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

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.

Authors:
 [1];  [1]; ORCiD logo [2];  [1];  [1];  [1]; ORCiD logo [1];  [1];  [3];  [1]; ORCiD logo [4];  [1];  [1];  [1];  [2];  [1];  [5];  [6];  [7];  [8] more »;  [9];  [10];  [11]; ORCiD logo [12];  [13];  [14];  [15];  [16]; ORCiD logo [17];  [18];  [19];  [20];  [21];  [22];  [23];  [24];  [25];  [26];  [27]; ORCiD logo [28];  [29];  [29];  [30];  [31]; ORCiD logo [31];  [1];  [32];  [9];  [31]; ORCiD logo [12]; ORCiD logo [13];  [33];  [13];  [34]; ORCiD logo [28];  [29];  [29];  [30]; ORCiD logo [35];  [33]; ORCiD logo [13]; ORCiD logo [31]; ORCiD logo [36];  [32];  [37];  [31];  [4] « less
+ Show Author Affiliations
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Bigelow Lab. for Ocean Sciences, East Boothbay, ME (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); United States Dept. of Agriculture, Gainesville, FL (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Merced, CA (United States)
  5. Broad Institute, Cambridge, MA (United States)
  6. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  7. European Molecular Biology Lab., Heidelberg (Germany)
  8. The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
  9. Michigan State Univ., East Lansing, MI (United States)
  10. California State Univ., San Bernardino, CA (United States)
  11. J. Craig Venter Institute, San Diego, CA (United States)
  12. J. Craig Venter Institute, Rockville, MD (United States)
  13. Max Planck Institute for Marine Microbiology, Bremen (Germany)
  14. Univ. of Chicago, Chicago, IL (United States)
  15. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  16. Univ. of British Columbia, Vancouver, BC (Canada)
  17. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Southern California, Los Angeles, CA (United States)
  18. Uppsala Univ., Uppsala (Sweden)
  19. Univ. of Vermont Cancer Center, Burlington, VT (United States)
  20. Georgia Inst. of Technology, Atlanta, GA (United States)
  21. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
  22. Univ. of Texas-Austin, Austin, TX (United States)
  23. Univ. of Vienna, Vienna (Austria)
  24. Univ. of California, Davis, CA (United States)
  25. Univ. of Nevada, Las Vegas, NV (United States)
  26. Univ. of Wisconsin, Madison, WI (United States)
  27. Univ. of Colorado, Boulder, CO (United States)
  28. Univ. of California San Diego, La Jolla, CA (United States)
  29. European Molecular Biology Lab., Cambridge (United Kingdom)
  30. National Institutes of Health, Bethesda, MD (United States)
  31. The Univ. of Queensland, Queensland (Australia)
  32. National Cancer Institute, Frederick, MD (United States)
  33. Argonne National Lab. (ANL), Argonne, IL (United States)
  34. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
  35. St. Petersburg State Univ., St. Petersburg (Russia)
  36. Knapp Center for Biomedical Discovery, Chicago, IL (United States)
  37. Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1375044
Alternate Identifier(s):
OSTI ID: 1394303; OSTI ID: 1414520; OSTI ID: 1459393
Report Number(s):
PNNL-SA-125978
Journal ID: ISSN 1087-0156; 137394
Grant/Contract Number:  
AC02-06CH11357; AC05-00OR22725; AC05-76RL01830; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Biotechnology
Additional Journal Information:
Journal Volume: 35; Journal Issue: 8; Journal ID: ISSN 1087-0156
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen -Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Kyrpides, Nikos C., Schriml, Lynn, Garrity, George M., Hugenholtz, Philip, Sutton, Granger, Yilmaz, Pelin, Meyer, Folker, Glockner, Frank O., Gilbert, Jack A., Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. United States: N. p., 2017. Web. doi:10.1038/nbt.3893.
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Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen -Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Kyrpides, Nikos C., Schriml, Lynn, Garrity, George M., Hugenholtz, Philip, Sutton, Granger, Yilmaz, Pelin, Meyer, Folker, Glockner, Frank O., Gilbert, Jack A., Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, & Woyke, Tanja. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. United States. https://doi.org/10.1038/nbt.3893
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Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen -Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Kyrpides, Nikos C., Schriml, Lynn, Garrity, George M., Hugenholtz, Philip, Sutton, Granger, Yilmaz, Pelin, Meyer, Folker, Glockner, Frank O., Gilbert, Jack A., Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja. Tue . "Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea". United States. https://doi.org/10.1038/nbt.3893. https://www.osti.gov/servlets/purl/1375044.
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@article{osti_1375044,
title = {Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea},
author = {Bowers, Robert M. and Kyrpides, Nikos C. and Stepanauskas, Ramunas and Harmon-Smith, Miranda and Doud, Devin and Reddy, T. B. K. and Schulz, Frederik and Jarett, Jessica and Rivers, Adam R. and Eloe-Fadrosh, Emiley A. and Tringe, Susannah G. and Ivanova, Natalia N. and Copeland, Alex and Clum, Alicia and Becraft, Eric D. and Malmstrom, Rex R. and Birren, Bruce and Podar, Mircea and Bork, Peer and Weinstock, George M. and Garrity, George M. and Dodsworth, Jeremy A. and Yooseph, Shibu and Sutton, Granger and Glockner, Frank O. and Gilbert, Jack A. and Nelson, William C. and Hallam, Steven J. and Jungbluth, Sean P. and Ettema, Thijs J. G. and Tighe, Scott and Konstantinidis, Konstantinos T. and Liu, Wen -Tso and Baker, Brett J. and Rattei, Thomas and Eisen, Jonathan A. and Hedlund, Brian and McMahon, Katherine D. and Fierer, Noah and Knight, Rob and Finn, Rob and Cochrane, Guy and Karsch-Mizrachi, Ilene and Tyson, Gene W. and Rinke, Christian and Kyrpides, Nikos C. and Schriml, Lynn and Garrity, George M. and Hugenholtz, Philip and Sutton, Granger and Yilmaz, Pelin and Meyer, Folker and Glockner, Frank O. and Gilbert, Jack A. and Knight, Rob and Finn, Rob and Cochrane, Guy and Karsch-Mizrachi, Ilene and Lapidus, Alla and Meyer, Folker and Yilmaz, Pelin and Parks, Donovan H. and Eren, A. M. and Schriml, Lynn and Banfield, Jillian F. and Hugenholtz, Philip and Woyke, Tanja},
abstractNote = {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.},
doi = {10.1038/nbt.3893},
journal = {Nature Biotechnology},
number = 8,
volume = 35,
place = {United States},
year = {Tue Aug 08 00:00:00 EDT 2017},
month = {Tue Aug 08 00:00:00 EDT 2017}
}
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  • Nature Communications, Vol. 7, Issue 1
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  • Glass, Elizabeth M.; Dribinsky, Yekaterina; Yilmaz, Pelin
  • The ISME Journal, Vol. 8, Issue 1
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  • Marcy, Y.; Ouverney, C.; Bik, E. M.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 29, p. 11889-11894
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  • The ISME Journal, Vol. 10, Issue 11
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Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
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ProDeGe: a computational protocol for fully automated decontamination of genomes
text, January 2016

