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

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Author manuscript; available in PMC: 2012 Jun 5.</div> <div> <em>Published in final edited form as: </em>Nat Biotechnol. 2011 May;29(5):415–420. doi: <a href="https://doi.org/10.1038/nbt.1823" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">10.1038/nbt.1823</a> </div> <nav id="journal_context_menu" hidden="hidden"><ul class="menu-list font-family-ui" role="menu"> <li role="presentation"><a href="https://www.ncbi.nlm.nih.gov/pmc/?term=%22Nat%20Biotechnol%22%5Bjour%5D" class="usa-link" role="menuitem">Search in PMC</a></li> <li role="presentation"><a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Nat%20Biotechnol%22%5Bjour%5D" lang="en" class="usa-link" role="menuitem">Search in PubMed</a></li> <li role="presentation"><a href="https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Nat%20Biotechnol%22%5BTitle%20Abbreviation%5D" class="usa-link" role="menuitem">View in NLM Catalog</a></li> <li role="presentation"><a href="?term=%22Nat%20Biotechnol%22%5Bjour%5D" class="usa-link" role="menuitem" data-add-to-search="true">Add to search</a></li> </ul></nav></section><section class="front-matter"><div class="ameta p font-secondary font-xs"> <hgroup><h1>Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications</h1></hgroup><div class="cg p"> <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Yilmaz%20P%22%5BAuthor%5D" class="usa-link" aria-describedby="id1"><span class="name western">Pelin Yilmaz</span></a><div hidden="hidden" id="id1"> <h3><span class="name western">Pelin Yilmaz</span></h3> <div class="p"> <sup>1</sup>Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.</div> <div class="p"> <sup>2</sup>Jacobs University Bremen gGmbH, Bremen, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Yilmaz%20P%22%5BAuthor%5D" class="usa-link"><span class="name western">Pelin Yilmaz</span></a> </div> </div> <sup>1,</sup><sup>2</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kottmann%20R%22%5BAuthor%5D" class="usa-link" aria-describedby="id2"><span class="name western">Renzo Kottmann</span></a><div hidden="hidden" id="id2"> <h3><span class="name western">Renzo Kottmann</span></h3> <div class="p"> <sup>1</sup>Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kottmann%20R%22%5BAuthor%5D" class="usa-link"><span class="name western">Renzo Kottmann</span></a> </div> </div> <sup>1</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Field%20D%22%5BAuthor%5D" class="usa-link" aria-describedby="id3"><span class="name western">Dawn Field</span></a><div hidden="hidden" id="id3"> <h3><span class="name western">Dawn Field</span></h3> <div class="p"> <sup>3</sup>Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Field%20D%22%5BAuthor%5D" class="usa-link"><span class="name western">Dawn Field</span></a> </div> </div> <sup>3</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Knight%20R%22%5BAuthor%5D" class="usa-link" aria-describedby="id4"><span class="name western">Rob Knight</span></a><div hidden="hidden" id="id4"> <h3><span class="name western">Rob Knight</span></h3> <div class="p"> <sup>4</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.</div> <div class="p"> <sup>5</sup>Howard Hughes Medical Institute, San Francisco, California, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Knight%20R%22%5BAuthor%5D" class="usa-link"><span class="name western">Rob Knight</span></a> </div> </div> <sup>4,</sup><sup>5</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Cole%20JR%22%5BAuthor%5D" class="usa-link" aria-describedby="id5"><span class="name western">James R Cole</span></a><div hidden="hidden" id="id5"> <h3><span class="name western">James R Cole</span></h3> <div class="p"> <sup>6</sup>Ribosomal Database Project, Michigan State University, East Lansing, Michigan, USA.</div> <div class="p"> <sup>7</sup>Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Cole%20JR%22%5BAuthor%5D" class="usa-link"><span class="name western">James R Cole</span></a> </div> </div> <sup>6,</sup><sup>7</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Amaral-Zettler%20L%22%5BAuthor%5D" class="usa-link" aria-describedby="id6"><span class="name western">Linda Amaral-Zettler</span></a><div hidden="hidden" id="id6"> <h3><span class="name western">Linda Amaral-Zettler</span></h3> <div class="p"> <sup>8</sup>The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Amaral-Zettler%20L%22%5BAuthor%5D" class="usa-link"><span class="name western">Linda Amaral-Zettler</span></a> </div> </div> <sup>8</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gilbert%20JA%22%5BAuthor%5D" class="usa-link" aria-describedby="id7"><span class="name western">Jack A Gilbert</span></a><div hidden="hidden" id="id7"> <h3><span class="name western">Jack A Gilbert</span></h3> <div class="p"> <sup>9</sup>Plymouth Marine Laboratory, Plymouth, UK.</div> <div class="p"> <sup>10</sup>Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.</div> <div class="p"> <sup>11</sup>Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gilbert%20JA%22%5BAuthor%5D" class="usa-link"><span class="name western">Jack A Gilbert</span></a> </div> </div> <sup>9,</sup><sup>10,</sup><sup>11</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Karsch-Mizrachi%20I%22%5BAuthor%5D" class="usa-link" aria-describedby="id8"><span class="name western">Ilene Karsch-Mizrachi</span></a><div hidden="hidden" id="id8"> <h3><span class="name western">Ilene Karsch-Mizrachi</span></h3> <div class="p"> <sup>12</sup>National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Karsch-Mizrachi%20I%22%5BAuthor%5D" class="usa-link"><span class="name western">Ilene Karsch-Mizrachi</span></a> </div> </div> <sup>12</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Johnston%20A%22%5BAuthor%5D" class="usa-link" aria-describedby="id9"><span class="name western">Anjanette Johnston</span></a><div hidden="hidden" id="id9"> <h3><span class="name western">Anjanette Johnston</span></h3> <div class="p"> <sup>12</sup>National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Johnston%20A%22%5BAuthor%5D" class="usa-link"><span class="name western">Anjanette Johnston</span></a> </div> </div> <sup>12</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Cochrane%20G%22%5BAuthor%5D" class="usa-link" aria-describedby="id10"><span class="name western">Guy Cochrane</span></a><div hidden="hidden" id="id10"> <h3><span class="name western">Guy Cochrane</span></h3> <div class="p"> <sup>13</sup>European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Cochrane%20G%22%5BAuthor%5D" class="usa-link"><span class="name western">Guy Cochrane</span></a> </div> </div> <sup>13</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Vaughan%20R%22%5BAuthor%5D" class="usa-link" aria-describedby="id11"><span class="name western">Robert Vaughan</span></a><div hidden="hidden" id="id11"> <h3><span class="name western">Robert Vaughan</span></h3> <div class="p"> <sup>13</sup>European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Vaughan%20R%22%5BAuthor%5D" class="usa-link"><span class="name western">Robert Vaughan</span></a> </div> </div> <sup>13</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Hunter%20C%22%5BAuthor%5D" class="usa-link" aria-describedby="id12"><span class="name western">Christopher Hunter</span></a><div hidden="hidden" id="id12"> <h3><span class="name western">Christopher Hunter</span></h3> <div class="p"> <sup>13</sup>European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Hunter%20C%22%5BAuthor%5D" class="usa-link"><span class="name western">Christopher Hunter</span></a> </div> </div> <sup>13</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Park%20J%22%5BAuthor%5D" class="usa-link" aria-describedby="id13"><span class="name western">Joonhong Park</span></a><div hidden="hidden" id="id13"> <h3><span class="name western">Joonhong Park</span></h3> <div class="p"> <sup>14</sup>WCU Center for Green Metagenomics, School of Civil and Environmental Engineering, Yonsei University, Seoul, Republic of Korea.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Park%20J%22%5BAuthor%5D" class="usa-link"><span class="name western">Joonhong Park</span></a> </div> </div> <sup>14</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Morrison%20N%22%5BAuthor%5D" class="usa-link" aria-describedby="id14"><span class="name western">Norman Morrison</span></a><div hidden="hidden" id="id14"> <h3><span class="name western">Norman Morrison</span></h3> <div class="p"> <sup>3</sup>Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.</div> <div class="p"> <sup>15</sup>School of Computer Science, University of Manchester, Manchester, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Morrison%20N%22%5BAuthor%5D" class="usa-link"><span class="name western">Norman Morrison</span></a> </div> </div> <sup>3,</sup><sup>15</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Rocca-Serra%20P%22%5BAuthor%5D" class="usa-link" aria-describedby="id15"><span class="name western">Philippe Rocca-Serra</span></a><div hidden="hidden" id="id15"> <h3><span class="name western">Philippe Rocca-Serra</span></h3> <div class="p"> <sup>16</sup>Oxford e-Research Centre, University of Oxford, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Rocca-Serra%20P%22%5BAuthor%5D" class="usa-link"><span class="name western">Philippe Rocca-Serra</span></a> </div> </div> <sup>16</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Sterk%20P%22%5BAuthor%5D" class="usa-link" aria-describedby="id16"><span class="name western">Peter Sterk</span></a><div hidden="hidden" id="id16"> <h3><span class="name western">Peter Sterk</span></h3> <div class="p"> <sup>3</sup>Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Sterk%20P%22%5BAuthor%5D" class="usa-link"><span class="name western">Peter Sterk</span></a> </div> </div> <sup>3</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Arumugam%20M%22%5BAuthor%5D" class="usa-link" aria-describedby="id17"><span class="name western">Manimozhiyan Arumugam</span></a><div hidden="hidden" id="id17"> <h3><span class="name western">Manimozhiyan Arumugam</span></h3> <div class="p"> <sup>17</sup>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Arumugam%20M%22%5BAuthor%5D" class="usa-link"><span class="name western">Manimozhiyan Arumugam</span></a> </div> </div> <sup>17</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Bailey%20M%22%5BAuthor%5D" class="usa-link" aria-describedby="id18"><span class="name western">Mark Bailey</span></a><div hidden="hidden" id="id18"> <h3><span class="name western">Mark Bailey</span></h3> <div class="p"> <sup>3</sup>Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Bailey%20M%22%5BAuthor%5D" class="usa-link"><span class="name western">Mark Bailey</span></a> </div> </div> <sup>3</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Baumgartner%20L%22%5BAuthor%5D" class="usa-link" aria-describedby="id19"><span class="name western">Laura Baumgartner</span></a><div hidden="hidden" id="id19"> <h3><span class="name western">Laura Baumgartner</span></h3> <div class="p"> <sup>18</sup>Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Baumgartner%20L%22%5BAuthor%5D" class="usa-link"><span class="name western">Laura Baumgartner</span></a> </div> </div> <sup>18</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Birren%20BW%22%5BAuthor%5D" class="usa-link" aria-describedby="id20"><span class="name western">Bruce W Birren</span></a><div hidden="hidden" id="id20"> <h3><span