High-resolution metagenomics targets specific functional types in complex microbial communities

被引：191

作者：

Kalyuzhnaya, Marina G. ^{[2
]}

Lapidus, Alla ^{[3
]}

Ivanova, Natalia ^{[3
]}

Copeland, Alex C. ^{[3
]}

McHardy, Alice C. ^{[4
]}

Szeto, Ernest ^{[5
]}

Salamov, Asaf ^{[3
]}

Grigoriev, Igor V. ^{[3
]}

Suciu, Dominic ^{[6
]}

Levine, Samuel R. ^{[1
]}

Markowitz, Victor M. ^{[5
]}

Rigoutsos, Isidore ^{[4
]}

Tringe, Susannah G. ^{[3
]}

Bruce, David C. ^{[7
]}

Richardson, Paul M. ^{[3
]}

Lidstrom, Mary E. ^{[1
,2
]}

Chistoserdova, Ludmila ^{[1
]}

机构：

[1] Univ Washington, Dept Chem Engn, Seattle, WA 98105 USA

[2] Univ Washington, Dept Microbiol, Seattle, WA 98105 USA

[3] DOE Joint Genome Inst, Prod Genom Facil, Walnut Creek, CA 94596 USA

[4] IBM Thomas J Watson Res Ctr, Bioinformat & Pattern Discovery Grp, Yorktown Hts, NY 10598 USA

[5] Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA

[6] Combimatrix Corp, Mukilteo, WA 98275 USA

[7] DOE Joint Genome Inst, Los Alamos Natl Lab, Los Alamos, NM 87545 USA

来源：

NATURE BIOTECHNOLOGY | 2008年 / 26卷 / 09期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1038/nbt.1488

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Most microbes in the biosphere remain unculturable(1). Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) can be used to study the genetic and metabolic properties of natural microbial communities(2-4). However, in communities of high complexity, metagenomics fails to link specific microbes to specific ecological functions. To overcome this limitation, we developed a method to target microbial subpopulations by labeling DNA through stable isotope probing ( SIP), followed by WGS sequencing. Metagenome analysis of microbes from Lake Washington in Seattle that oxidize single-carbon (C-1) compounds shows specific sequence enrichments in response to different C-1 substrates, revealing the ecological roles of individual phylotypes. We also demonstrate the utility of our approach by extracting a nearly complete genome of a novel methylotroph, Methylotenera mobilis, reconstructing its metabolism and conducting genome-wide analyses. This high-resolution, targeted metagenomics approach may be applicable to a wide variety of ecosystems.

引用

页码：1029 / 1034

页数：6

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