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Metabolic profiling and automated dereplication of microbial extracts from underexplored habitats

This project is no longer listed on and may not be available.

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  • Full or part time
    Dr R Ebel
    Prof M Jaspars
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

One of the key challenges in natural product chemistry when screening for new natural products with interesting biological activity is the increasing tendency to encounter known compounds already described by other research groups in the literature. To avoid the costly re-isolation of such known compounds, and to rather focus ones attention on microbial strains with a high chance to yield new compounds, various dereplication protocols have been developed by the research community, with the aim to detect and identify known compounds as early as possible, preferably already at the level of the crude extracts.

This PhD project aims at improving existing dereplication strategies based on high resolution ESI-LC/MS by identifying suitable experimental parameters for peak detection, alignment, deisotopisation, calculation of candidate molecular formulae, and database querying in an automated fashion. Secondary metabolites identified as potentially new through this protocol will be isolated, and their structures will be established through state-of-the-art spectroscopic techniques.

1) Extracts of selected microorganisms (fungi and actinobacteria) will be analysed in parallel on two different ESI-LC/MS systems, i.e. ion trap (Thermo Finnigan LCQ deca) and QTOF (Bruker maXis II)
2) Optimum parameters and settings for both systems will be identified, making use of a scripting platform that processes entire chromatograms, and which has been developed within the framework of the FP7 research consortium “PharmaSea”
3) Candidate molecular formulae for individual peaks thus obtained will be queried in an automated fashion against a commercial database
4) Various validation approaches will be followed, for example by spiking the microbial extracts with known natural products at various concentrations
5) New natural products with biological activity will be isolated and their structures will be established by modern spectroscopic techniques including one- and two-dimensional NMR pulse sequences and mass spectrometry

This PhD research project will be tightly embedded into the natural product discovery programme at the Marine Biodiscovery Centre (MBC) in Aberdeen. Through “PharmaSea” and its follow-up consortium (ITN “MarPipe”), we will provide chemically prolific microbial strains which have been shown to possess promising anti-infective or anti-inflammatory properties.

These microbial extracts analysed using two ESI-LC/MS systems, i.e. an ion trap and a QTOF, and thus are expected to provide complimentary information, and processed by software tools currently under development for automated dereplication and database querying. Existing LC-MS-based dereplication protocols will be refined in close correlation with a specialised developer of dereplication software and established academics. The feasibility of this approach will be demonstrated by a directed isolation, followed by full structural characterisation of new natural products with promising biological activity.

The successful candidate will have or expect to have a UK Honours Degree at 2.1 (or equivalent) in Chemistry.

Strong background in organic chemistry, in particular natural product chemistry
Desired skills: strong background in mass spectrometry including LC-MS, natural product isolation techniques, basic microbiological techniques including fermentation, 1D and 2D NMR techniques

This project is advertised in relation to the research areas of the discipline of Chemistry. Formal applications can be completed online: You should apply for Degree of Doctor of Philosophy in Chemistry, to ensure that your application is passed to the correct person for processing. NOTE CLEARLY THE NAME OF THE SUPERVISOR and EXACT PROJECT TITLE ON THE APPLICATION FORM.

Informal inquiries can be made to Dr R Ebel ([Email Address Removed]) with a copy of your curriculum vitae and cover letter indicating your interest in the project and why you wish to undertake it. All general enquiries should be directed to the Postgraduate Research School )[Email Address Removed]).

Funding Notes

There is no funding attached to this project, it is for self-funded students only.


Chervin, J.; Stierhof, M.; Tong, M. H.; Peace, D.; Hansen, K. O.; Urgast, D. S.; Andersen, J. H.; Yu, Y.; Ebel, R.; Kyeremeh, K.; Paget, V.; Cimpan, G.; Van Wyk, A.; Deng, H.; Jaspars, M.; Tabudravu, J. N. “Targeted dereplication of microbial natural products by high-resolution MS and predicted LC retention time”, J. Nat. Prod. 2017, 5, 1370-1377.

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