Format

Send to

Choose Destination
See comment in PubMed Commons below
Nat Biotechnol. 2013 Jun;31(6):533-8. doi: 10.1038/nbt.2579. Epub 2013 May 26.

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.

Author information

1
Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark.

Abstract

Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition-independent approach to recover high-quality microbial genomes from deeply sequenced metagenomes. Multiple metagenomes of the same community, which differ in relative population abundances, were used to assemble 31 bacterial genomes, including rare (<1% relative abundance) species, from an activated sludge bioreactor. Twelve genomes were assembled into complete or near-complete chromosomes. Four belong to the candidate bacterial phylum TM7 and represent the most complete genomes for this phylum to date (relative abundances, 0.06-1.58%). Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than other currently used methods, which are primarily based on sequence composition. This approach will be an important addition to the standard metagenome toolbox and greatly improve access to genomes of uncultured microorganisms.

PMID:
23707974
DOI:
10.1038/nbt.2579
[Indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Nature Publishing Group
    Loading ...
    Support Center