Integration of silicon chip microstructures in soft microfluidic device for in-line microbial cell lysis and characterization

Recent advances enable single-cell genomics in human tissues to identify constituent cell types and their functions. However, this technology has largely failed to translate to microbes that include fungi, bacteria, etc. and the microbiomes they constitute. There is no rapid, high-throughput technique that can be applied to multiple microbial species in an unbiased way. We aim to perform scRNA-seq of the microbiome to detect the constituent species, along with their genomic and biochemical activity. We developed a Silicon Chip-Integrated Soft Microfluidics (SCISM) platform to perform lysis of microbial cells rapidly and efficiently using micromechanical impact and demonstrated it on Saccharomyces cerevisiae and Candida albicans. As next step, we are integrating optical spectroscopy on the SCISM platform to characterize the cells and their lysates, to be compared with RNA-seq data.