New Paper in PNAS reports on superfast single cell functional analyses of microbiome members

Stimulated Raman Spectroscopy instrument

In close collaboration with the Cheng group in Boston, members of our Division of Microbial Ecology (DOME) developed a high-throughput technique to simultaneously determine the identity and metabolic activity of individual bacterial cells in milliseconds. To this end, they combined two-photon fluorescence with Stimulated Raman Spectroscopy (SRS) for coupling FISH with single cell isotope probing. In their study, recently published in PNAS, they successfully applied their imaging-based approach termed stimulated Raman scattering–two-photon fluorescence in situ hybridization (SRS-FISH) to investigate mucosal sugar degradation by human gut microbiome members. Thereby, the researchers unexpectedly revealed that Clostridia can outperform Bacteroidales at foraging fucose.

With this new technique imaging and quantification of isotope incorporation of FISH-identified cells in complex samples is 2-3 orders of magnitude faster than with other state of the art methods. Excitingly, the unique instrument used for these experiments is currently assembled at DOME. The large-scale device, which is unique in Europe in its optimised configuration for microbiome research, will be available for research projects by interested researchers as of autumn 2022.