title: High-resolution metagenomics targets specific functional types in complex microbial communities.
abstract: Most microbes in the biosphere remain unculturable. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) can be used to study the genetic and metabolic properties of natural microbial communities. 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 (C1) compounds shows specific sequence enrichments in response to different C1 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.
authors: Department of Microbiology, University of Washington, Benjamin Hall IRB, 616 NE Northlake Place, Seattle, Washington 98105, USA.
authors: Marina G
authors: MG
authors: Kalyuzhnaya
authors: Alla
authors: A
authors: Lapidus
authors: Natalia
authors: N
authors: Ivanova
authors: Alex C
authors: AC
authors: Copeland
authors: Alice C
authors: AC
authors: McHardy
authors: Ernest
authors: E
authors: Szeto
authors: Asaf
authors: A
authors: Salamov
authors: Igor V
authors: IV
authors: Grigoriev
authors: Dominic
authors: D
authors: Suciu
authors: Samuel R
authors: SR
authors: Levine
authors: Victor M
authors: VM
authors: Markowitz
authors: Isidore
authors: I
authors: Rigoutsos
authors: Susannah G
authors: SG
authors: Tringe
authors: David C
authors: DC
authors: Bruce
authors: Paul M
authors: PM
authors: Richardson
authors: Mary E
authors: ME
authors: Lidstrom
authors: Ludmila
authors: L
authors: Chistoserdova
mesh_terms: D001419:Bacteria / Q000145:classification / Q000166:cytology* / Q000235:genetics / Q000302:isolation & purification; D001709:Biotechnology / Q000379:methods / Q000639:trends; D042521:Burkholderiaceae / Q000235:genetics; D042621:Comamonadaceae / Q000235:genetics; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D019015:Geologic Sediments / Q000382:microbiology; D008772:Methylococcaceae / Q000235:genetics; D042762:Methylophilaceae / Q000235:genetics; D008829:Microbiology; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D010100:Oxygen / Q000737:chemistry; D043362:Rhodocyclaceae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012988:Soil Microbiology
chemical_list: D010100:Oxygen