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1. CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Author

Emiley A. Eloe-Fadrosh, Antonio P. Camargo, Stephen Nayfach, Simon Roux, Nikos C. Kyrpides, and Frederik Schulz

Subjects
viruses, Biomedical Engineering, Bioengineering, Genome, Viral, Computational biology, Biology, Genome informatics, Applied Microbiology and Biotechnology, Genome, Article, 03 medical and health sciences, Completeness (order theory), Human virome, Viral, Gene, 030304 developmental biology, 0303 health sciences, 030302 biochemistry & molecular biology, Molecular Sequence Annotation, Viral genomes, Metagenomics, Metagenome, Molecular Medicine, Infection, Software, Biotechnology, Systematic search
Abstract

Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions., The quality of viral genomes assembled from metagenome data is assessed by CheckV.

Published
2020
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2. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Seth R. Bordenstein, Frederik Schulz, Pelin Yilmaz, Rebecca Vega Thurber, Natalia Ivanova, Christelle Desnues, Shinichi Sunagawa, Karyna Rosario, Simon Roux, Steven W. Wilhelm, Nicole S. Webster, Mart Krupovic, Lisa Zeigler Allen, Catherine Putonti, K. Eric Wommack, Tanja Woyke, Eugene V. Koonin, Joanne B. Emerson, Jed A. Fuhrman, Hiroyuki Ogata, Ramy K. Aziz, Arvind Varsani, Marie-Agnès Petit, Bonnie L. Hurwitz, Evelien M. Adriaenssens, Andrew M. Kropinski, Katrine Whiteson, Thomas Rattei, Kyung Bum Lee, Peer Bork, David Paez-Espino, Mark J. Young, Jens H. Kuhn, Ben Temperton, Rebecca A. Daly, Natalya Yutin, Emiley A. Eloe-Fadrosh, Manuel Martinez-Garcia, Curtis A. Suttle, Susannah G. Tringe, Alejandro Reyes, Bas E. Dutilh, Nikos C. Kyrpides, Rex R. Malmstrom, Ilene Karsch Mizrachi, Kelly C. Wrighton, Rob Lavigne, Mya Breitbart, Lynn M. Schriml, Philip Hugenholtz, Melissa B. Duhaime, François Enault, Pascal Hingamp, Francisco Rodriguez-Valera, Clara Amid, Matthew B. Sullivan, Jessica M. Labonté, Grieg F. Steward, J. Rodney Brister, Takashi Yoshida, Guy Cochrane, DOE Joint Genome Institute [Walnut Creek], University of Liverpool, Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Radboud University Medical Center [Nijmegen], National Center for Biotechnology Information (NCBI), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Arizona State University [Tempe] (ASU), University of Cape Town, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Cairo University, Vanderbilt University [Nashville], European Molecular Biology Laboratory [Heidelberg] (EMBL), University of South Florida [Tampa] (USF), Colorado State University [Fort Collins] (CSU), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Michigan [Ann Arbor], University of Michigan System, University of California [Davis] (UC Davis), University of California (UC), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), University of Queensland [Brisbane], University of Arizona, Texas A&M University [Galveston], National Institute of Genetics (NIG), Universidad de Alicante, Kyoto University, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Chicago, Department of Microbiology and Ecosystem Science [Vienna], University of Vienna [Vienna], Universidad de los Andes [Bogota] (UNIANDES), Universidad Miguel Hernández [Elche] (UMH), University of Maryland School of Medicine, University of Maryland System, University of Hawai‘i [Mānoa] (UHM), Ohio State University [Columbus] (OSU), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of British Columbia (UBC), University of Exeter, Oregon State University (OSU), Australian Institute of Marine Science [Townsville] (AIMS Townsville), Australian Institute of Marine Science (AIMS), University of California [Irvine] (UC Irvine), The University of Tennessee [Knoxville], University of Delaware [Newark], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Montana State University (MSU), J. Craig Venter Institute, University of California [San Diego] (UC San Diego), This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under US Department of Energy Contract No. DE-AC02-05CH11231 for S.R., the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 for B.E.D., the Intramural Research Program of the National Library of Medicine, National Institutes of Health for E.V.K., I.K.M., J.R.B. and N.Y., the