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Understanding and dissecting microbial communities with Raman spectroscopy

   Institute of Integrative Biology

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  Prof R Goodacre  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

We have shown that it is possible to label bacteria with heavy isotopes of carbon (13C) and nitrogen (15N) and this incorporation within cellular biomass of heavy isotopes has led to significant shifts in certain vibrational modes from amino acids and nucleic acids that can be readily detected with Raman spectroscopy. This approach potentially allows the metabolic and biological functions of specific bacteria in mixed communities to be investigated.

This project will explore the use of new high throughput and high-resolution methods based on stimulated Raman spectroscopy and nanoscale infrared microscopy to identify bacteria at the single cell level as well as to assign function to these microorganisms. A specific focus will be in bioremediation where screening environmental isolates for desirable traits (e.g., contaminant cleanup) may then allow isolation of novel enzymes for decontamination, sensing and for enhanced production.

Roy Goodacre –

The student will receive broad training in bioanalysis within the post-genomics sciences / systems biology interface. Specific training will be given in Raman and infrared spectroscopies as well as multivariate data analysis and metabolomics.

The student will join a dynamic research group based in the IIB where the focus is to investigate cellular metabolism. Details of the current projects and diversity of work, as well as more general papers, can be found here:

Funding Notes

Open to both UK/International students with their own funding/scholarship.

Assistance will be given to those who are applying to international funding schemes. The successful applicant will be expected to provide the funding for tuition fees and living expenses as well as research costs of £3000 per year.

Details of costs can be found on the University website:


Chisanga, M., Muhamadali, H., Kimber R. & Goodacre, R. (2017) Quantitative detection of isotopically enriched E. coli cells by SERS. Faraday Discussion 205, 331-343.

Wang, Y., Song, Y., Tao, Y., Muhamadali, H., Goodacre, R., Zhou, N-Y., Gail, P., Xu, J. & Huang, W. (2016) Reverse and multiple stable isotope probing to study bacterial metabolism and interactions at the single cell level. Analytical Chemistry 88, 9443-9450.

Muhamadali, H., Chisanga, M., Subaihi, A. & Goodacre, R. (2015) Combining Raman and FT-IR spectroscopy with quantitative isotopic labelling for differentiation of E. coli cells at community and single cell levels. Analytical Chemistry 87, 4578-4586.
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