Microbial single-cell RNA sequencing by split-pool barcoding
Anna Kuchina, Leandra Brettner, Luana Paleologu, Charles M. Roco, Alexander Rosenberg, Alberto Carignano, Ryan D. Kibler, Matthew Hirano, R. William DePaolo, Georg Seelig
Abstract
Bacterial cell gene expression Single-cell genomics in bacteria has lagged relative to in eukaryotes because of their tough bacterial cell walls, low messenger RNA content, and lack of many posttranscriptional modifications. To tackle this challenge, Kuchina et al. developed microbial split-pool ligation transcriptomics, or microSPLiT, a single-cell sequencing method for both Gram-negative and Gram-positive bacteria. Sequencing both Escherichia coli and Bacillus subtilis showed differences in the heat shock response. Examining B. subtilis transcriptional patterns revealed that a small fraction of cells grown in laboratory medium express a myo-inositol catabolism pathway, which the cell could use in nonlaboratory environments, thus highlighting how microSPLiT can identify rare cellular states. Science , this issue p. eaba5257