacteria can indeed utilise the expected substrates, and identify key metabolites produced. The substrate specificity of selected enzymes may be further investigated through gene cloning and expression assays.

Mining the gut microbiome to identify novel carbohydrate active enzymes that could potentially be applied in genetic engineering for biotechnological purposes, including bioremediation and to improve the digestibility of current ‘waste-stream by-products’ has potential value for society and industry going forward.

The project has two key aims:

  1. Perform extensive bioinformatic analysis on bacterial whole genome sequence data to identify genes involved in carbohydrate degradation.
  2. Investigate the functionality of these genes in bacterial growth experiments.

And a third additional aim:

Assess the expression of targeted genes following cloning into an expression vector.

Skills developed

The project will give the student experience in both dry-lab and wet-lab techniques. Training will be provided in Bioinformatic analysis, including script writing (Python, shell and/or R/Rstudio), bacterial whole genome sequence data analysis, gene function annotation using online databases (COG, KEGG) and investigating genomes for carbohydrate utilisation (CAZymes), antimicrobial resistance (CARD), virulence factors (VFDB) etc, and in managing large datasets.

Lab-based training will also be provided in anaerobic microbiology methodology (aseptic technique, bacterial culturing, bacterial metabolite (volatile fatty acid) analysis) and molecular biology techniques (PCR amplification, cloning and gene expression).

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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 Professor Karen Scott () 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 
Biological Sciences (4) Medicine (26)

Funding Notes

This is a self-funding project open to students worldwide. Our typical start dates for this programme are February or October.
Fees for this programme are £4,712 for home/UK students, and £24,860 for international students.
Additional research costs / Bench fees of £3,000 will also apply.
The Scottish Government offers postgraduate loans to those due to start a Masters (taught or research) programme.

References

1) S.H. Duncan et al. (2023) Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health. Biomedicines Vol.11(5), p.1338. https://doi.org/10.3390/biomedicines11051338
2) I. Mukhopadhya et al. (2022) Remarkable conservation of microbial signatures between paired faecal and rectal biopsy samples from healthy volunteers revealed using next generation sequencing and culturomics. Microbiome. doi.org/10.1186/s40168-022-01354-4
3) K.P. Scott et al (2011) Substrate-driven gene expression in Roseburia inulinivorans: Importance of inducible enzymes in the utilization of inulin and starch. Proceedings of the National Academy of Sciences USA 108, 4672-4679.

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