class="name western">Bruce W Birren</span></h3> <div class="p"> <sup>19</sup>Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Birren%20BW%22%5BAuthor%5D" class="usa-link"><span class="name western">Bruce W Birren</span></a> </div> </div> <sup>19</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Blaser%20MJ%22%5BAuthor%5D" class="usa-link" aria-describedby="id21"><span class="name western">Martin J Blaser</span></a><div hidden="hidden" id="id21"> <h3><span class="name western">Martin J Blaser</span></h3> <div class="p"> <sup>20</sup>Department of Medicine and the Department of Microbiology, New York University Langone Medical Center, New York, New York, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Blaser%20MJ%22%5BAuthor%5D" class="usa-link"><span class="name western">Martin J Blaser</span></a> </div> </div> <sup>20</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Bonazzi%20V%22%5BAuthor%5D" class="usa-link" aria-describedby="id22"><span class="name western">Vivien Bonazzi</span></a><div hidden="hidden" id="id22"> <h3><span class="name western">Vivien Bonazzi</span></h3> <div class="p"> <sup>21</sup>National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Bonazzi%20V%22%5BAuthor%5D" class="usa-link"><span class="name western">Vivien Bonazzi</span></a> </div> </div> <sup>21</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Booth%20T%22%5BAuthor%5D" class="usa-link" aria-describedby="id23"><span class="name western">Tim Booth</span></a><div hidden="hidden" id="id23"> <h3><span class="name western">Tim Booth</span></h3> <div class="p"> <sup>3</sup>Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Booth%20T%22%5BAuthor%5D" class="usa-link"><span class="name western">Tim Booth</span></a> </div> </div> <sup>3</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Bork%20P%22%5BAuthor%5D" class="usa-link" aria-describedby="id24"><span class="name western">Peer Bork</span></a><div hidden="hidden" id="id24"> <h3><span class="name western">Peer Bork</span></h3> <div class="p"> <sup>17</sup>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Bork%20P%22%5BAuthor%5D" class="usa-link"><span class="name western">Peer Bork</span></a> </div> </div> <sup>17</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Bushman%20FD%22%5BAuthor%5D" class="usa-link" aria-describedby="id25"><span class="name western">Frederic D Bushman</span></a><div hidden="hidden" id="id25"> <h3><span class="name western">Frederic D Bushman</span></h3> <div class="p"> <sup>22</sup>Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Bushman%20FD%22%5BAuthor%5D" class="usa-link"><span class="name western">Frederic D Bushman</span></a> </div> </div> <sup>22</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Buttigieg%20PL%22%5BAuthor%5D" class="usa-link" aria-describedby="id26"><span class="name western">Pier Luigi Buttigieg</span></a><div hidden="hidden" id="id26"> <h3><span class="name western">Pier Luigi Buttigieg</span></h3> <div class="p"> <sup>1</sup>Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.</div> <div class="p"> <sup>2</sup>Jacobs University Bremen gGmbH, Bremen, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Buttigieg%20PL%22%5BAuthor%5D" class="usa-link"><span class="name western">Pier Luigi Buttigieg</span></a> </div> </div> <sup>1,</sup><sup>2</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Chain%20PSG%22%5BAuthor%5D" class="usa-link" aria-describedby="id27"><span class="name western">Patrick S G Chain</span></a><div hidden="hidden" id="id27"> <h3><span class="name western">Patrick S G Chain</span></h3> <div class="p"> <sup>7</sup>Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA.</div> <div class="p"> <sup>23</sup>DOE Joint Genome Institute, Walnut Creek, California, USA.</div> <div class="p"> <sup>24</sup>Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Chain%20PSG%22%5BAuthor%5D" class="usa-link"><span class="name western">Patrick S G Chain</span></a> </div> </div> <sup>7,</sup><sup>23,</sup><sup>24</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Charlson%20E%22%5BAuthor%5D" class="usa-link" aria-describedby="id28"><span class="name western">Emily Charlson</span></a><div hidden="hidden" id="id28"> <h3><span class="name western">Emily Charlson</span></h3> <div class="p"> <sup>22</sup>Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Charlson%20E%22%5BAuthor%5D" class="usa-link"><span class="name western">Emily Charlson</span></a> </div> </div> <sup>22</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Costello%20EK%22%5BAuthor%5D" class="usa-link" aria-describedby="id29"><span class="name western">Elizabeth K Costello</span></a><div hidden="hidden" id="id29"> <h3><span class="name western">Elizabeth K Costello</span></h3> <div class="p"> <sup>4</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Costello%20EK%22%5BAuthor%5D" class="usa-link"><span class="name western">Elizabeth K Costello</span></a> </div> </div> <sup>4</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Huot-Creasy%20H%22%5BAuthor%5D" class="usa-link" aria-describedby="id30"><span class="name western">Heather Huot-Creasy</span></a><div hidden="hidden" id="id30"> <h3><span class="name western">Heather Huot-Creasy</span></h3> <div class="p"> <sup>25</sup>Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Huot-Creasy%20H%22%5BAuthor%5D" class="usa-link"><span class="name western">Heather Huot-Creasy</span></a> </div> </div> <sup>25</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Dawyndt%20P%22%5BAuthor%5D" class="usa-link" aria-describedby="id31"><span class="name western">Peter Dawyndt</span></a><div hidden="hidden" id="id31"> <h3><span class="name western">Peter Dawyndt</span></h3> <div class="p"> <sup>26</sup>Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Dawyndt%20P%22%5BAuthor%5D" class="usa-link"><span class="name western">Peter Dawyndt</span></a> </div> </div> <sup>26</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22DeSantis%20T%22%5BAuthor%5D" class="usa-link" aria-describedby="id32"><span class="name western">Todd DeSantis</span></a><div hidden="hidden" id="id32"> <h3><span class="name western">Todd DeSantis</span></h3> <div class="p"> <sup>27</sup>Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, California, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22DeSantis%20T%22%5BAuthor%5D" class="usa-link"><span class="name western">Todd DeSantis</span></a> </div> </div> <sup>27</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Fierer%20N%22%5BAuthor%5D" class="usa-link" aria-describedby="id33"><span class="name western">Noah Fierer</span></a><div hidden="hidden" id="id33"> <h3><span class="name western">Noah Fierer</span></h3> <div class="p"> <sup>28</sup>Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Fierer%20N%22%5BAuthor%5D" class="usa-link"><span class="name western">Noah Fierer</span></a> </div> </div> <sup>28</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Fuhrman%20JA%22%5BAuthor%5D" class="usa-link" aria-describedby="id34"><span class="name western">Jed A Fuhrman</span></a><div hidden="hidden" id="id34"> <h3><span class="name western">Jed A Fuhrman</span></h3> <div class="p"> <sup>29</sup>Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Fuhrman%20JA%22%5BAuthor%5D" class="usa-link"><span class="name western">Jed A Fuhrman</span></a> </div> </div> <sup>29</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gallery%20RE%22%5BAuthor%5D" class="usa-link" aria-describedby="id35"><span class="name western">Rachel E Gallery</span></a><div hidden="hidden" id="id35"> <h3><span class="name western">Rachel E Gallery</span></h3> <div class="p"> <sup>30</sup>National Ecological Observatory Network, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gallery%20RE%22%5BAuthor%5D" class="usa-link"><span class="name western">Rachel E Gallery</span></a> </div> </div> <sup>30</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gevers%20D%22%5BAuthor%5D" class="usa-link" aria-describedby="id36"><span class="name western">Dirk Gevers</span></a><div hidden="hidden" id="id36"> <h3><span class="name western">Dirk Gevers</span></h3> <div class="p"> <sup>19</sup>Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gevers%20D%22%5BAuthor%5D" class="usa-link"><span class="name western">Dirk Gevers</span></a> </div> </div> <sup>19</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gibbs%20RA%22%5BAuthor%5D" class="usa-link" aria-describedby="id37"><span class="name western">Richard A Gibbs</span></a><div hidden="hidden" id="id37"> <h3><span class="name western">Richard A Gibbs</span></h3> <div class="p"> <sup>31</sup>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.</div> <div class="p"> <sup>32</sup>Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gibbs%20RA%22%5BAuthor%5D" class="usa-link"><span class="name western">Richard A Gibbs</span></a> </div> </div> <sup>31,</sup><sup>32</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gil%20IS%22%5BAuthor%5D" class="usa-link" aria-describedby="id38"><span class="name western">Inigo San Gil</span></a><div hidden="hidden" id="id38"> <h3><span class="name western">Inigo San Gil</span></h3> <div class="p"> <sup>33</sup>Department of Biology, University of New Mexico, LTER Network Office, Albuquerque, New Mexico, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gil%20IS%22%5BAuthor%5D" class="usa-link"><span class="name western">Inigo San Gil</span></a> </div> </div> <sup>33</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gonzalez%20A%22%5BAuthor%5D" class="usa-link" aria-describedby="id39"><span class="name western">Antonio Gonzalez</span></a><div hidden="hidden" id="id39"> <h3><span class="name western">Antonio Gonzalez</span></h3> <div class="p"> <sup>34</sup>Department of Computer Science, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gonzalez%20A%22%5BAuthor%5D" class="usa-link"><span class="name western">Antonio Gonzalez</span></a> </div> </div> <sup>34</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gordon%20JI%22%5BAuthor%5D" class="usa-link" aria-describedby="id40"><span class="name western">Jeffrey I Gordon</span></a><div hidden="hidden" id="id40"> <h3><span class="name western">Jeffrey I Gordon</span></h3> <div class="p"> <sup>35</sup>Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gordon%20JI%22%5BAuthor%5D" class="usa-link"><span class="name western">Jeffrey I Gordon</span></a> </div> </div> <sup>35</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Guralnick%20R%22%5BAuthor%5D" class="usa-link" aria-describedby="id41"><span class="name western">Robert Guralnick</span></a><div hidden="hidden" id="id41"> <h3><span class="name western">Robert Guralnick</span></h3> <div class="p"> <sup>28</sup>Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.</div> <div class="p"> <sup>36</sup>University of Colorado Museum of Natural History, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Guralnick%20R%22%5BAuthor%5D" class="usa-link"><span class="name western">Robert Guralnick</span></a> </div> </div> <sup>28,</sup><sup>36</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Hankeln%20W%22%5BAuthor%5D" class="usa-link" aria-describedby="id42"><span class="name western">Wolfgang Hankeln</span></a><div hidden="hidden" id="id42"> <h3><span class="name western">Wolfgang Hankeln</span></h3> <div class="p"> <sup>1</sup>Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.