Even isogenic bacteria may heterogeneously express different subsets of genes, assuming distinct roles for the survival of the community. There is limited knowledge about the diversity of phenotypic states within complex bacterial communities which are ill-suited for reporter-based approaches. Overcoming technical challenges associated with bringing the technology used for eukaryotic cells to prokaryotes, we developed a high-throughput single-cell RNA sequencing technology tailored specifically for bacteria. We validated the method for both gram-positive and gram-negative organisms and revealed a plethora of gene expression states in >25,000 Bacillus subtilis cells. We are continuing to adapt and apply emergent single-cell RNA sequencing technologies for single-cell gene expression studies of natural and engineered bacterial consortia.