Revealing within-species diversity in uncultivated human gut bacteria with single-cell long-read sequencing

Bacteria change the structure of their genome dynamically, and the structural variants sometimes change the bacterial phenotype, but acquiring the complete genome of uncultured bacteria has been difficult so far. Here we present a workflow to construct the circular single-amplified genomes (cSAG) from long-read single-cell sequencing of targeted uncultured bacteria. Our workflow, scALA, generates cSAGs from nanopore long-read sequencing of the single-cell amplified genome by producing contiguous sequences with repeated bias reduction and assembly processing. The method developed here would further expand the bacterial genome database with the cSAGs and our understanding of the within-species diversities in uncultured bacteria.