</div> <div class="p"> <sup>2</sup>Jacobs University Bremen gGmbH, Bremen, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Hankeln%20W%22%5BAuthor%5D" class="usa-link"><span class="name western">Wolfgang Hankeln</span></a> </div> </div> <sup>1,</sup><sup>2</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Highlander%20S%22%5BAuthor%5D" class="usa-link" aria-describedby="id43"><span class="name western">Sarah Highlander</span></a><div hidden="hidden" id="id43"> <h3><span class="name western">Sarah Highlander</span></h3> <div class="p"> <sup>31</sup>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.</div> <div class="p"> <sup>37</sup>Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Highlander%20S%22%5BAuthor%5D" class="usa-link"><span class="name western">Sarah Highlander</span></a> </div> </div> <sup>31,</sup><sup>37</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Hugenholtz%20P%22%5BAuthor%5D" class="usa-link" aria-describedby="id44"><span class="name western">Philip Hugenholtz</span></a><div hidden="hidden" id="id44"> <h3><span class="name western">Philip Hugenholtz</span></h3> <div class="p"> <sup>38</sup>Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Hugenholtz%20P%22%5BAuthor%5D" class="usa-link"><span class="name western">Philip Hugenholtz</span></a> </div> </div> <sup>38</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Jansson%20J%22%5BAuthor%5D" class="usa-link" aria-describedby="id45"><span class="name western">Janet Jansson</span></a><div hidden="hidden" id="id45"> <h3><span class="name western">Janet Jansson</span></h3> <div class="p"> <sup>23</sup>DOE Joint Genome Institute, Walnut Creek, California, USA.</div> <div class="p"> <sup>39</sup>Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Jansson%20J%22%5BAuthor%5D" class="usa-link"><span class="name western">Janet Jansson</span></a> </div> </div> <sup>23,</sup><sup>39</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kau%20AL%22%5BAuthor%5D" class="usa-link" aria-describedby="id46"><span class="name western">Andrew L Kau</span></a><div hidden="hidden" id="id46"> <h3><span class="name western">Andrew L Kau</span></h3> <div class="p"> <sup>35</sup>Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kau%20AL%22%5BAuthor%5D" class="usa-link"><span class="name western">Andrew L Kau</span></a> </div> </div> <sup>35</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kelley%20ST%22%5BAuthor%5D" class="usa-link" aria-describedby="id47"><span class="name western">Scott T Kelley</span></a><div hidden="hidden" id="id47"> <h3><span class="name western">Scott T Kelley</span></h3> <div class="p"> <sup>40</sup>Department of Biology, San Diego State University, San Diego, California, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kelley%20ST%22%5BAuthor%5D" class="usa-link"><span class="name western">Scott T Kelley</span></a> </div> </div> <sup>40</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kennedy%20J%22%5BAuthor%5D" class="usa-link" aria-describedby="id48"><span class="name western">Jerry Kennedy</span></a><div hidden="hidden" id="id48"> <h3><span class="name western">Jerry Kennedy</span></h3> <div class="p"> <sup>4</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kennedy%20J%22%5BAuthor%5D" class="usa-link"><span class="name western">Jerry Kennedy</span></a> </div> </div> <sup>4</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Knights%20D%22%5BAuthor%5D" class="usa-link" aria-describedby="id49"><span class="name western">Dan Knights</span></a><div hidden="hidden" id="id49"> <h3><span class="name western">Dan Knights</span></h3> <div class="p"> <sup>34</sup>Department of Computer Science, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Knights%20D%22%5BAuthor%5D" class="usa-link"><span class="name western">Dan Knights</span></a> </div> </div> <sup>34</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Koren%20O%22%5BAuthor%5D" class="usa-link" aria-describedby="id50"><span class="name western">Omry Koren</span></a><div hidden="hidden" id="id50"> <h3><span class="name western">Omry Koren</span></h3> <div class="p"> <sup>41</sup>Department of Microbiology, Cornell University, Ithaca, New York, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Koren%20O%22%5BAuthor%5D" class="usa-link"><span class="name western">Omry Koren</span></a> </div> </div> <sup>41</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kuczynski%20J%22%5BAuthor%5D" class="usa-link" aria-describedby="id51"><span class="name western">Justin Kuczynski</span></a><div hidden="hidden" id="id51"> <h3><span class="name western">Justin Kuczynski</span></h3> <div class="p"> <sup>18</sup>Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kuczynski%20J%22%5BAuthor%5D" class="usa-link"><span class="name western">Justin Kuczynski</span></a> </div> </div> <sup>18</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kyrpides%20N%22%5BAuthor%5D" class="usa-link" aria-describedby="id52"><span class="name western">Nikos Kyrpides</span></a><div hidden="hidden" id="id52"> <h3><span class="name western">Nikos Kyrpides</span></h3> <div class="p"> <sup>23</sup>DOE Joint Genome Institute, Walnut Creek, California, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Kyrpides%20N%22%5BAuthor%5D" class="usa-link"><span class="name western">Nikos Kyrpides</span></a> </div> </div> <sup>23</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Larsen%20R%22%5BAuthor%5D" class="usa-link" aria-describedby="id53"><span class="name western">Robert Larsen</span></a><div hidden="hidden" id="id53"> <h3><span class="name western">Robert Larsen</span></h3> <div class="p"> <sup>4</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Larsen%20R%22%5BAuthor%5D" class="usa-link"><span class="name western">Robert Larsen</span></a> </div> </div> <sup>4</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Lauber%20CL%22%5BAuthor%5D" class="usa-link" aria-describedby="id54"><span class="name western">Christian L Lauber</span></a><div hidden="hidden" id="id54"> <h3><span class="name western">Christian L Lauber</span></h3> <div class="p"> <sup>42</sup>Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Lauber%20CL%22%5BAuthor%5D" class="usa-link"><span class="name western">Christian L Lauber</span></a> </div> </div> <sup>42</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Legg%20T%22%5BAuthor%5D" class="usa-link" aria-describedby="id55"><span class="name western">Teresa Legg</span></a><div hidden="hidden" id="id55"> <h3><span class="name western">Teresa Legg</span></h3> <div class="p"> <sup>28</sup>Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Legg%20T%22%5BAuthor%5D" class="usa-link"><span class="name western">Teresa Legg</span></a> </div> </div> <sup>28</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ley%20RE%22%5BAuthor%5D" class="usa-link" aria-describedby="id56"><span class="name western">Ruth E Ley</span></a><div hidden="hidden" id="id56"> <h3><span class="name western">Ruth E Ley</span></h3> <div class="p"> <sup>41</sup>Department of Microbiology, Cornell University, Ithaca, New York, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ley%20RE%22%5BAuthor%5D" class="usa-link"><span class="name western">Ruth E Ley</span></a> </div> </div> <sup>41</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Lozupone%20CA%22%5BAuthor%5D" class="usa-link" aria-describedby="id57"><span class="name western">Catherine A Lozupone</span></a><div hidden="hidden" id="id57"> <h3><span class="name western">Catherine A Lozupone</span></h3> <div class="p"> <sup>4</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Lozupone%20CA%22%5BAuthor%5D" class="usa-link"><span class="name western">Catherine A Lozupone</span></a> </div> </div> <sup>4</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ludwig%20W%22%5BAuthor%5D" class="usa-link" aria-describedby="id58"><span class="name western">Wolfgang Ludwig</span></a><div hidden="hidden" id="id58"> <h3><span class="name western">Wolfgang Ludwig</span></h3> <div class="p"> <sup>43</sup>Lehrstuhl für Mikrobiologie, Technische Universität München, Freising, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ludwig%20W%22%5BAuthor%5D" class="usa-link"><span class="name western">Wolfgang Ludwig</span></a> </div> </div> <sup>43</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Lyons%20D%22%5BAuthor%5D" class="usa-link" aria-describedby="id59"><span class="name western">Donna Lyons</span></a><div hidden="hidden" id="id59"> <h3><span class="name western">Donna Lyons</span></h3> <div class="p"> <sup>42</sup>Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Lyons%20D%22%5BAuthor%5D" class="usa-link"><span class="name western">Donna Lyons</span></a> </div> </div> <sup>42</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Maguire%20E%22%5BAuthor%5D" class="usa-link" aria-describedby="id60"><span class="name western">Eamonn Maguire</span></a><div hidden="hidden" id="id60"> <h3><span class="name western">Eamonn Maguire</span></h3> <div class="p"> <sup>16</sup>Oxford e-Research Centre, University of Oxford, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Maguire%20E%22%5BAuthor%5D" class="usa-link"><span class="name western">Eamonn Maguire</span></a> </div> </div> <sup>16</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Meth%C3%A9%20BA%22%5BAuthor%5D" class="usa-link" aria-describedby="id61"><span class="name western">Barbara A Methé</span></a><div hidden="hidden" id="id61"> <h3><span class="name western">Barbara A Methé</span></h3> <div class="p"> <sup>44</sup>J. Craig Venter Institute, Rockville, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Meth%C3%A9%20BA%22%5BAuthor%5D" class="usa-link"><span class="name western">Barbara A Methé</span></a> </div> </div> <sup>44</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Meyer%20F%22%5BAuthor%5D" class="usa-link" aria-describedby="id62"><span class="name western">Folker Meyer</span></a><div hidden="hidden" id="id62"> <h3><span class="name western">Folker Meyer</span></h3> <div class="p"> <sup>10</sup>Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Meyer%20F%22%5BAuthor%5D" class="usa-link"><span class="name western">Folker Meyer</span></a> </div> </div> <sup>10</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Muegge%20B%22%5BAuthor%5D" class="usa-link" aria-describedby="id63"><span class="name western">Brian Muegge</span></a><div hidden="hidden" id="id63"> <h3><span class="name western">Brian Muegge</span></h3> <div class="p"> <sup>35</sup>Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Muegge%20B%22%5BAuthor%5D" class="usa-link"><span class="name western">Brian Muegge</span></a> </div> </div> <sup>35</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Nakielny%20S%22%5BAuthor%5D" class="usa-link" aria-describedby="id64"><span class="name western">Sara Nakielny</span></a><div hidden="hidden" id="id64"> <h3><span class="name western">Sara Nakielny</span></h3> <div class="p"> <sup>4</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Nakielny%20S%22%5BAuthor%5D" class="usa-link"><span class="name western">Sara Nakielny</span></a> </div> </div> <sup>4</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Nelson%20KE%22%5BAuthor%5D" class="usa-link" aria-describedby="id65"><span class="name western">Karen E Nelson</span></a><div hidden="hidden" id="id65"> <h3><span class="name western">Karen E Nelson</span></h3> <div class="p"> <sup>44</sup>J. Craig Venter Institute, Rockville, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Nelson%20KE%22%5BAuthor%5D" class="usa-link"><span class="name western">Karen E Nelson</span></a> </div> </div> <sup>44</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Nemergut%20D%22%5BAuthor%5D" class="usa-link" aria-describedby="id66"><span class="name western">Diana Nemergut</span></a><div hidden="hidden" id="id66"> <h3><span class="name western">Diana Nemergut</span></h3> <div class="p"> <sup>45</sup>Department of Environmental Sciences, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Nemergut%20D%22%5BAuthor%5D" class="usa-link"><span class="name western">Diana Nemergut</span></a> </div> </div> <sup>45</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Neufeld%20JD%22%5BAuthor%5D" class="usa-link" aria-describedby="id67"><span class="name western">Josh D Neufeld</span></a><div hidden="hidden" id="id67"> <h3><span class="name western">Josh D Neufeld</span></h3> <div class="p"> <sup>46</sup>Department of Biology, University of Waterloo, Ontario, Canada.