Unravelling bacterial complexity at high resolution with single-cell transcriptomics

Phenotypic heterogeneity, a feature of both bacteria and eukaryotic cells, arises from inherent cell-to-cell variability. In eukaryotes, single-cell RNA sequencing has led to an explosion in understanding how heterogeneity impacts different cell types and states in organs and tissues. While single-cell RNA sequencing analyses in bacteria have lagged behind eukaryotic studies, recent technological advances now enable similar, high-resolution studies to be performed at scale in bacteria, yielding fundamental insights into how heterogeneity influences bacterial physiology, metabolism, antibiotic resistance, pathogenesis and interactions within complex microbial communities. Here we review recent advances in bacterial single-cell RNA sequencing, including the methods developed so far and what has been learned from their application. We also discuss technological and computational challenges going forwards, the need for standardization and how that could be achieved, and how this emerging field is now poised to revolutionize our understanding of bacterial physiology, infection biology and interactions within bacterial communities, such as the microbiota.