Raman-based sorting of microbial cells to link functions to their genes

Abstract

In our recent work, we developed an optofluidic plat-form that allows a direct link to be made between the phenotypes (functions) and the genotypes (genes) of microbial cells within natural communities. By combin-ing stable isotope probing, optical tweezers, Raman microspectroscopy, and microfluidics, the platform performs automated Raman-based sorting of taxa from within a complex community in terms of their functional properties. In comparison with manual sort-ing approaches, our method provides high throughput (up to 500 cells per hour) and very high sorting accura-cy (98.3 ± 1.7%), and significantly reduces the human labour required. The system provides an efficient manner to untangle the contributions of individual members within environmental and host-associated microbiomes. In this News and Thoughts, we provide an overview of our platform, describe potential appli-cations, suggest ways in which the system could be improved, and discuss future directions in which Ra-man-based analysis of microbial populations might be developed.