Abstract
<h3>Abstract</h3> Bacterial populations are highly adaptive, enabling them to respond to and surviving in shifting environments or stresses. Yet, how these single-cell organisms vary and organize their behavior to tolerate stressors is poorly understood. This is because many bacterial subpopulations are rare and cannot be readily discovered by existing single-cell sequencing methods due to limitations in cell number and sequencing depth. Here we develop Massively-parallel Microbial mRNA sequencing (M3-Seq), which addresses these challenges by using combinatorially-indexed cells to overload droplets in combination with RNA amplification and post-hoc rRNA depletion. In a single M3-Seq experiment, we profile hundreds of thousands of bacterial cells from multiple species under a wide range of conditions. In addition to validating our approach and findings, we exploit the scale of M3-Seq to make several unexpected discoveries, including new insights into bet hedging strategies in stress responses, bacterial responses to antibiotics, and host responses to phage infection.
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