Virus-X project (EU Horizon 2020, No. 685778) for F.E. and M.K., Battelle Memorial Institute's prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I for J.H.K., the GOA grant 'Bacteriophage Biosystems' from KU Leuven for R.L., the European Molecular Biology Laboratory for C.A. and G.R.C., Cairo University Grant 2016-57 for R.K.A., National Science Foundation award 1456778, National Institutes of Health awards R01 AI132581 and R21 HD086833, and The Vanderbilt Microbiome Initiative award for S.R.B., National Science Foundation awards DEB-1239976 for M.B. and K.R. and DEB-1555854 for M.B., the NSF Early Career award DEB-1555854 and NSF Dimensions of Biodiversity #1342701 for K.C.W. and R.A.D., the Agence Nationale de la Recherche JCJC grant ANR-13-JSV6-0004 and Investissements d'Avenir Méditerranée Infection 10-IAHU-03 for C.D., the Gordon and Betty Moore Foundation Marine Microbiology Initiative No. 3779 and the Simons Foundation for J.A.F., the French government 'Investissements d'Avenir' program OCEANOMICS ANR-11-BTBR-0008 and European FEDER Fund 1166-39417 for P. Hingamp, Australian Research Council Laureate Fellowship FL150100038 to P. Hugenholtz the National Science Foundation award 1801367 and C-DEBI Research Grant for J.M.L., the Gordon and Betty Moore Foundation grant 5334 and Ministry of Economy and Competitivity refs. CGL2013-40564-R and SAF2013-49267-EXP for M.M.-G., the Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan No. 16H06429, 16K21723, and 16H06437 for H.O. and T.Y., National Science Foundation award DBI-1661357 to C.P., the Ministry of Economy and Competitivity ref CGL2016-76273-P (cofunded with FEDER funds) for F.R.-V., the Gordon and Betty Moore Foundation awards 3305 and 3790 and NSF Biological Oceanography OCE 1536989 for M.B.S., the ETH Zurich and Helmut Horten Foundation and the Novartis Foundation for Medical-Biological Research (17B077) for S.S., a BIOS-SCOPE award from Simons Foundation International and NERC award NE/P008534/1 to B.T., NSF Biological Oceanography Grant 1635913 for R.V.T., the Australian Research Council Future Fellowship FT120100480 for N.S.W., a Gilead Sciences Cystic Fibrosis Research Scholarship for K.L.W., Gordon and Better Moore Foundation Grant 4971 for S.W.W., the NSF EPSCoR grant 1736030 for K.E.W., the National Science Foundation award DEB-4W4596 and National Institutes of Health award R01 GM117361 for M.J.Y., the Gordon and Betty Moore Foundation No. 7000 and the National Oceanic and Atmospheric Administration (NOAA) under award NA15OAR4320071 for L.Z.A. DDBJ is supported by ROIS and MEXT. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. B.E.D., A.K., M.K., J.H.K., R.L. and A.V. are members of the ICTV Executive Committee, but the views and opinions expressed are those of the authors and not those of the ICTV., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular, Institut Pasteur [Paris], University of South Florida (USF), University of California, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Universidad de los Andes [Bogota], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of California [Irvine] (UCI), J Craig Venter Institute, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Sub Bioinformatics, and Theoretical Biology and Bioinformatics

Subjects
[SDV]Life Sciences [q-bio], Microbiología, 2.2 Factors relating to physical environment, Applied Microbiology and Biotechnology, Genome, 0302 clinical medicine, Databases, Genetic, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], phage, Viral, 0303 health sciences, Genetic Databases, Environmental microbiology, pipeline, Genome project, dynamics, Genomics, annotation, Viruses, Molecular Medicine, tacomony, Infection, Genetic databases, Biotechnology, Virus Cultivation, In silico, Biomedical Engineering, Phage biology, Bioengineering, Computational biology, Genome, Viral, Biology, Virus, dna viruses, Article, Uncultivated virus genomes, Databases, 03 medical and health sciences, Annotation, Genetic, Virology, MD Multidisciplinary, Genetics, 030304 developmental biology, Human Genome, Biological classification, commitee, prediction, Metagenomics, Minimum Information about any (x) Sequence (MIxS), 030217 neurology & neurosurgery, discovery
Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere., Nature Biotechnology, 37 (1), ISSN:1546-1696, ISSN:1087-0156

