Functional metagenomic profiling of nine biomes (original) (raw)

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

Authors

  1. Elizabeth A. Dinsdale
  2. Robert A. Edwards
  3. Dana Hall
  4. Florent Angly
  5. Mya Breitbart
  6. Jennifer M. Brulc
  7. Mike Furlan
  8. Christelle Desnues
  9. Matthew Haynes
  10. Linlin Li
  11. Lauren McDaniel
  12. Mary Ann Moran
  13. Karen E. Nelson
  14. Christina Nilsson
  15. Robert Olson
  16. John Paul
  17. Beltran Rodriguez Brito
  18. Yijun Ruan
  19. Brandon K. Swan
  20. Rick Stevens
  21. David L. Valentine
  22. Rebecca Vega Thurber
  23. Linda Wegley
  24. Bryan A. White
  25. Forest Rohwer

Corresponding author

Correspondence toElizabeth A. Dinsdale.

Supplementary information

Supplementary Information (download PDF )

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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