Metabolism in Action: Developing stable isotope probing using Raman and infrared imaging for understanding metabolic flux at the single cell level

Posted on: 14 April 2021 by Prof Roy Goodacre in Case studies

D20 labelling

Complex microbial communities are found throughout ecosystems on the planet and these play essential functions that support animal and aquatic life.

Despite the vital role that bacteria play, linking these microbes with specific metabolic functions is difficult, since microbial communities consist of numerous and phylogenetically diverse microbes.  This is compounded by the microscopic size of these microorganism (1-2 µm).

There is therefore a need to develop metabolomics solutions that generate images that are based on the biochemistry of the sample under analysis, and that provide information at micron and sub-micrometre scales.  With the advent of spontaneous Raman and variants that can be tuned to specific vibrations (viz SRS and CARS), these, along with optical-photothermal infrared (O-PTIR) microscopy open up the tantalising opportunity to follow metabolism in microbial communities.



In a recent series of papers published in Analytical Chemistry and Analyst we have shown that the cellular uptake of stable isotope-labelled compounds by bacteria can be probed at the single-cell level using both Raman and infrared spectroscopies.  This is due to the ability of these imaging techniques to monitor chemical vibrations that are affected by the incorporation of “heavy” atoms by cells and thus can be used to understand microbial systems.  In this series of experiments, we have shown that it is possible to measure incorporation of 13C and 15N substrates, follow the dynamics of the rate of incorporation, as well as employing deuterated water to assess cross feeding in microbial communities.

This research has opened up the exciting prospect that these enabling chemical imaging technologies will guide the identification of primary substrate consumers in complex microbial communities in situ.  This we believe represents a key step towards the characterisation of novel genes, enzymes and metabolic flux analysis in microbial consortia.

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