Published
2018
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3. Publisher Correction: A genomic catalog of Earth’s microbiomes

Author

José P. Faria, Edward Kirton, Nikos C. Kyrpides, Joshua Ladau, Torben Nielsen, Stephen Nayfach, David Paez-Espino, Nigel J Mouncey, Tanja Woyke, Christopher S. Henry, T. B. K. Reddy, Rekha Seshadri, Neha Varghese, Susannah G. Tringe, Daniel W. Udwary, Sean P. Jungbluth, Axel Visel, Dongying Wu, Emiley A. Eloe-Fadrosh, Supratim Mukherjee, Krishna Palaniappan, I-Min Chen, Frederik Schulz, Adam P. Arkin, Natalia Ivanova, Simon Roux, Dylan Chivian, Elisha M. Wood-Charlson, Janaka N. Edirisinghe, Marcel Huntemann, and Paramvir S. Dehal

Subjects
0303 health sciences, Published Erratum, Biomedical Engineering, Medical school, Library science, Bioengineering, Applied Microbiology and Biotechnology, Publisher Correction, Microbiology, Computational biology and bioinformatics, 03 medical and health sciences, 0302 clinical medicine, Molecular Medicine, Environmental systems, 030217 neurology & neurosurgery, 030304 developmental biology, Biotechnology
Abstract

In the version of this article initially published, four people were missing from the alphabetical list of IMG/M Data Consortium members: Lauren V. Alteio of the Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria; Jeffrey L. Blanchard of the Biology Department, University of Massachusetts Amherst, Amherst, MA, USA; Kristen M. DeAngelis of the Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA; and William Rodriguez-Reillo of the Research Computing Division, Harvard Medical School, Boston, MA, USA. The error has been corrected in the PDF and HTML versions of the article.

Published
2020

4. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author

Granger G. Sutton, Pelin Yilmaz, Robert D. Finn, Jessica K. Jarett, Rob Knight, Gene W. Tyson, Frank Oliver Gloeckner, Jack A. Gilbert, Jeremy A. Dodsworth, T. B. K. Reddy, Noah Fierer, Jillian F. Banfield, Nikos C. Kyrpides, Mircea Podar, Philip Hugenholtz, Ilene Karsch-Mizrachi, Adam R. Rivers, Donovan H. Parks, Lynn M. Schriml, Miranda Harmon-Smith, Jonathan A. Eisen, Frederik Schulz, Shibu Yooseph, Folker Meyer, Sean P. Jungbluth, Brian P. Hedlund, Brett J. Baker, Natalia Ivanova, Tanja Woyke, Ramunas Stepanauskas, Steven J. Hallam, George M. Garrity, Eric D. Becraft, Susannah G. Tringe, George M. Weinstock, Bruce W. Birren, Konstantinos T. Konstantinidis, Alla Lapidus, Alicia Clum, A. M. Eren, Thomas Rattei, Scott Tighe, William C. Nelson, Peer Bork, Christian Rinke, Thijs J. G. Ettema, Devin F. R. Doud, Emiley A. Eloe-Fadrosh, Guy Cochrane, Katherine D. McMahon, Alex Copeland, Wen Tso Liu, Rex R. Malmstrom, and Robert M. Bowers

Subjects
0301 basic medicine, Sequence analysis, 030106 microbiology, Biomedical Engineering, Bioengineering, Genomics, Computational biology, Biology, Applied Microbiology and Biotechnology, Genome, Genome Standards Consortium, Article, Microbiology, 03 medical and health sciences, Genome, Archaeal, Life Science, Biologiska vetenskaper, Whole genome sequencing, Multiple displacement amplification, Genome project, Sequence Analysis, DNA, Biological Sciences, 030104 developmental biology, Metagenomics, Molecular Medicine, Erratum, Genome, Bacterial, Biotechnology, Reference genome
Abstract

