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Multiple displacement amplification compromises quantitative analysis of metagenomes

Nature Methods volume 7, pages 943–944 (2010)Cite this article

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Nucleic acid concentration is often a limiting factor for 'omic' characterization of low-biomass habitats or small-sized samples. Multiple displacement amplification (MDA) with phi29 DNA polymerase is increasingly being used to overcome this hurdle1,2,3. Despite its enormous potential, MDA has several recognized limitations, including amplification bias that may compromise subsequent quantitative analysis3. MDA of picogram quantities of genomic DNA introduced pronounced skewing of most members of an eight-species synthetic microbial community based on small-subunit ribosomal RNA gene profiling4. We found that MDA also introduced a bias in natural and more complex communities.

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Figure 1: Correlations between OTU skewing and estimated genomic G+C content for the three environmental samples and three MDA protocols tested.

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Acknowledgements

We thank R. Scheffrahn and D. Jacobson for providing samples of worker termites and garden compost, respectively. This work was supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy.

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Author notes

  1. Suzan Yilmaz and Martin Allgaier: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Energy Joint Genome Institute, Microbial Ecology Program, Walnut Creek, California, USA

    Suzan Yilmaz, Martin Allgaier & Philip Hugenholtz

  2. Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, USA

    Martin Allgaier & Philip Hugenholtz

  3. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia

    Philip Hugenholtz

Authors
  1. Suzan Yilmaz
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  2. Martin Allgaier
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  3. Philip Hugenholtz
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Corresponding author

Correspondence to Philip Hugenholtz.

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The authors declare no competing financial interests.

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Supplementary Figures 1–2, Supplementary Tables 1–4, Supplementary Methods (PDF 1034 kb)

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Yilmaz, S., Allgaier, M. & Hugenholtz, P. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 7, 943–944 (2010). https://doi.org/10.1038/nmeth1210-943

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