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Functional metagenomic profiling of nine biomes

Nature volume 452, pages 629–632 (2008)Cite this article

A Corrigendum to this article was published on 09 October 2008

Abstract

Microbial activities shape the biogeochemistry of the planet1,2 and macroorganism health3. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.

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Figure 1: Functional analysis of microbial and viral metagenomes.
Figure 2: A one-dimensional representation of the environmental metabolic profiles for the microbial and viral metagenomes sampled from the nine environments.
Figure 3: A comparison of the distribution of sequences similar to motility and chemotaxis genes identified within the microbiomes ( n = 43) and viromes ( n = 41).

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Data deposits

The metagenomes used in this paper are freely available from the SEED platform and are being made accessible from CAMERA and the NCBI Short Read Archive. The accession numbers are shown in Supplementary Table 1. The NCBI genome project IDs used in this study are: 28619, 28613, 28611, 28609, 28607, 28605, 28603, 28601, 28599, 28597, 28469, 28467, 28465, 28463, 28461, 28459, 28457, 28455, 28453, 28451, 28449, 28447, 28445, 28443, 28441, 28439, 28437, 28435, 28433, 28431, 28429, 28427, 28425, 28423, 28421, 28419, 28417, 28415, 28413, 28411, 28409, 28407, 28405, 28403, 28401, 28395, 28393, 28391, 28389, 28387, 28385, 28383, 28381, 28379, 28377, 28375, 28373, 28371, 28361, 28359, 28357, 28355, 28353 and 28351.

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Acknowledgements

This project was supported by the Gordon and Betty Moore Foundation Marine Microbial Initiative, National Science Foundation grants (F.R. and D.L.V.), a Department of Commerce ATP grant (F.R.), a National Research Initiative Competitive Grant from the USDA Cooperative State Research, Education and Extension Service (B.W.), the National Institute of Allergy and Infectious Diseases, the National Institutes of Health and the Department of Health and Human Services (R.S.).

Author Contributions E.A.D. conceptualized the project, conducted the CDA and wrote the manuscript. R.A.E., R.O. and R.S. performed the bioinformatics. D.H. conducted the non-parametric statistical analysis. F.R. oversaw most of the metagenomic projects. All other authors collected the metagenomes and provided comments on the manuscript.

Author information

Author notes

  1. Christelle Desnues

    Present address: Present address: Unité des Rickettsies, CNRS-UMR 6020, Faculté de médecine, 13385 Marseille, France.,

  2. Elizabeth A. Dinsdale and Robert A. Edwards: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biology,,

    Elizabeth A. Dinsdale, Robert A. Edwards, Dana Hall, Florent Angly, Mike Furlan, Christelle Desnues, Matthew Haynes, Linlin Li, Beltran Rodriguez Brito, Rebecca Vega Thurber, Linda Wegley & Forest Rohwer

  2. Center for Microbial Sciences,,

    Robert A. Edwards & Forest Rohwer

  3. Department of Computer Sciences, and,

    Robert A. Edwards

  4. Computational Science Research Centre, San Diego State University, San Diego, California 92182, USA ,

    Florent Angly & Beltran Rodriguez Brito

  5. School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia ,

    Elizabeth A. Dinsdale

  6. Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA,

    Robert A. Edwards, Robert Olson & Rick Stevens

  7. University of South Florida, College of Marine Science, 140 7th Avenue South, St Petersburg, Florida 33701, USA ,

    Mya Breitbart, Lauren McDaniel & John Paul

  8. Department of Animal Sciences, and,

    Jennifer M. Brulc & Bryan A. White

  9. The Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA ,

    Bryan A. White

  10. Department of Marine Sciences, University of Georgia, Athens, 30602 Georgia, USA,

    Mary Ann Moran

  11. The J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA ,

    Karen E. Nelson

  12. Genome Institute of Singapore, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore ,

    Christina Nilsson & Yijun Ruan

  13. Department of Earth Science, University of California Santa Barbara, Santa Barbara, California 93106, USA,

    Brandon K. Swan & David L. Valentine

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  1. Elizabeth A. Dinsdale
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Corresponding author

Correspondence to Elizabeth A. Dinsdale.

Supplementary information

Supplementary Information

The file contains Supplementary Tables S1-S4 and Supplementary Figures S1-S6 with Legends. The Supplementary Tables present accession numbers and descriptions of metagenomes, phage and prophage content of each metagenome, the motility proteins present in the microbial and viral metagenomes and statistical comparisons of the proportions of metabolic processes across the nine biomes. The Supplementary Figures provide information about the geographic separation of samples, diversity versus sequences number, comparison of diversity between metagenomes and sequenced whole bacterial genomes, the fine-scale details about the sulfur metabolic processes, and two experiments that show the strength of the CDA across multiple groupings. (PDF 855 kb)

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Dinsdale, E., Edwards, R., Hall, D. et al. Functional metagenomic profiling of nine biomes. Nature 452, 629–632 (2008). https://doi.org/10.1038/nature06810

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