Raman-activated microbial cell sorting (RACS)

Single-cell studies have the potential to transform environmental as well as human microbiome research. However, progress is currently limited by the difficulty of sorting cells according to function and thus most studies are performed on randomly selected cells. Recently, we have developed a fully automated optofluidic platform for high-throughput Raman-activated cell sorting (RACS) of unfixed microbial cells that are active under environmental conditions of interest. Our platform combines confocal Raman microspectroscopy, optical tweezers, microfluidics, and heavy-water (D₂O) based activity labeling of microbes. A commercial Raman microspectroscope is customized for simultaneous Raman measurements and microscopic image acquisition. In a microfluidic device, individual cells are captured by optical tweezers, their Raman spectrum is measured to assess their labeling status, and they are then automatically released to either collection or waste outlets. The entire process is controlled by a graphical interface. The RACS platform achieves a throughput of >200 cells per hour with very high sorting accuracy (>98%), opening the door to high-throughput functional and genomic studies of bacteria with specific traits of interest. For more information, please contact Kang Soo Lee (leeka@ethz.ch), Jen Nguyen (nguyenje@ethz.ch) or Vicente Fernandez (fernandez@ifu.baug.ethz.ch).