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

Published
2016
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5. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Author

Neha Varghese, David Paez-Espino, Axel Visel, Michalis Hadjithomas, George M. Garrity, Hans-Peter Klenk, Nikos C. Kyrpides, Amrita Pati, Philip Hugenholtz, Emiley A. Eloe-Fadrosh, Tanja Woyke, Yasuo Yoshikuni, Markus Göker, William B. Whitman, Rekha Seshadri, Georgios A. Pavlopoulos, Supratim Mukherjee, Natalia Ivanova, Jonathan A. Eisen, Jan P. Meier-Kolthoff, and R. Cameron Coates

Subjects
0301 basic medicine, Encyclopedias as Topic, Knowledge Bases, 030106 microbiology, Biomedical Engineering, Datasets as Topic, Bioengineering, Genomics, Computational biology, Applied Microbiology and Biotechnology, Genome, Bacterial genetics, 03 medical and health sciences, Databases, Genetic, Genome, Archaeal, Reference Values, Databases, Genetic, Genetics, biology, Phylogenetic tree, Bacterial, Chromosome Mapping, High-Throughput Nucleotide Sequencing, biology.organism_classification, Phylogenetic diversity, 030104 developmental biology, Metagenomics, Archaeal, Molecular Medicine, Database Management Systems, Sequence space (evolution), Infection, Genome, Bacterial, Biotechnology, Archaea
Abstract

© 2017 Nature America, Inc., part of Springer Nature. All rights reserved. We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

Published
2016
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6. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Author

Jed A. Fuhrman, Justin Kuczynski, Dawn Field, Renzo Kottmann, Jack A. Gilbert, Dan Knights, Lynn M. Schriml, Patrick D. Schloss, Linda A. Amaral-Zettler, Jeroen Raes, Ruth E. Ley, Mark J. Bailey, Jacques Ravel, Andreas Wilke, David A. Relman, Martin J. Blaser, Wolfgang Ludwig, Lindsay K. Newbold, Rob Knight, Josh D. Neufeld, Frederic D. Bushman, Pier Luigi Buttigieg, Peer Bork, Scott T. Kelley, Michelle I. Smith, Norman Morrison, Christopher I. Hunter, Rohini Sinha, Omry Koren, Catherine A. Lozupone, Christian L. Lauber, Diana R. Nemergut, Tanya Yatsunenko, George M. Weinstock, Patrick S. G. Chain, Sara Nakielny, Elizabeth K. Costello, Timothy F. Booth, Anjanette Johnston, Brian D. Muegge, Sarah K. Highlander, Christian Quast, Susanna Assunta-Sansone, Aymé Spor, Bruce W. Birren, Sujeevan Ratnasingham, Peter Sterk, Andrew S. Whiteley, Antonio Gonzalez, Owen White, Robert P. Guralnick, Pelin Yilmaz, Jeffrey I. Gordon, Emily S. Charlson, Doug Wendel, Dirk Gevers, Eamonn Maguire, Erica Sodergren, Ilene Karsch-Mizrachi, Joseph F. Petrosino, Elmar Pruesse, Folker Meyer, Andrew L. Kau, Jörg Peplies, Giriprakash Palanisamy, Richard A. Gibbs, Jerry Kennedy, Doyle V. Ward, Nikos C. Kyrpides, Karen E. Nelson, Wolfgang Hankeln, Manimozhiyan Arumugam, Philippe Rocca-Serra, Philip Hugenholtz, James M. Tiedje, Robert Larsen, Jesse Stombaugh, Rachel E. Gallery, Lita M. Proctor, Janet K. Jansson, Todd Z. DeSantis, Vivien Bonazzi, Anna Oliver, Laura K. Baumgartner, Robert Vaughan, James R. Cole, Joonhong Park, Frank Oliver Glöckner, Donna Lyons, Heather Huot-Creasy, Teresa M. Legg, Norman R. Pace, Noah Fierer, Jennifer R. Wortman, Barbara A. Methé, Inigo San Gil, Guy Cochrane, Peter Dawyndt, and Department of Bio-engineering Sciences