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Neufeld%20JD%22%5BAuthor%5D" class="usa-link"><span class="name western">Josh D Neufeld</span></a> </div> </div> <sup>46</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Newbold%20LK%22%5BAuthor%5D" class="usa-link" aria-describedby="id68"><span class="name western">Lindsay K Newbold</span></a><div hidden="hidden" id="id68"> <h3><span class="name western">Lindsay K Newbold</span></h3> <div class="p"> <sup>3</sup>Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Newbold%20LK%22%5BAuthor%5D" class="usa-link"><span class="name western">Lindsay K Newbold</span></a> </div> </div> <sup>3</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Oliver%20AE%22%5BAuthor%5D" class="usa-link" aria-describedby="id69"><span class="name western">Anna E Oliver</span></a><div hidden="hidden" id="id69"> <h3><span class="name western">Anna E Oliver</span></h3> <div class="p"> <sup>3</sup>Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Oliver%20AE%22%5BAuthor%5D" class="usa-link"><span class="name western">Anna E Oliver</span></a> </div> </div> <sup>3</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Pace%20NR%22%5BAuthor%5D" class="usa-link" aria-describedby="id70"><span class="name western">Norman R Pace</span></a><div hidden="hidden" id="id70"> <h3><span class="name western">Norman R Pace</span></h3> <div class="p"> <sup>18</sup>Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Pace%20NR%22%5BAuthor%5D" class="usa-link"><span class="name western">Norman R Pace</span></a> </div> </div> <sup>18</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Palanisamy%20G%22%5BAuthor%5D" class="usa-link" aria-describedby="id71"><span class="name western">Giriprakash Palanisamy</span></a><div hidden="hidden" id="id71"> <h3><span class="name western">Giriprakash Palanisamy</span></h3> <div class="p"> <sup>47</sup>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Palanisamy%20G%22%5BAuthor%5D" class="usa-link"><span class="name western">Giriprakash Palanisamy</span></a> </div> </div> <sup>47</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Peplies%20J%22%5BAuthor%5D" class="usa-link" aria-describedby="id72"><span class="name western">Jörg Peplies</span></a><div hidden="hidden" id="id72"> <h3><span class="name western">Jörg Peplies</span></h3> <div class="p"> <sup>48</sup>Ribocon GmbH, Bremen, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Peplies%20J%22%5BAuthor%5D" class="usa-link"><span class="name western">Jörg Peplies</span></a> </div> </div> <sup>48</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Petrosino%20J%22%5BAuthor%5D" class="usa-link" aria-describedby="id73"><span class="name western">Joseph Petrosino</span></a><div hidden="hidden" id="id73"> <h3><span class="name western">Joseph Petrosino</span></h3> <div class="p"> <sup>31</sup>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.</div> <div class="p"> <sup>37</sup>Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Petrosino%20J%22%5BAuthor%5D" class="usa-link"><span class="name western">Joseph Petrosino</span></a> </div> </div> <sup>31,</sup><sup>37</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Proctor%20L%22%5BAuthor%5D" class="usa-link" aria-describedby="id74"><span class="name western">Lita Proctor</span></a><div hidden="hidden" id="id74"> <h3><span class="name western">Lita Proctor</span></h3> <div class="p"> <sup>21</sup>National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Proctor%20L%22%5BAuthor%5D" class="usa-link"><span class="name western">Lita Proctor</span></a> </div> </div> <sup>21</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Pruesse%20E%22%5BAuthor%5D" class="usa-link" aria-describedby="id75"><span class="name western">Elmar Pruesse</span></a><div hidden="hidden" id="id75"> <h3><span class="name western">Elmar Pruesse</span></h3> <div class="p"> <sup>1</sup>Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.</div> <div class="p"> <sup>2</sup>Jacobs University Bremen gGmbH, Bremen, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Pruesse%20E%22%5BAuthor%5D" class="usa-link"><span class="name western">Elmar Pruesse</span></a> </div> </div> <sup>1,</sup><sup>2</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Quast%20C%22%5BAuthor%5D" class="usa-link" aria-describedby="id76"><span class="name western">Christian Quast</span></a><div hidden="hidden" id="id76"> <h3><span class="name western">Christian Quast</span></h3> <div class="p"> <sup>1</sup>Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Quast%20C%22%5BAuthor%5D" class="usa-link"><span class="name western">Christian Quast</span></a> </div> </div> <sup>1</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Raes%20J%22%5BAuthor%5D" class="usa-link" aria-describedby="id77"><span class="name western">Jeroen Raes</span></a><div hidden="hidden" id="id77"> <h3><span class="name western">Jeroen Raes</span></h3> <div class="p"> <sup>49</sup>VIB - Vrije Universiteit Brussel, Brussels, Belgium.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Raes%20J%22%5BAuthor%5D" class="usa-link"><span class="name western">Jeroen Raes</span></a> </div> </div> <sup>49</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ratnasingham%20S%22%5BAuthor%5D" class="usa-link" aria-describedby="id78"><span class="name western">Sujeevan Ratnasingham</span></a><div hidden="hidden" id="id78"> <h3><span class="name western">Sujeevan Ratnasingham</span></h3> <div class="p"> <sup>50</sup>Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ratnasingham%20S%22%5BAuthor%5D" class="usa-link"><span class="name western">Sujeevan Ratnasingham</span></a> </div> </div> <sup>50</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ravel%20J%22%5BAuthor%5D" class="usa-link" aria-describedby="id79"><span class="name western">Jacques Ravel</span></a><div hidden="hidden" id="id79"> <h3><span class="name western">Jacques Ravel</span></h3> <div class="p"> <sup>25</sup>Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ravel%20J%22%5BAuthor%5D" class="usa-link"><span class="name western">Jacques Ravel</span></a> </div> </div> <sup>25</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Relman%20DA%22%5BAuthor%5D" class="usa-link" aria-describedby="id80"><span class="name western">David A Relman</span></a><div hidden="hidden" id="id80"> <h3><span class="name western">David A Relman</span></h3> <div class="p"> <sup>51</sup>Departments of Microbiology and Immunology and Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.</div> <div class="p"> <sup>52</sup>Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Relman%20DA%22%5BAuthor%5D" class="usa-link"><span class="name western">David A Relman</span></a> </div> </div> <sup>51,</sup><sup>52</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Assunta-Sansone%20S%22%5BAuthor%5D" class="usa-link" aria-describedby="id81"><span class="name western">Susanna Assunta-Sansone</span></a><div hidden="hidden" id="id81"> <h3><span class="name western">Susanna Assunta-Sansone</span></h3> <div class="p"> <sup>16</sup>Oxford e-Research Centre, University of Oxford, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Assunta-Sansone%20S%22%5BAuthor%5D" class="usa-link"><span class="name western">Susanna Assunta-Sansone</span></a> </div> </div> <sup>16</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Schloss%20PD%22%5BAuthor%5D" class="usa-link" aria-describedby="id82"><span class="name western">Patrick D Schloss</span></a><div hidden="hidden" id="id82"> <h3><span class="name western">Patrick D Schloss</span></h3> <div class="p"> <sup>53</sup>Department of Microbiology and Immunology, Ann Arbor, Michigan, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Schloss%20PD%22%5BAuthor%5D" class="usa-link"><span class="name western">Patrick D Schloss</span></a> </div> </div> <sup>53</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Schriml%20L%22%5BAuthor%5D" class="usa-link" aria-describedby="id83"><span class="name western">Lynn Schriml</span></a><div hidden="hidden" id="id83"> <h3><span class="name western">Lynn Schriml</span></h3> <div class="p"> <sup>25</sup>Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Schriml%20L%22%5BAuthor%5D" class="usa-link"><span class="name western">Lynn Schriml</span></a> </div> </div> <sup>25</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Sinha%20R%22%5BAuthor%5D" class="usa-link" aria-describedby="id84"><span class="name western">Rohini Sinha</span></a><div hidden="hidden" id="id84"> <h3><span class="name western">Rohini Sinha</span></h3> <div class="p"> <sup>22</sup>Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Sinha%20R%22%5BAuthor%5D" class="usa-link"><span class="name western">Rohini Sinha</span></a> </div> </div> <sup>22</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Smith%20MI%22%5BAuthor%5D" class="usa-link" aria-describedby="id85"><span class="name western">Michelle I Smith</span></a><div hidden="hidden" id="id85"> <h3><span class="name western">Michelle I Smith</span></h3> <div class="p"> <sup>35</sup>Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Smith%20MI%22%5BAuthor%5D" class="usa-link"><span class="name western">Michelle I Smith</span></a> </div> </div> <sup>35</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Sodergren%20E%22%5BAuthor%5D" class="usa-link" aria-describedby="id86"><span class="name western">Erica Sodergren</span></a><div hidden="hidden" id="id86"> <h3><span class="name western">Erica Sodergren</span></h3> <div class="p"> <sup>54</sup>The Genome Center, Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Sodergren%20E%22%5BAuthor%5D" class="usa-link"><span class="name western">Erica Sodergren</span></a> </div> </div> <sup>54</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Spor%20A%22%5BAuthor%5D" class="usa-link" aria-describedby="id87"><span class="name western">Aymé Spor</span></a><div hidden="hidden" id="id87"> <h3><span class="name western">Aymé Spor</span></h3> <div class="p"> <sup>41</sup>Department of Microbiology, Cornell University, Ithaca, New York, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Spor%20A%22%5BAuthor%5D" class="usa-link"><span class="name western">Aymé Spor</span></a> </div> </div> <sup>41</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Stombaugh%20J%22%5BAuthor%5D" class="usa-link" aria-describedby="id88"><span class="name western">Jesse Stombaugh</span></a><div hidden="hidden" id="id88"> <h3><span class="name western">Jesse Stombaugh</span></h3> <div class="p"> <sup>4</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Stombaugh%20J%22%5BAuthor%5D" class="usa-link"><span