High-quality Genome Sequences of Uncultured Microbes by Assembly of Read Clouds

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2018 Oct 16

PMID 30320765

Citations 52

Authors

Alex Bishara

Eli L Moss

Mikhail Kolmogorov

Alma E Parada

Ziming Weng

Arend Sidow

Anne E Dekas

Serafim Batzoglou

Ami S Bhatt

Affiliations

Soon will be listed here.

Abstract

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 (>200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20×) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which were complete (>90% complete, <5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.

Citing Articles

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Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.

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