Raman-activated cell sorting can identify living cells by their chemical fingerprints without fluorescent labels. Yet researchers have faced a trade-off: fast, flowing systems struggle to measure weak Raman signals, while systems that allow longer measurements sort cells slowly. Collecting the selected cells in a large volume can also make subsequent experiments difficult.

Researchers at the Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, together with Qingdao Single-Cell Biotech. Co., Ltd., Kweichow Moutai Co., Ltd., and other partners, developed an optical-tweezer-assisted platform called Pit-RACS to address both challenges.

Their study was published in Small Methods on Sep. 12.

Pit-RACS operates in two modes on the same microfluidic chip. For strong resonance Raman signals, cells are measured and sorted as they flow through the device. This mode sorted up to 836 ± 1 events per minute with a 10-millisecond spectral acquisition time. For weaker non-resonance signals, optical tweezers move individual cells into a cell-free buffer stream, allowing longer measurements without interference from nearby cells. That mode sorted approximately 50 cells per minute. Switching modes requires no hardware changes.

The chip also temporarily stores selected cells and releases them together in approximately 10 microliters of liquid. In the reported tests, the collected cells exceeded 97% purity and could proceed to cultivation or genomic analysis without an additional concentration step.

“Raman signals vary greatly between biological targets. We designed the two modes so researchers can choose the measurement time their question requires while using the same sorting platform,” said Prof. MA Bo from the Single-Cell Center at QIBEBT, a corresponding author of the study.

To demonstrate industrial strain screening, the team sorted a mutant library of Yarrowia lipolytica and identified a strain with 77.4% higher β-carotene yield than the control. In a second demonstration, they combined heavy-water labeling with Pit-RACS to enrich phosphate-solubilizing microorganisms from river water. The concentrated output was used directly for metagenomic sequencing, revealing 12 phosphate-solubilizing bacteria species across nine genera.

“The small collection volume helps connect a cell’s measured metabolic phenotype to what we can learn from its genome or cultivation,” said Prof. XU Jian, the head of Single-Cell Center and another corresponding author.

The researchers say the platform could support microbial strain development and the study of functional microorganisms in environmental samples.

This methodological advance will serve iMAPS (in-situ Metabolic Atlas Projects @ Single-cell, https://www.imaps.info/), an international consortium building a global network of Microbiome Metabolic Observatories to profile, mine and biobank microbes by their in-situ metabolic function at single-cell resolution.

Pit-RACS combines two Raman-activated cell sorting modes on one microfluidic chip