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

Albertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W. and Nielsen, Per H. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31 6: 533-538+. doi:10.1038/nbt.2579


Author Albertsen, Mads
Hugenholtz, Philip
Skarshewski, Adam
Nielsen, Kare L.
Tyson, Gene W.
Nielsen, Per H.
Title Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
Journal name Nature Biotechnology   Check publisher's open access policy
ISSN 1087-0156
1546-1696
Publication date 2013-06-01
Year available 2013
Sub-type Article (original research)
DOI 10.1038/nbt.2579
Open Access Status
Volume 31
Issue 6
Start page 533
End page 538+
Total pages 9
Place of publication New York, NY United States
Publisher Nature Publishing Group
Language eng
Subject 2402 Applied Microbiology and Biotechnology
1305 Biotechnology
1313 Molecular Medicine
1502 Bioengineering
2204 Biomedical Engineering
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.
Keyword Biological Phosphorus Removal
Gram positive bacteria
Microbial Communities
Archaea
Cells
Amplification
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID DP120103498
DP1093175
Institutional Status UQ

 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 365 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 399 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Sun, 21 Jul 2013, 10:04:37 EST by System User on behalf of School of Chemistry & Molecular Biosciences