class="name western">Jesse Stombaugh</span></a> </div> </div> <sup>4</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Tiedje%20JM%22%5BAuthor%5D" class="usa-link" aria-describedby="id89"><span class="name western">James M Tiedje</span></a><div hidden="hidden" id="id89"> <h3><span class="name western">James M Tiedje</span></h3> <div class="p"> <sup>7</sup>Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Tiedje%20JM%22%5BAuthor%5D" class="usa-link"><span class="name western">James M Tiedje</span></a> </div> </div> <sup>7</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ward%20DV%22%5BAuthor%5D" class="usa-link" aria-describedby="id90"><span class="name western">Doyle V Ward</span></a><div hidden="hidden" id="id90"> <h3><span class="name western">Doyle V Ward</span></h3> <div class="p"> <sup>19</sup>Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Ward%20DV%22%5BAuthor%5D" class="usa-link"><span class="name western">Doyle V Ward</span></a> </div> </div> <sup>19</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Weinstock%20GM%22%5BAuthor%5D" class="usa-link" aria-describedby="id91"><span class="name western">George M Weinstock</span></a><div hidden="hidden" id="id91"> <h3><span class="name western">George M Weinstock</span></h3> <div class="p"> <sup>54</sup>The Genome Center, Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Weinstock%20GM%22%5BAuthor%5D" class="usa-link"><span class="name western">George M Weinstock</span></a> </div> </div> <sup>54</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Wendel%20D%22%5BAuthor%5D" class="usa-link" aria-describedby="id92"><span class="name western">Doug Wendel</span></a><div hidden="hidden" id="id92"> <h3><span class="name western">Doug Wendel</span></h3> <div class="p"> <sup>4</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Wendel%20D%22%5BAuthor%5D" class="usa-link"><span class="name western">Doug Wendel</span></a> </div> </div> <sup>4</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22White%20O%22%5BAuthor%5D" class="usa-link" aria-describedby="id93"><span class="name western">Owen White</span></a><div hidden="hidden" id="id93"> <h3><span class="name western">Owen White</span></h3> <div class="p"> <sup>25</sup>Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22White%20O%22%5BAuthor%5D" class="usa-link"><span class="name western">Owen White</span></a> </div> </div> <sup>25</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Whiteley%20A%22%5BAuthor%5D" class="usa-link" aria-describedby="id94"><span class="name western">Andrew Whiteley</span></a><div hidden="hidden" id="id94"> <h3><span class="name western">Andrew Whiteley</span></h3> <div class="p"> <sup>3</sup>Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Whiteley%20A%22%5BAuthor%5D" class="usa-link"><span class="name western">Andrew Whiteley</span></a> </div> </div> <sup>3</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Wilke%20A%22%5BAuthor%5D" class="usa-link" aria-describedby="id95"><span class="name western">Andreas Wilke</span></a><div hidden="hidden" id="id95"> <h3><span class="name western">Andreas Wilke</span></h3> <div class="p"> <sup>10</sup>Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Wilke%20A%22%5BAuthor%5D" class="usa-link"><span class="name western">Andreas Wilke</span></a> </div> </div> <sup>10</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Wortman%20JR%22%5BAuthor%5D" class="usa-link" aria-describedby="id96"><span class="name western">Jennifer R Wortman</span></a><div hidden="hidden" id="id96"> <h3><span class="name western">Jennifer R Wortman</span></h3> <div class="p"> <sup>25</sup>Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Wortman%20JR%22%5BAuthor%5D" class="usa-link"><span class="name western">Jennifer R Wortman</span></a> </div> </div> <sup>25</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Yatsunenko%20T%22%5BAuthor%5D" class="usa-link" aria-describedby="id97"><span class="name western">Tanya Yatsunenko</span></a><div hidden="hidden" id="id97"> <h3><span class="name western">Tanya Yatsunenko</span></h3> <div class="p"> <sup>35</sup>Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Yatsunenko%20T%22%5BAuthor%5D" class="usa-link"><span class="name western">Tanya Yatsunenko</span></a> </div> </div> <sup>35</sup>, <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gl%C3%B6ckner%20FO%22%5BAuthor%5D" class="usa-link" aria-describedby="id98"><span class="name western">Frank Oliver Glöckner</span></a><div hidden="hidden" id="id98"> <h3><span class="name western">Frank Oliver Glöckner</span></h3> <div class="p"> <sup>1</sup>Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.</div> <div class="p"> <sup>2</sup>Jacobs University Bremen gGmbH, Bremen, Germany.</div> <div class="p">Find articles by <a href="https://pubmed.ncbi.nlm.nih.gov/?term=%22Gl%C3%B6ckner%20FO%22%5BAuthor%5D" class="usa-link"><span class="name western">Frank Oliver Glöckner</span></a> </div> </div> <sup>1,</sup><sup>2</sup> </div> <ul class="d-buttons inline-list"> <li><button class="d-button" aria-controls="aip_a" aria-expanded="false">Author information</button></li> <li><button class="d-button" aria-controls="clp_a" aria-expanded="false">Copyright and License information</button></li> </ul> <div class="d-panels font-secondary-light"> <div id="aip_a" class="d-panel p" style="display: none"> <div class="p" id="A1"> <sup>1</sup>Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.</div> <div id="A2"> <sup>2</sup>Jacobs University Bremen gGmbH, Bremen, Germany.</div> <div id="A3"> <sup>3</sup>Natural Environment Research Council Environmental Bioinformatics Centre, Wallington CEH, Oxford, UK.</div> <div id="A4"> <sup>4</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA.</div> <div id="A5"> <sup>5</sup>Howard Hughes Medical Institute, San Francisco, California, USA.</div> <div id="A6"> <sup>6</sup>Ribosomal Database Project, Michigan State University, East Lansing, Michigan, USA.</div> <div id="A7"> <sup>7</sup>Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA.</div> <div id="A8"> <sup>8</sup>The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA.</div> <div id="A9"> <sup>9</sup>Plymouth Marine Laboratory, Plymouth, UK.</div> <div id="A10"> <sup>10</sup>Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.</div> <div id="A11"> <sup>11</sup>Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.</div> <div id="A12"> <sup>12</sup>National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.</div> <div id="A13"> <sup>13</sup>European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.</div> <div id="A14"> <sup>14</sup>WCU Center for Green Metagenomics, School of Civil and Environmental Engineering, Yonsei University, Seoul, Republic of Korea.</div> <div id="A15"> <sup>15</sup>School of Computer Science, University of Manchester, Manchester, UK.</div> <div id="A16"> <sup>16</sup>Oxford e-Research Centre, University of Oxford, Oxford, UK.</div> <div id="A17"> <sup>17</sup>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.</div> <div id="A18"> <sup>18</sup>Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA.</div> <div id="A19"> <sup>19</sup>Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.</div> <div id="A20"> <sup>20</sup>Department of Medicine and the Department of Microbiology, New York University Langone Medical Center, New York, New York, USA.</div> <div id="A21"> <sup>21</sup>National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.</div> <div id="A22"> <sup>22</sup>Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.</div> <div id="A23"> <sup>23</sup>DOE Joint Genome Institute, Walnut Creek, California, USA.</div> <div id="A24"> <sup>24</sup>Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.</div> <div id="A25"> <sup>25</sup>Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.</div> <div id="A26"> <sup>26</sup>Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium.</div> <div id="A27"> <sup>27</sup>Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, California, USA.</div> <div id="A28"> <sup>28</sup>Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.</div> <div id="A29"> <sup>29</sup>Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.</div> <div id="A30"> <sup>30</sup>National Ecological Observatory Network, Boulder, Colorado, USA.</div> <div id="A31"> <sup>31</sup>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.</div> <div id="A32"> <sup>32</sup>Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.</div> <div id="A33"> <sup>33</sup>Department of Biology, University of New Mexico, LTER Network Office, Albuquerque, New Mexico, USA.</div> <div id="A34"> <sup>34</sup>Department of Computer Science, University of Colorado, Boulder, Colorado, USA.</div> <div id="A35"> <sup>35</sup>Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.</div> <div id="A36"> <sup>36</sup>University of Colorado Museum of Natural History, University of Colorado, Boulder, Colorado, USA.</div> <div id="A37"> <sup>37</sup>Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.</div> <div id="A38"> <sup>38</sup>Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.</div> <div id="A39"> <sup>39</sup>Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.</div> <div id="A40"> <sup>40</sup>Department of Biology, San Diego State University, San Diego, California, USA.</div> <div id="A41"> <sup>41</sup>Department of Microbiology, Cornell University, Ithaca, New York, USA.</div> <div id="A42"> <sup>42</sup>Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.</div> <div id="A43"> <sup>43</sup>Lehrstuhl für Mikrobiologie, Technische Universität München, Freising, Germany.</div> <div id="A44"> <sup>44</sup>J. Craig Venter Institute, Rockville, Maryland, USA.</div> <div id="A45"> <sup>45</sup>Department of Environmental Sciences, University of Colorado, Boulder, Colorado, USA.</div> <div id="A46"> <sup>46</sup>Department of Biology, University of Waterloo, Ontario, Canada.</div> <div id="A47"> <sup>47</sup>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.</div> <div id="A48"> <sup>48</sup>Ribocon GmbH, Bremen, Germany.</div> <div id="A49"> <sup>49</sup>VIB - Vrije Universiteit Brussel, Brussels, Belgium.</div> <div id="A50"> <sup>50</sup>Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.</div> <div id="A51"> <sup>51</sup>Departments of Microbiology and Immunology and Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.</div> <div id="A52"> <sup>52</sup>Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA.</div> <div id="A53"> <sup>53</sup>Department of Microbiology and Immunology, Ann Arbor, Michigan, USA.</div> <div id="A54"> <sup>54</sup>The Genome Center, Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.</div> <div class="author-notes p"><div class="fn" id="cor1"> <sup>✉</sup><p class="display-inline">Correspondence should be addressed to F.O.G. (<span>fog@mpi-bremen.de</span>)</p> </div></div> </div> <div id="clp_a" class="d-panel p" style="display: none"> <div>© 2011 Nature America, Inc. All rights reserved.</div> <div class="p"><a href="/about/copyright/" class="usa-link">PMC Copyright notice</a></div> </div> </div> <div>PMCID: PMC3367316 NIHMSID: NIHMS370143 PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/21552244/" class="usa-link">21552244</a> </div> <div class="ra xbox p" role="complementary" aria-label="Related or updated information about this article"><div>The publisher's version of this article is available at <a href="https://doi.org/10.1038/nbt.1823" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">Nat Biotechnol</a> </div></div> </div></section></section><section aria-label="Article content"><section class="body main-article-body"><section class="abstract" id="abstract1"><h2>Abstract</h2> <p id="P1">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.