Subjects
Sequence analysis, Biomedical Engineering, Information Storage and Retrieval, Bioengineering, Computational biology, Environment, Biology, Applied Microbiology and Biotechnology, Marker gene, Article, DNA sequencing, chemistry.chemical_compound, Molecular marker, Databases, Genetic, Humans, Sequence (medicine), Genetics, Whole genome sequencing, Internet, fungi, Nucleic acid sequence, Genetic Variation, Genes, rRNA, Sequence Analysis, DNA, Checklist, mimimarks, chemistry, Metagenomics, Molecular Medicine, Programming Languages, Biomarkers, Software, Biotechnology
Abstract

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

Published
2011
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7. Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author

George M. Weinstock, Rex R. Malmstrom, Robert M. Bowers, Alex Copeland, Thijs J. G. Ettema, Devin F. R. Doud, Jessica K. Jarett, Rob Knight, Alicia Clum, Wen Tso Liu, Tanja Woyke, Gene W. Tyson, Brett J. Baker, Sean P. Jungbluth, Ramunas Stepanauskas, William C. Nelson, George M. Garrity, Jack A. Gilbert, Susannah G. Tringe, Steven J. Hallam, Guy Cochrane, Ilene Karsch-Mizrachi, Adam R. Rivers, Nikos C. Kyrpides, Lynn M. Schriml, Mircea Podar, Folker Meyer, Noah Fierer, Philip Hugenholtz, Katherine D. McMahon, Jonathan A. Eisen, Donovan H. Parks, Frank Oliver Glöckner, Eric D. Becraft, Thomas Rattei, Jeremy A. Dodsworth, Konstantinos T. Konstantinidis, Robert D. Finn, T. B. K. Reddy, Brian P. Hedlund, A. Murat Eren, Frederik Schulz, Shibu Yooseph, Natalia Ivanova, Miranda Harmon-Smith, Pelin Yilmaz, Alla Lapidus, Peer Bork, Christian Rinke, Granger G. Sutton, Jillian F. Banfield, Bruce W. Birren, Scott Tighe, and Emiley A. Eloe-Fadrosh

Subjects
0301 basic medicine, biology, Biomedical Engineering, Library science, Bioengineering, Computational biology, biology.organism_classification, Applied Microbiology and Biotechnology, Genome, 03 medical and health sciences, 030104 developmental biology, Geography, Metagenomics, Molecular Medicine, Erratum, Bacteria, Biotechnology, Archaea
Abstract

In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.

Published
2018
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8. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream

Author

Nikos C. Kyrpides

Subjects
Microbial Genomes, Emerging technologies, business.industry, Biomedical Engineering, Bioengineering, Genomics, Biology, Applied Microbiology and Biotechnology, Data science, Biotechnology, Microbial genomics, Databases, Genetic, Database Management Systems, Molecular Medicine, business, Genome, Bacterial
Abstract

As we approach the completed sequencing of 1,000 microbial genomes, the field of microbial genomics is poised at a crossroads. The future holds great promise for far-reaching advancements in microbiology as well as in diverse, related sciences. But realizing that potential will require meeting the challenges that have accompanied the rapid development of the underlying technology and the exponential growth of data. New technologies provide unprecedented opportunities but also call for conceptual shifts. Experience gained in the first decade of genomics can guide the improved approaches now needed for the selection of genome sequencing projects and their funding, for genome publication and annotation, as well as for data analysis and access. Equipped with these new tools and policies, microbiologists will have a unique opportunity for unprecedented exploration of our microbial planet.

