Single-cell methods are the state of the art in biological research. Zheng et al. developed a high-throughput technique called Microbe-seq designed to analyze single bacterial cells from a microbiota. Microbe-seq uses microfluidics to separate individual bacterial cells within droplets and then extract, amplify, and barcode their DNA, which is then subject to pooled Illumina sequencing. The technique was tested by sequencing multiple human fecal samples to generate barcoded reads for thousands of single amplified genomes (SAGs) per sample. Pooling the SAGs corresponding to the same bacterial species allowed consensus assemblies of these genomes to provide insights into strain-level diversity and revealed a phage association and the limits on horizontal gene-transfer events between strains.