Selective isolation of bacterial cells within a microfluidic device using magnetic probe-based cell fishing

This paper demonstrates the selective isolation of bacterial cells from a mixture by combining magnetic probe-based cell fishing with the use of microfluidics. A microfluidic cell sorter was obtained by integrating permanent micromagnets in a PDMS microchannel. While non-target cells pass through the device, the magnetically labeled target cells can be efficiently captured thanks to the high magnetic field gradients generated by the micro-flux sources. The sorting device capabilities were evaluated by performing enrichment of Escherichia coli DH10β from a bacterial cell mixture containing an initial concentration of 0.04% E. coli DH10β and 99.96% Acinetobacter sp. ADP1. The probes used to specifically target E. coli cells were RNA transcripts from PCR amplicons of 23S rRNA genes from E. coli DH10β DNA. Those probes were biotinylated to enable magnetic labeling with 50 nm streptavidin-coated superparamagnetic particles after in situ hybridization. qPCR analysis of the sorted fractions revealed that the target cells were enriched from an initial concentration of 0.04% to a final concentration of 98.46%, with a 50% recovery rate, at a throughput of 109 cells per hour. This approach offers great potential to address issues linked to exploration of bacterial diversity in complex ecosystems, where labeling strategies applicable to unculturable bacteria are required.