</p></section><hr class="headless"> <p id="P2">Without specific guidelines, most genomic, metagenomic and marker gene sequences in databases are sparsely annotated with the information required to guide data integration, comparative studies and knowledge generation. Even with complex keyword searches, it is currently impossible to reliably retrieve sequences that have originated from certain environments or particular locations on Earth—for example, all sequences from ‘soil’ or ‘freshwater lakes’ in a certain region of the world. Because public databases of the International Nucleotide Sequence Database Collaboration (INSDC; comprising DNA Data Bank of Japan (DDBJ), the European Nucleotide Archive (EBI-ENA) and GenBank (<a href="http://www.insdc.org/" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://www.insdc.org/</a>)) depend on author-submitted information to enrich the value of sequence data sets, we argue that the only way to change the current practice is to establish a standard of reporting that requires contextual data to be deposited at the time of sequence submission. The adoption of such a standard would elevate the quality, accessibility and utility of information that can be collected from INSDC or any other data repository.</p> <p id="P3">The GSC has previously proposed standards for describing genomic sequences— the “minimum information about a genome sequence” (MIGS)—and metagenomic sequences—the “minimum information about a metagenome sequence” (MIMS)<sup><a href="#R1" class="usa-link" aria-describedby="R1">1</a></sup>. Here we introduce an extension of these standards for capturing information about marker genes. Additionally, we introduce ‘environmental packages’ that standardize sets of measurements and observations describing particular habitats that are applicable across all GSC checklists and beyond<sup><a href="#R2" class="usa-link" aria-describedby="R2">2</a></sup>. We define ‘environment’ as any location in which a sample or organism is found, e.g., soil, air, water, human-associated, plant-associated or laboratory. The original MIGS/MIMS checklists included contextual data about the location from which a sample was isolated and how the sequence data were produced. However, standard descriptions for a more comprehensive range of environmental parameters, which would help to better contextualize a sample, were not included. The environmental packages presented here are relevant to any genome sequence of known origin and are designed to be used in combination with MIGS, MIMS and MIMARKS checklists.</p> <p id="P4">To create a single entry point to all minimum information checklists from the GSC and to the environmental packages, we propose an overarching framework, the MIxS standard (<a href="http://gensc.org/gc_wiki/index.php/MIxS" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://gensc.org/gc_wiki/index.php/MIxS</a>). MIxS includes the technology-specific checklists from the previous MIGS and MIMS standards, provides a way of introducing additional checklists such as MIMARKS, and also allows annotation of sample data using environmental packages. A schematic overview of MIxS along with the MIxS environmental packages is shown in <a href="#F1" class="usa-link">Figure 1</a>.</p> <figure class="fig xbox font-sm" id="F1"><h2 class="obj_head">Figure 1.</h2> <p class="img-box line-height-none margin-x-neg-2 tablet:margin-x-0 text-center"><a class="tileshop" target="_blank" href="https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=3367316_nihms370143f1.jpg"><img class="graphic zoom-in" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed1c/3367316/96b63e8e9957/nihms370143f1.jpg" loading="lazy" height="776" width="1050" alt="Figure 1"></a></p> <div class="p text-right font-secondary"><a href="figure/F1/" class="usa-link" target="_blank" rel="noopener noreferrer">Open in a new tab</a></div> <figcaption><p id="P26">Schematic overview about the GSC MIxS standard (brown), including combination with specific environmental packages (blue). Shared descriptors apply to all MIxS checklists; however, each checklist has its own specific descriptors as well. Environmental packages can be applied to any of the checklists. EU, eukarya; BA, bacteria/archaea; PL, plasmid; VI, virus; ORG, organelle.</p></figcaption></figure><section id="S1"><h2 class="pmc_sec_title">Development of MIMARKS and the environmental packages</h2> <p id="P5">Over the past three decades, the 16S rRNA, 18S rRNA and internal transcribed spacer gene sequences (ITS) from <em>Bacteria</em>, <em>Archaea</em> and microbial <em>Eukaryotes</em> have provided deep insights into the topology of the tree of life<sup><a href="#R3" class="usa-link" aria-describedby="R3">3</a>,<a href="#R4" class="usa-link" aria-describedby="R4">4</a></sup> and the composition of communities of organisms that live in diverse environments, ranging from deep sea hydrothermal vents to ice sheets in the Arctic<sup><a href="#R5" class="usa-link" aria-describedby="R5">5</a>–<a href="#R16" class="usa-link" aria-describedby="R16">16</a></sup>. Numerous other phylogenetic marker genes have proven useful, including RNA polymerase subunits (<em>rpoB</em>), DNA gyrases (<em>gyrB</em>), DNA recombination and repair proteins (<em>recA</em>) and heat shock proteins (<em>HSP70</em>)<sup><a href="#R3" class="usa-link" aria-describedby="R3">3</a></sup>. Marker genes can also reveal key metabolic functions rather than phylogeny; examples include nitrogen cycling (<em>amoA, nifH, ntcA</em>)<sup><a href="#R17" class="usa-link" aria-describedby="R17">17</a>,<a href="#R18" class="usa-link" aria-describedby="R18">18</a></sup>, sulfate reduction (<em>dsrAB</em>)<sup><a href="#R19" class="usa-link" aria-describedby="R19">19</a></sup> or phosphorus metabolism (<em>phnA, phnI, phnJ</em>)<sup><a href="#R20" class="usa-link" aria-describedby="R20">20</a>,<a href="#R21" class="usa-link" aria-describedby="R21">21</a></sup>. In this paper we define all phylogenetic and functional genes (or gene fragments) used to profile natural genetic diversity as ‘marker genes’. MIMARKS (<a href="#T1" class="usa-link">Table 1</a>) complements the MIGS/MIMS checklists for genomes and metagenomes by adding two new checklists, a MIMARKS survey, for uncultured diversity marker gene surveys, and a MIMARKS specimen, for marker gene sequences obtained from any material identifiable by means of specimens. The MIMARKS extension adopts and incorporates the standards being developed by the Consortium for the Barcode of Life (CBOL)<sup><a href="#R22" class="usa-link" aria-describedby="R22">22</a></sup>. Therefore, the checklist can be universally applied to any marker gene, from small subunit rRNA to cytochrome oxidase I (COI), to all taxa, and to studies ranging from single individuals to complex communities.</p> <section class="tw xbox font-sm" id="T1"><h3 class="obj_head">Table 1.</h3> <div class="caption p"><p id="P27">The core items of the MIMARKS checklists, along with the value types, descriptions and requirement status</p></div> <div class="tbl-box p" tabindex="0"><table class="content" frame="hsides" rules="groups"> <thead> <tr> <th align="left" rowspan="1" colspan="1"></th> <th align="left" rowspan="1" colspan="1"></th> <th align="center" colspan="2" rowspan="1">Report type</th> </tr> <tr> <th align="left" rowspan="1" colspan="1"></th> <th align="left" rowspan="1" colspan="1"></th> <th align="center" colspan="2" valign="bottom" rowspan="1"><hr></th> </tr> <tr> <th align="left" valign="bottom" rowspan="1" colspan="1">Item</th> <th align="left" valign="bottom" rowspan="1" colspan="1">Description</th> <th align="center" rowspan="1" colspan="1">MIMARKS<br>survey</th> <th align="center" rowspan="1" colspan="1">MIMARKS<br>specimen</th> </tr> </thead> <tbody> <tr> <td align="left" rowspan="1" colspan="1"><strong>Investigation</strong></td> <td align="left" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Submitted to INSDC<sup>[boolean]</sup> </td> <td align="left" valign="top" rowspan="1" colspan="1">Depending on the study (large-scale, e.g., done with next-generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archives), DRA (DDBJ Sequence Read Archive) or through the classical Webin/Sequin systems to GenBank, ENA and DDBJ</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Investigation type<sup>[mimarks-survey or mimarks-specimen]</sup> </td> <td align="left" valign="top" rowspan="1" colspan="1">Nucleic Acid Sequence Report is the root element of all MIMARKS compliant reports as standardized by Genomic Standards Consortium (GSC). This field is either MIMARKS survey or MIMARKS specimen</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Project name</td> <td align="left" valign="top" rowspan="1" colspan="1">Name of the project within which the sequencing was organized</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" rowspan="1" colspan="1"><strong>Environment</strong></td> <td align="left" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Geographic location (latitude and longitude<sup>[float, point, transect and region]</sup>)</td> <td align="left" valign="top" rowspan="1" colspan="1">The geographical origin of the sample as defined by latitude and longitude.<br>The values should be reported in decimal degrees and in WGS84 system</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Geographic location (depth<sup>[integer, point, interval, unit]</sup>)</td> <td align="left" valign="top" rowspan="1" colspan="1">Please refer to the definitions of depth in the environmental packages</td> <td align="center" valign="top" rowspan="1" colspan="1">E</td> <td align="center" valign="top" rowspan="1" colspan="1">E</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Geographic location (elevation of site<sup>[integer, unit]</sup>; altitude of sample<sup>[integer, unit]</sup>)</td> <td align="left" valign="top" rowspan="1" colspan="1">Please refer to the definitions of either altitude or elevation in the environmental packages</td> <td align="center" valign="top" rowspan="1" colspan="1">E</td> <td align="center" valign="top" rowspan="1" colspan="1">E</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Geographic location (country and/or sea<sup>[INSDC or GAZ]</sup>; region<sup>[GAZ]</sup>)</td> <td align="left" valign="top" rowspan="1" colspan="1">The geographical origin of the sample as defined by the country or sea name. Country, sea or region names should be chosen from the INSDC list (<a href="http://insdc.org/country.html" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://insdc.org/country.html</a>), or the GAZ (Gazetteer, v1.446) ontology (<a href="http://bioportal.bioontology.org/visualize/40651" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://bioportal.bioontology.org/visualize/40651</a>)</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Collection date<sup>[ISO8601]</sup> </td> <td align="left" valign="top" rowspan="1" colspan="1">The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated, that is, all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; except for 2008-01 and 2008, all are ISO6801 compliant</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Environment (biome<sup>[EnvO]</sup>)</td> <td align="left" valign="top" rowspan="1" colspan="1">In environmental biome level are the major classes of ecologically similar communities of plants, animals and other organisms. Biomes are defined based on factors such as plant structures, leaf types, plant spacing and other factors like climate. Examples include desert, taiga, deciduous woodland or coral reef. Environment Ontology (EnvO) (v1.53) terms listed under environmental biome can be found at <a href="http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00000428" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00000428</a> </td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Environment (feature<sup>[EnvO]</sup>)</td> <td align="left" valign="top" rowspan="1" colspan="1">Environmental feature level includes geographic environmental features. Examples include harbor, cliff or lake. EnvO (v1.53) terms listed under environmental feature can be found at <a href="http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00002297" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00002297</a> </td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Environment (material<sup>[EnvO]</sup>)</td> <td align="left" valign="top" rowspan="1" colspan="1">The environmental material level refers to the matter that was displaced by the sample, before the sampling event. Environmental matter terms are generally mass nouns. Examples include: air, soil or water. EnvO (v1.53) terms listed under environmental matter can be found at <a href="http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00010483" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00010483</a> </td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" rowspan="1" colspan="1"><strong>MIGS/MIMS/MIMARKS extension</strong></td> <td align="left" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Environmental package<sup>[air, host-associated, human-associated, human-skin, human-oral, human-gut, human-vaginal, microbial mat/biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater/sludge, water]</sup> </td> <td align="left" valign="top" rowspan="1" colspan="1">MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" rowspan="1" colspan="1"><strong>Nucleic acid sequence source</strong></td> <td align="left" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Isolation and growth conditions<sup>[PMID, DOI or URL]</sup> </td> <td align="left" valign="top" rowspan="1" colspan="1">Publication reference in the form of PubMed ID (PMID), digital object identifier (DOI) or URL for isolation and growth condition specifications of the organism/material</td> <td align="center" valign="top" rowspan="1" colspan="1">–</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" rowspan="1" colspan="1"><strong>Sequencing</strong></td> <td align="left" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> <td align="center" rowspan="1" colspan="1"></td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Target gene or locus (e.g., 16S rRNA, 18S rRNA, nif, amoA, rpo)</td> <td align="left" valign="top" rowspan="1" colspan="1">Targeted gene or locus name for marker gene study</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> <tr> <td align="left" valign="top" rowspan="1" colspan="1"> Sequencing method (e.g., dideoxysequencing, pyrosequencing, polony)</td> <td align="left" valign="top" rowspan="1" colspan="1">Sequencing method used, e.g., Sanger, pyrosequencing, ABI-solid</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> <td align="center" valign="top" rowspan="1" colspan="1">M</td> </tr> </tbody> </table></div> <div class="p text-right font-secondary"><a href="table/T1/" class="usa-link" target="_blank" rel="noopener noreferrer">Open in a new tab</a></div> <div class="tw-foot p"><div class="fn" id="TFN1"><p id="P28">Items for the MIMARKS specification and their mandatory (M), status for both MIMARKS-survey and MIMARKS-specimen checklists. Furthermore, “–” denotes that an item is not applicable for a given checklist. E denotes that a field has environment-specific requirements. For example, whereas “depth” is mandatory for the environments water, sediment or soil, it is optional for human-associated environments. MIMARKS-survey is applicable to contextual data for marker gene sequences, obtained directly from the environment, without culturing or identification of the organisms. MIMARKS-specimen, on the other hand, applies to the contextual data for marker gene sequences from cultured or voucher-identifiable specimens. Both MIMARKS-survey and specimen checklists can be used for any type of marker gene sequence data, ranging from 16S, 18S, 23S, 28S rRNA to COI, hence the checklists are universal for all three domains of life. Item names are followed by a short description of the value of the item in parentheses and/or value type in brackets as a superscript. Whenever applicable, value types are chosen from a controlled vocabulary (CV) or an ontology from the Open Biological and Biomedical Ontologies (OBO) foundry (<a href="http://www.obofoundry.org/" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://www.obofoundry.org/</a>). This table only presents the very core of MIMARKS checklists, that is, only mandatory items for each checklist. <a href="#SD3" class="usa-link">Supplementary Results 2</a> contains all MIMARKS items, the tables for environmental packages in the MIGS/MIMS/MIMARKS extension and GenBank structured comment name that should be used for submitting MIMARKS data to GenBank. In case of submitting to EBI-ENA, the full names can be used.</p></div></div></section><p id="P6">Both MIMARKS and the environmental packages were developed by collating information from several sources and evaluating it in the framework of the existing MIGS/MIMS checklists. These include four independent community-led surveys, examination of the parameters reported in published studies and examination of compliance with optional features in INSDC documents. The overall goal of these activities was to design the backbone of the MIMARKS checklist, which describes the most important aspects of marker gene contextual data.</p></section><section id="S2"><h2 class="pmc_sec_title">Results of community-led surveys</h2> <p id="P7">Four online surveys about descriptors for marker genes have been conducted to determine researcher preferences for core descriptors. The Department of Energy Joint Genome Institute and SILVA<sup><a href="#R23" class="usa-link" aria-describedby="R23">23</a></sup> surveys focused on general descriptor contextual data for a marker gene, whereas the Ribosomal Database Project (RDP)<sup><a href="#R24" class="usa-link" aria-describedby="R24">24</a></sup> focused on prevalent habitats for rRNA gene surveys, and the Terragenome Consortium<sup><a href="#R25" class="usa-link" aria-describedby="R25">25</a></sup> focused on soil metagenome project contextual data (<a href="#SD2" class="usa-link">Supplementary Results 1</a>). The above recommendations were combined with an extensive set of contextual data items suggested by an International Census of Marine Microbes (ICoMM) working group that met in 2005. These collective resources provided valuable insights into community requests for contextual data items to be included in the MIMARKS checklist and the main habitats constituting the environmental packages.</p></section><section id="S3"><h2 class="pmc_sec_title">Survey of published parameters</h2> <p id="P8">We reviewed published rRNA gene studies, retrieved from SILVA and the ICoMM database MICROBIS (The Microbial Oceanic Biogeographic Information System, <a href="http://icomm.mbl.edu/microbis/" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://icomm.mbl.edu/microbis/</a>) to further supplement contextual data items that are included in the respective environmental packages. In total, 39 publications from SILVA and >40 ICoMM projects were scanned for contextual data items to constitute the core of the environmental package subtables (<a href="#SD2" class="usa-link">Supplementary Results 1</a>).</p> <p id="P9">In a final analysis step, we surveyed usage statistics of INSDC source feature key qualifier values of rRNA gene sequences contained in SILVA (<a href="#SD2" class="usa-link">Supplementary Results 1</a>). Notably, <10% of the 1.2 million 16S rRNA gene sequences (SILVA release 100) were associated with even basic information such as latitude and longitude, collection date or PCR primers.</p></section><section id="S4"><h2 class="pmc_sec_title">The MIMARKS checklist</h2> <p id="P10">The MIMARKS checklist provides users with an ‘electronic laboratory notebook’ containing core contextual data items required for consistent reporting of marker gene investigations. MIMARKS uses the MIGS/MIMS checklists with respect to the nucleic acid sequence source and sequencing contextual data, but extends them with further experimental contextual data such as PCR primers and conditions, or target gene name.</p> <p id="P11">For clarity and ease of use, all items within the MIMARKS checklist are presented with a value syntax description, as well as a clear definition of the item. Whenever terms from a specific ontology are required as the value of an item, these terms can be readily found in the respective ontology browsers linked by URLs in the item definition. Although this version of the MIMARKS checklist does not contain unit specifications, we recommend all units to be chosen from and follow the International System of Units (SI) recommendations. In addition, we strongly urge the community to provide feedback regarding the best unit recommendations for given parameters. Unit standardization across data sets will be vital to facilitate comparative studies in future. An Excel version of the MIMARKS checklist is provided on the GSC web site (<a href="http://gensc.org/gc_wiki/index.php/MIMARKS" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://gensc.org/gc_wiki/index.php/MIMARKS</a>).</p></section><section id="S5"><h2 class="pmc_sec_title">The MIxS environmental packages</h2> <p id="P12">Fourteen environmental packages provide a wealth of environmental and epidemiological contextual data fields for a complete description of sampling environments. The environmental packages can be combined with any of the GSC checklists (<a href="#F1" class="usa-link">Fig. 1</a> and <a href="#SD3" class="usa-link">Supplementary Results 2</a>). Researchers within The Human Microbiome Project<sup><a href="#R26" class="usa-link" aria-describedby="R26">26</a></sup> contributed the host-associated and all human packages. The Terragenome Consortium contributed sediment and soil packages. Finally, ICoMM, Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites and the Max Planck Institute for Marine Microbiology contributed the water package. The MIMARKS working group developed the remaining packages (air, microbial mat/biofilm, miscellaneous natural or artificial environment, plant-associated and wastewater/sludge). The package names describe high-level habitat terms in order to be exhaustive. The miscellaneous natural or artificial environment package contains a generic set of parameters, and is included for any other habitat that does not fall into the other thirteen categories. Whenever needed, multiple packages may be used for the description of the environment.