  • James, Han,; L., Dangl, Jeff; Scott, Clingenpeel,
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/xvw7-9p10

The bacterial species definition in the genomic era
text, January 2006

  • Ramette, Alban Nicolas; Konstantinidis, K. T.; Tiedje, J. M.
  • Royal Society of London
  • DOI: 10.7892/boris.91421
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    The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities
    journal, February 2020

    • Michaelsen, Thomas Yssing; Brandt, Jakob; Singleton, Caitlin Margaret
    • mSystems, Vol. 5, Issue 1
    • DOI: 10.1128/msystems.00587-19

    Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer
    journal, March 2020

    Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly
    journal, December 2019

    • Kang, Joyce B.; Siranosian, Benjamin A.; Moss, Eli L.
    • BMC Bioinformatics, Vol. 20, Issue S16
    • DOI: 10.1186/s12859-019-3073-1

    Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
    journal, November 2017

    CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes
    journal, December 2018

    • Benavides, Andres; Isaza, Juan Pablo; Niño-García, Juan Pablo
    • BMC Genomics, Vol. 19, Issue S8
    • DOI: 10.1186/s12864-018-5191-y

    bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
    journal, February 2019

    Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
    journal, October 2019

    Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
    journal, December 2019

    Assessment of urban microbiome assemblies with the help of targeted in silico gold standards
    journal, October 2018

    Integrated multi-omic analysis of host-microbiota interactions in acute oak decline
    journal, January 2018

    Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity
    journal, January 2018

    Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua)
    journal, April 2019

    Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem
    journal, February 2020

    A pipeline for targeted metagenomics of environmental bacteria
    journal, February 2020

    Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages
    journal, September 2019

    Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics
    journal, November 2019

    Parasite microbiome project: Grand challenges
    journal, October 2019

    Dietary Oligosaccharides Attenuate Stress-Induced Disruptions in Immune Reactivity and Microbial B-Vitamin Metabolism
    journal, July 2019

    • Allen, Jacob M.; Jaggers, Robert M.; Solden, Lindsey M.
    • Frontiers in Immunology, Vol. 10
    • DOI: 10.3389/fimmu.2019.01774

    Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla
    journal, November 2017

    Genomic Description of ‘Candidatus Abyssubacteria,’ a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes
    journal, August 2018

    Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments
    journal, November 2018

    Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments
    journal, December 2018

    • Timmers, Peer H. A.; Vavourakis, Charlotte D.; Kleerebezem, Robbert
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.03039

    Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach
    journal, February 2019

    Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments
    journal, March 2019

    An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids
    journal, July 2019

    Genome of a Novel Bacterium “Candidatus Jettenia ecosi” Reconstructed From the Metagenome of an Anammox Bioreactor
    journal, October 2019

    • Mardanov, Andrey V.; Beletsky, Alexey V.; Ravin, Nikolai V.
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.02442

    A Bioinformatics Guide to Plant Microbiome Analysis
    journal, October 2019

    • Lucaciu, Rares; Pelikan, Claus; Gerner, Samuel M.
    • Frontiers in Plant Science, Vol. 10
    • DOI: 10.3389/fpls.2019.01313

    Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
    journal, January 2018

    • Linz, Alexandra M.; He, Shaomei; Stevens, Sarah L. R.
    • PeerJ, Vol. 6
    • DOI: 10.7717/peerj.6075
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