Lan, F. et al. Nat. Biotechnol. http://dx.doi.org/10.1038/nbt.3880 (2017).

The power of metagenomics is that it can identify microbes on the basis of pooled sequences recovered from any sample. But it is difficult to assign every sequence fragment to the organism it came from, which limits taxonomic accuracy and the amount of functional information that can be gleaned. Lan et al. use the latest mantra of high-throughput genomics—compartmentalize, barcode, pool and sequence—to perform single-cell genomic sequencing (SiC-seq) on microbial communities. SiC-seq is a microfluidic approach that traps single cells in oligo-barcoded agarose microspheres and carries out enzymatic lysis and pooled library prep on over 50,000 cells in a single run. Because many sequence reads are linked to each genome, the researchers were able to classify microbes and identify patterns of antibiotic resistance, virulence factors and viral transduction potential in tens of thousands of microbes from San Francisco seawater.