High-quality genome sequences of uncultured microbes by assembly of read clouds

Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of the strain-level community structure, it remains difficult to obtain high-quality microbial genome drafts without isolation and culture. Here we present a novel application of read clouds, short read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We apply this approach to sequence stool samples from two healthy individuals, and compare it to existing short-read and synthetic long-read metagenomic sequencing techniques. Read cloud metagenomic sequencing and Athena assembly produce the most complete individual genome drafts with high contiguity (>200 kbp N50, <10 contigs), even for bacteria that have relatively low (20x) raw short-read sequence coverage. We also sequence a complex marine sediment sample and generate 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which are complete (>90% complete, <5% contaminated). Thus, our approach allows culture-free generation of high-quality microbial genome drafts using a single shotgun experiment.