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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Nature Biotechnology volume 29, pages 415420 (2011) | Download Citation

Abstract

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

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Acknowledgements

Funding sources are listed in the Supplementary Note.

Author information

Affiliations

  1. Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

    • Pelin Yilmaz
    • , Renzo Kottmann
    • , Pier Luigi Buttigieg
    • , Wolfgang Hankeln
    • , Elmar Pruesse
    • , Christian Quast
    •  & Frank Oliver Glöckner
  2. Jacobs University Bremen gGmbH, Bremen, Germany.

    • Pelin Yilmaz
    • , Pier Luigi Buttigieg
    • , Wolfgang Hankeln
    • , Elmar Pruesse
    •  & Frank Oliver Glöckner
  3. Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.

    • Dawn Field
    • , Norman Morrison
    • , Peter Sterk
    • , Mark Bailey
    • , Tim Booth
    • , Lindsay K Newbold
    • , Anna E Oliver
    •  & Andrew Whiteley
  4. Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.

    • Rob Knight
    • , Elizabeth K Costello
    • , Jerry Kennedy
    • , Robert Larsen
    • , Catherine A Lozupone
    • , Sara Nakielny
    • , Jesse Stombaugh
    •  & Doug Wendel
  5. Howard Hughes Medical Institute, San Francisco, California, USA.

    • Rob Knight
  6. Ribosomal Database Project, Michigan State University, East Lansing, Michigan, USA.

    • James R Cole
  7. Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA.

    • James R Cole
    • , Patrick S G Chain
    •  & James M Tiedje
  8. The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA.

    • Linda Amaral-Zettler
  9. Plymouth Marine Laboratory, Plymouth, UK.

    • Jack A Gilbert
  10. Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.

    • Jack A Gilbert
    • , Folker Meyer
    •  & Andreas Wilke
  11. Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.

    • Jack A Gilbert
  12. National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

    • Ilene Karsch-Mizrachi
    •  & Anjanette Johnston
  13. European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

    • Guy Cochrane
    • , Robert Vaughan
    •  & Christopher Hunter
  14. WCU Center for Green Metagenomics, School of Civil and Environmental Engineering, Yonsei University, Seoul, Republic of Korea.

    • Joonhong Park
  15. School of Computer Science, University of Manchester, Manchester, UK.

    • Norman Morrison
  16. Oxford e-Research Centre, University of Oxford, Oxford, UK.

    • Philippe Rocca-Serra
    • , Eamonn Maguire
    •  & Susanna Assunta-Sansone
  17. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

    • Manimozhiyan Arumugam
    •  & Peer Bork
  18. Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA.

    • Laura Baumgartner
    • , Justin Kuczynski
    •  & Norman R Pace
  19. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.

    • Bruce W Birren
    • , Dirk Gevers
    •  & Doyle V Ward
  20. Department of Medicine and the Department of Microbiology, New York University Langone Medical Center, New York, New York, USA.

    • Martin J Blaser
  21. National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.

    • Vivien Bonazzi
    •  & Lita Proctor
  22. Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.

    • Frederic D Bushman
    • , Emily Charlson
    •  & Rohini Sinha
  23. DOE Joint Genome Institute, Walnut Creek, California, USA.

    • Patrick S G Chain
    • , Janet Jansson
    •  & Nikos Kyrpides
  24. Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.

    • Patrick S G Chain
  25. Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.

    • Heather Huot-Creasy
    • , Jacques Ravel
    • , Lynn Schriml
    • , Owen White
    •  & Jennifer R Wortman
  26. Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium.

    • Peter Dawyndt
  27. Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

    • Todd DeSantis
  28. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.

    • Noah Fierer
    • , Robert Guralnick
    •  & Teresa Legg
  29. Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.

    • Jed A Fuhrman
  30. National Ecological Observatory Network, Boulder, Colorado, USA.

    • Rachel E Gallery
  31. Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.

    • Richard A Gibbs
    • , Sarah Highlander
    •  & Joseph Petrosino
  32. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

    • Richard A Gibbs
  33. Department of Biology, University of New Mexico, LTER Network Office, Albuquerque, New Mexico, USA.

    • Inigo San Gil
  34. Department of Computer Science, University of Colorado, Boulder, Colorado, USA.

    • Antonio Gonzalez
    •  & Dan Knights
  35. Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.

    • Jeffrey I Gordon
    • , Andrew L Kau
    • , Brian Muegge
    • , Michelle I Smith
    •  & Tanya Yatsunenko
  36. University of Colorado Museum of Natural History, University of Colorado, Boulder, Colorado, USA.

    • Robert Guralnick
  37. Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.

    • Sarah Highlander
    •  & Joseph Petrosino
  38. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.

    • Philip Hugenholtz
  39. Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

    • Janet Jansson
  40. Department of Biology, San Diego State University, San Diego, California, USA.

    • Scott T Kelley
  41. Department of Microbiology, Cornell University, Ithaca, New York, USA.

    • Omry Koren
    • , Ruth E Ley
    •  & Aymé Spor
  42. Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.

    • Christian L Lauber
    •  & Donna Lyons
  43. Lehrstuhl für Mikrobiologie, Technische Universität München, Freising, Germany.

    • Wolfgang Ludwig
  44. J. Craig Venter Institute, Rockville, Maryland, USA.

    • Barbara A Methé
    •  & Karen E Nelson
  45. Department of Environmental Sciences, University of Colorado, Boulder, Colorado, USA.

    • Diana Nemergut
  46. Department of Biology, University of Waterloo, Ontario, Canada.

    • Josh D Neufeld
  47. Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

    • Giriprakash Palanisamy
  48. Ribocon GmbH, Bremen, Germany.

    • Jörg Peplies
  49. VIB - Vrije Universiteit Brussel, Brussels, Belgium.

    • Jeroen Raes
  50. Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.

    • Sujeevan Ratnasingham
  51. Departments of Microbiology and Immunology and Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.

    • David A Relman
  52. Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA.

    • David A Relman
  53. Department of Microbiology and Immunology, Ann Arbor, Michigan, USA.

    • Patrick D Schloss
  54. The Genome Center, Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.

    • Erica Sodergren
    •  & George M Weinstock

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Frank Oliver Glöckner.

Supplementary information

PDF files

  1. 1.

    Supplementary Results 1

    Community led surveys

Excel files

  1. 1.

    Supplementary Results 2

    MIMARKS checklist

  2. 2.

    Supplementary Results 3

    MIMARKS compliant datasets

  3. 3.

    Supplementary Note

    Funding sources

About this article

Publication history

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DOI

https://doi.org/10.1038/nbt.1823

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