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

Nature Biotechnology volume 26, pages 1029–1034 (2008)Cite this article

Abstract

Most microbes in the biosphere remain unculturable1. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) can be used to study the genetic and metabolic properties of natural microbial communities2,3,4. 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 (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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Figure 1: Taxonomic distribution of 16S rRNA gene sequences from metagenomes.
Figure 2: Metabolic features of M. mobilis (left) compared to metabolic features of M. flagellatus (right) as deduced from genomic comparisons.
Figure 3: Comparison of gene clusters involved in methylotrophy in M. mobilis and M. flagellatus.

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Acknowledgements

This research was supported by the National Science Foundation as part of the Microbial Observatories program (MCB-0604269). This work was performed, in part, under the auspices of the US Department of Energy's Office of Science Biological and Environmental Research Program, and by the University of California, Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract no. DE-AC02-05CH11231 and Los Alamos National Laboratory under contract no. DE-AC02-06NA25396. The sequencing for the project was provided through the US Department of Energy Community Sequencing Program (http://www.jgi.doe.gov/CSP/index.html).

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Author notes

  1. Alice C McHardy

    Present address: Present address: Computational Genomics and Epidemiology Group, Max Planck Institute for Computer Science, Campus E1 4, 66123 Saarbruecken, Germany.,

Authors and Affiliations

  1. Department of Microbiology, University of Washington, Benjamin Hall IRB, 616 NE Northlake Place, Seattle, 98105, Washington, USA

    Marina G Kalyuzhnaya & Mary E Lidstrom

  2. Department of Chemical Engineering, University of Washington, Benjamin Hall IRB, 616 NE Northlake Place, Seattle, 98105, Washington, USA

    Samuel R Levine, Mary E Lidstrom & Ludmila Chistoserdova

  3. Production Genomics Facility, DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg. 400, Walnut Creek, 94596, California, USA

    Alla Lapidus, Natalia Ivanova, Alex C Copeland, Asaf Salamov, Igor V Grigoriev, Susannah G Tringe & Paul M Richardson

  4. Bioinformatics and Pattern Discovery Group, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, 10598, New York, USA

    Alice C McHardy & Isidore Rigoutsos

  5. Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 50A-1148, Berkeley, 94720, California, USA

    Ernest Szeto & Victor M Markowitz

  6. Combimatrix Corporation, 6500 Harbour Heights Pkwy., Mukilteo, 98275, Washington, USA

    Dominic Suciu

  7. DOE Joint Genome Institute, Los Alamos National Laboratory, PO Box 1663, Los Alamos, 87545, New Mexico, USA

    David C Bruce

Authors
  1. Marina G Kalyuzhnaya
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Contributions

M.G.K., M.E.L. and L.C. conceived the project. M.E.L. and L.C. coordinated project execution. M.G.K. collected samples, performed SIP, purified DNA for sequencing and performed microarray hybridizations. D.C.B. and P.M.R. oversaw library construction and sequencing. S.G.T. oversaw sequence assembly and analysis. A.C.C. and A.L. carried out assemblies. A.S. and I.V.G. conducted gene prediction and annotation. A.C.M. and I.R. carried out binning. E.S. and V.M.M. carried out data processing and loading into IMG/M. L.C. and N.I. carried out metabolic reconstruction. S.R.L. and M.G.K. performed species richness estimates. D.S. carried our microarray design. M.G.K., M.E.L. and L.C. wrote the initial draft of the paper; all other authors contributed.

Corresponding author

Correspondence to Ludmila Chistoserdova.

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Figures 1–7, Tables 1–11, Methods (PDF 2145 kb)

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Kalyuzhnaya, M., Lapidus, A., Ivanova, N. et al. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol 26, 1029–1034 (2008). https://doi.org/10.1038/nbt.1488

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