High throughput detection and sorting of substrate labelled microbial clusters

Phenotypic profiling of populations of single cells or cell clusters is a valuable tool in microbial ecology, bioengineering and biomedicine. A label free approach to phenotypic profiling is enabled by Raman spectroscopy. This allows studying cellular metabolism by tracking intake of stable isotopes of carbon, nitrogen or hydrogen. It has been applied to profile bacteria resistant to antimicrobials, survey yeast or algal phenotypic diversity.

This study presents a high-throughput platform for collecting Raman spectra in a viscoelastically focused stream of cells. The implementation of viscoelastic focusing requires only a single pump and offers a stable operation over several hours. This relatively simple and extendable setup offers a throughput of 80 detections/minute in cultures of the dinoflagellate alga Alexandrium ostenfeldii. The trigger design enables further implementation of cell sorting or other analysis and the relatively low-cost design lowers the technical barrier for adoption of Raman cytometry in diverse laboratory settings.