Article

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

Department of Microbiology, University of Washington, Benjamin Hall IRB, 616 NE Northlake Place, Seattle, Washington 98105, USA.
Nature Biotechnology (Impact Factor: 39.08). 09/2008; 26(9):1029-34. DOI: 10.1038/nbt.1488
Source: PubMed

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.

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    • "Analysis based on 16S rRNA gene sequences is informative regarding the composition and diversity of a microbial community; however, its ability to elucidate the functional gene content and metabolic pathways is limited (Kalyuzhnaya et al., 2008). Metagenomics can provide detailed information on global metabolic functions; however, it typically achieves limited depth of coverage for any one pathway or gene family of interest, and as a result has low ability to detect small polymorphisms or rare genes (Kalyuzhnaya et al., 2008). Neither of these approaches has thus yet provided detailed information on the GH profile of the human gut. "
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    • "The rapid development of DNA sequencing technologies has also facilitated SIP study combined with metagenome sequencing for the full characterization of microorganisms in their metagenomic contexts. In particular , the almost complete genome of the methylotroph Methylotenera mobilis was obtained from DNA labelled with 13 C1 compounds using an SIP method combined with metagenome sequencing (Kalyuzhnaya et al., 2008). The MT Hebei Spirit oil spill (ca. 10 900 tons of crude oil) occurred near the coast of Taean in the Yellow Sea in December 2007, and most of the western side of the Korean Peninsula with tidal flats was heavily contaminated by the oil spill. "
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    • "As expected from prior analyses (Kalyuzhnaya et al., 2008), the community in the unamended sample revealed high complexity, being represented by a total of 1,486 sequence clusters (97% sequence identity; Kunin & Hugenholtz, 2010). The community was dominated by Proteobacteria (33.3%), of which phylotypes of the Methylococcaceae family that represents one class (called type I) of methane oxidizing bacteria were most prominently present (10% of all sequences). "
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