부산대학교 도서관

Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an 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 applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity ( [greater than] 200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20x) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts ( [greater than] 70% complete, [less than] 10% contaminated), nine of which were complete ( [greater than] 90% complete, [less than] 5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.
Author(s): Alex Bishara [1, 2]; Eli L Moss [2]; Mikhail Kolmogorov [3]; Alma E Parada [4]; Ziming Weng [5]; Arend Sidow [2, 5]; Anne E Dekas [4]; Serafim Batzoglou (corresponding [...]