</p></section><section id="S6"><h2 class="pmc_sec_title">Examples of MIMARKS-compliant data sets</h2> <p id="P13">Several MIMARKS-compliant reports are included in <a href="#SD4" class="usa-link">Supplementary Results 3</a>. These include a 16S rRNA gene survey from samples obtained in the North Atlantic, an 18S pyrosequencing tag study of anaerobic protists in a permanently anoxic basin of the North Sea, a <em>pmoA</em> survey from Negev Desert soils, a <em>dsrAB</em> survey of Gulf of Mexico sediments and a 16S pyrosequencing tag study of bacterial diversity in the western English Channel (SRA accession no. SRP001108).</p></section><section id="S7"><h2 class="pmc_sec_title">Adoption by major database and informatics resources</h2> <p id="P14">Support for adoption of MIMARKS and the MIxS standard has spread rapidly. Authors of this paper include representatives from genome sequencing centers, maintainers of major resources, principal investigators of large- and small-scale sequencing projects, and individual investigators who have provided compliant data sets, showing the breadth of support for the standard within the community.</p> <p id="P15">In the past, the INSDC has issued a reserved ‘barcode’ keyword for the CBOL<sup><a href="#R7" class="usa-link" aria-describedby="R7">7</a></sup>. Following this model, the INSDC has recently recognized the GSC as an authority for the MIxS standard and issued the standard with official keywords within INSDC nucleotide sequence records<sup><a href="#R27" class="usa-link" aria-describedby="R27">27</a></sup>. This greatly facilitates automatic validation of the submitted contextual data and provides support for data sets compliant with previous versions by including the checklist version as a keyword.</p> <p id="P16">GenBank accepts MIxS metadata in tabular format using the sequin and tbl2asn submission tools, validates MIxS compliance and reports the fields in the structured comment block. The EBI-ENA Webin submission system provides prepared web forms for the submission of MIxS compliant data; it presents all of the appropriate fields with descriptions, explanations and examples, and validates the data entered. One tool that can aid submitting contextual data is MetaBar<sup><a href="#R28" class="usa-link" aria-describedby="R28">28</a></sup>, a spreadsheet and web-based software, designed to assist users in the consistent acquisition, electronic storage and submission of contextual data associated with their samples in compliance with the MIxS standard. The online tool CDinFusion (<a href="http://www.megx.net/CDinFusion" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://www.megx.net/CDinFusion</a>) was created to facilitate the combination of contextual data with sequence data, and generation of submission-ready files.</p> <p id="P17">The next-generation Sequence Read Archive (SRA) collects and displays MIxS-compliant metadata in sample and experiment objects. There are several tools that are already available or under development to assist users in SRA submissions. The myRDP SRA PrepKit allows users to prepare and edit their submissions of reads generated from ultra-high-throughput sequencing technologies. A set of suggested attributes in the data forms assist researchers in providing metadata conforming to checklists such as MIMARKS. The Quantitative Insights Into Microbial Ecology (QIIME) web application (<a href="http://www.microbio.me/qiime" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://www.microbio.me/qiime</a>) allows users to generate and validate MIMARKS-compliant templates. These templates can be viewed and completed in the users’ spreadsheet editor of choice (e.g., Microsoft Excel). The QIIME web-platform also offers an ontology lookup and geo-referencing tool to aid users when completing the MIMARKS templates. The Investigation/Study/Assay (ISA) is a software suite that assists in the curation, reporting and local management of experimental metadata from studies using one or a combination of technologies, including high-throughput sequencing<sup><a href="#R29" class="usa-link" aria-describedby="R29">29</a></sup>. Specific ISA configurations (<a href="http://isa-tools.org/tools.html" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://isa-tools.org/tools.html</a>) have been developed to ensure MIxS compliance by providing templates and validation capability. Another tool, ISAconverter, produces SRA.xml documents, facilitating submission to the SRA repository. MIxS checklists are also registered with the BioSharing catalog of standards (<a href="http://biosharing.org/" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://biosharing.org/</a>), set to progressively link minimal information specifications to the respective exchange formats, ontologies and compliant tools.</p> <p id="P18">Further detailed guidance for submission processes can be found under the respective wiki pages (<a href="http://gensc.org/gc_wiki/index.php/MIxS" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://gensc.org/gc_wiki/index.php/MIxS</a>) of the standard.</p></section><section id="S8"><h2 class="pmc_sec_title">Maintenance of the MIxS standard</h2> <p id="P19">To allow further developments, extensions and enhancements of MIxS, we set up a public issue tracking system to track changes and accomplish feature requests (<a href="http://mixs.gensc.org/" class="usa-link usa-link--external" data-ga-action="click_feat_suppl" target="_blank" rel="noopener noreferrer">http://mixs.gensc.org/</a>). New versions will be released annually. Technically, the MIxS standard, including MIMARKS and the environmental packages, is maintained in a relational database system at the Max Planck Institute for Marine Microbiology Bremen on behalf of the GSC. This provides a secure and stable mechanism for updating the checklist suite and versioning. In the future, we plan to develop programmatic access to this database to allow automatic retrieval of the latest version of each checklist for INSDC databases and for GSC community resources. Moreover, the Genomic Contextual Data Markup Language is a reference implementation of the GSC checklists by the GSC and now implements the full range of MIxS standards. It is based on XML Schema technology and thus serves as an interoperable data exchange format for infrastructures based on web services<sup><a href="#R30" class="usa-link" aria-describedby="R30">30</a></sup>.</p></section><section id="S9"><h2 class="pmc_sec_title">Conclusions and call for action</h2> <p id="P20">The GSC is an international body with a stated mission of working towards richer descriptions of the complete collection of genomes and metagenomes through the MIxS standard. The present report extends the scope of GSC guidelines to marker gene sequences and environmental packages and establishes a single portal where experimentalists can gain access to and learn how to use GSC guidelines. The GSC is an open initiative that welcomes the participation of the wider community. This includes an open call to contribute to refinements of the MIxS standards and their implementations.</p> <p id="P21">The adoption of the GSC standards by major data providers and organizations, as well as the INSDC, supports efforts to contextually enrich sequence data and complements recent efforts to enrich other (meta) ‘omics data. The MIxS standard, including MIMARKS, has been developed to the point that it is ready for use in the publication of sequences. A defined procedure for requesting new features and stable release cycles will facilitate implementation of the standard across the community. Compliance among authors, adoption by journals and use by informatics resources will vastly improve our collective ability to mine and integrate invaluable sequence data collections for knowledge- and application-driven research. In particular, the ability to combine microbial community samples collected from any source, using the universal tree of life as a measure to compare even the most diverse communities, should provide new insights into the dynamic spatiotemporal distribution of microbial life on our planet and on the human body.</p></section><section id="SM"><h2 class="pmc_sec_title">Supplementary Material</h2> <section class="sm xbox font-sm" id="SD1"><div class="caption p"><span>S1</span></div> <div class="media p" id="d35e1372"><div class="caption"> <a href="/articles/instance/3367316/bin/NIHMS370143-supplement-S1.pdf" data-ga-action="click_feat_suppl" class="usa-link">NIHMS370143-supplement-S1.pdf</a><sup> (783.3KB, pdf) </sup> </div></div></section><section class="sm xbox font-sm" id="SD2"><div class="caption p"><span>S2</span></div> <div class="media p" id="d35e1376"><div class="caption"> <a href="/articles/instance/3367316/bin/NIHMS370143-supplement-S2.xls" data-ga-action="click_feat_suppl" class="usa-link">NIHMS370143-supplement-S2.xls</a><sup> (176.5KB, xls) </sup> </div></div></section><section class="sm xbox font-sm" id="SD3"><div class="caption p"><span>S3</span></div> <div class="media p" id="d35e1380"><div class="caption"> <a href="/articles/instance/3367316/bin/NIHMS370143-supplement-S3.xls" data-ga-action="click_feat_suppl" class="usa-link">NIHMS370143-supplement-S3.xls</a><sup> (110.5KB, xls) </sup> </div></div></section><section class="sm xbox font-sm" id="SD4"><div class="caption p"><span>S4</span></div> <div class="media p" id="d35e1384"><div class="caption"> <a href="/articles/instance/3367316/bin/NIHMS370143-supplement-S4.xls" data-ga-action="click_feat_suppl" class="usa-link">NIHMS370143-supplement-S4.xls</a><sup> (26KB, xls) </sup> </div></div></section></section><section id="S10" class="ack"><h2 class="pmc_sec_title">ACKNOWLEDGMENTS</h2> <p id="P25">Funding sources are listed in the <a href="#SD1" class="usa-link">Supplementary Note</a>.</p></section><section id="fn-group1" class="fn-group"><h2 class="pmc_sec_title">Footnotes</h2> <div class="fn-group p font-secondary-light font-sm"> <div class="fn p" id="FN1"><p id="P22">Note: Supplementary information is available on the Nature Biotechnology website.</p></div> <div class="fn p" id="FN2"> <p id="P23">COMPETING FINANCIAL INTERESTS</p> <p id="P24">The authors declare no competing financial interests.</p> </div> </div></section><section id="ref-list1" class="ref-list"><h2 class="pmc_sec_title">References</h2> <section id="ref-list1_sec2"><ul class="ref-list font-sm" style="list-style-type:none"> <li id="R1"> <span class="label">1.</span><cite>Field D, et al. 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class="pmc_sec_title">Associated Data</h2> <p class="font-secondary"><em>This section collects any data citations, data availability statements, or supplementary materials included in this article.</em></p> <section id="_adsm93_" lang="en" class="supplementary-materials"><h3 class="pmc_sec_title">Supplementary Materials</h3> <section class="sm xbox font-sm" id="db_ds_supplementary-material1_reqid_"><div class="caption p"><span>S1</span></div> <div class="media p"><div class="caption"> <a href="/articles/instance/3367316/bin/NIHMS370143-supplement-S1.pdf" data-ga-action="click_feat_suppl" class="usa-link">NIHMS370143-supplement-S1.pdf</a><sup> (783.3KB, pdf) </sup> </div></div></section><section class="sm xbox font-sm" id="db_ds_supplementary-material2_reqid_"><div class="caption p"><span>S2</span></div> <div class="media p"><div class="caption"> <a href="/articles/instance/3367316/bin/NIHMS370143-supplement-S2.xls" data-ga-action="click_feat_suppl" 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