Highly Multiplexed Spatial Transcriptomics in Bacteria

Many bacteria inhabit complex, spatially structured environments and exhibit behaviors not well captured by population averages. Image-based single-cell transcriptomic methods, which profile the transcriptome of cells in their local environments, offer a promising avenue for bacterial study. However, the extreme density of bacterial RNAs has challenged such methods. Sarfatis et al. solved this challenge by developing a method called bacterial-MERFISH, which combines up to 1000-fold volumetric expansion with image-based transcriptomics. With the ability to profile the transcriptome of single cells within complex native environments, this method promises an exciting new window into a range of bacterial phenomena.