Published
2009
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9. The minimum information about a genome sequence (MIGS) specification

Author

Dawn Field, Renzo Kottmann, Sandra L. Baldauf, Eugene Kolker, Phillip Lord, Ingio San Gil, George M. Garrity, Norman Morrison, Gareth A. Wilson, Nadeem Faruque, Bob Vaughan, Owen White, Tanya Gray, James R. Cole, Phil Hugenholtz, David W. Ussery, Peter Sterk, Robert Edwards, Henning Hermjakob, Barbara A. Methé, Naomi L. Ward, Samuel V. Angiuoli, Ilene Mizrachi, Anil Wipat, Paul De Vos, Andrew J. Spiers, Kelvin Li, Chris F. Taylor, Allyson L. Lister, Julian Parkhill, Frank Oliver Glöckner, George A. Kowalchuk, Jeffrey L. Boore, Leonid Kagan, Suzanna E. Lewis, Victor Markowitz, Robert G. Feldman, Paul Swift, Nikos C. Kyrpides, Guy Cochrane, Jack A. Gilbert, Daniel H. Haft, Natalia Maltsev, Trish Whetzel, Jennifer B. H. Martiny, Matthew D. Kane, Peter Dawyndt, Lita M. Proctor, Tatiana Tatusova, Claude W. dePamphilis, Saul A. Kravitz, Yoshio Tateno, Michael J. Allen, Nicholas R. Thomson, Nelson Axelrod, Karen E. Nelson, Ian Joint, Jim Leebens-Mack, Jeremy D. Selengut, Michael Ashburner, Robert P. Guralnick, Sarah L. Turner, Adrian Tett, David Hancock, S. Ballard, Christiane Hertz-Fowler, Richard Moxon, Susanna-Assunta Sansone, Philip Goldstein, Robert Stevens, Paul Gilna, Jessie Kennedy, and Terrestrial Microbial Ecology (TME)

Subjects
Genetics, Whole genome sequencing, Internationality, Standardization, Databases, Factual, Information Dissemination, Biomedical Engineering, Information Theory, Chromosome Mapping, Information Storage and Retrieval, Bioengineering, Genomics, Biology, Information theory, Applied Microbiology and Biotechnology, Transparency (behavior), Data science, Genome, Article, Metadata, Molecular Medicine, Biotechnology
Abstract

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

Published
2008

10. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

Author

Falk Warnecke, Nikos C. Kyrpides, Philip Hugenholtz, Victor Kunin, Nik Putnam, Ernest Szeto, Linda L. Blackall, Eileen Dalin, Alice C. McHardy, Jasmyn Pangilinan, Shaomei He, Katherine D. McMahon, Natalia Ivanova, Asaf Salamov, Hector Garcia Martin, Harris Shapiro, Christine Yeates, Isidore Rigoutsos, and Kerrie Barry

Subjects
biology, Sewage, Ecology, Biomedical Engineering, Candidatus Accumulibacter, Adaptation, Biological, Betaproteobacteria, Bioengineering, Phosphorus, biology.organism_classification, Applied Microbiology and Biotechnology, Candidatus Accumulibacter phosphatis, Waste Disposal, Fluid, Polyphosphate-accumulating organisms, Enhanced biological phosphorus removal, Metagenomics, Molecular Medicine, Evolutionary dynamics, Organism, Genome, Bacterial, Biotechnology, Waste disposal
Abstract

Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, "Candidatus Accumulibacter phosphatis." The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of A. phosphatis in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the A. phosphatis genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems.

Published
2006

11. A unified catalog of 204,938 reference genomes from the human gut microbiome

Author

Zhou Jason Shi, Katherine S. Pollard, Nikos C. Kyrpides, Robert D. Finn, Philip Hugenholtz, Francesco Strozzi, Donovan H. Parks, Nicola Segata, Ekaterina A. Sakharova, Miguel Boland, Stephen Nayfach, Martin Beracochea, and Alexandre Almeida

Subjects
Resource, Biomedical Engineering, Bioengineering, Computational biology, Biology, ENCODE, Applied Microbiology and Biotechnology, Genome, Bacterial genetics, 03 medical and health sciences, Phylogenetics, Databases, Genetic, Humans, Microbiome, Gene, Phylogeny, 030304 developmental biology, 0303 health sciences, Bacteria, 030306 microbiology, Phenotype, Gastrointestinal Microbiome, Metagenomics, Molecular Medicine, Metagenome, Genome, Bacterial, Biotechnology
Abstract

Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to individual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome., More than 200,000 gut prokaryotic reference genomes and the proteins they encode are collated, providing comprehensive resources for microbiome researchers.

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