. 2017 Aug 8;35(8):725-731.

doi: 10.1038/nbt.3893.

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

Robert M Bowers¹, Nikos C Kyrpides¹, Ramunas Stepanauskas², Miranda Harmon-Smith¹, Devin Doud¹, T B K Reddy¹, Frederik Schulz¹, Jessica Jarett¹, Adam R Rivers^{1

3}, Emiley A Eloe-Fadrosh¹, Susannah G Tringe^{1

4}, Natalia N Ivanova¹, Alex Copeland¹, Alicia Clum¹, Eric D Becraft², Rex R Malmstrom¹, Bruce Birren⁵, Mircea Podar⁶, Peer Bork⁷, George M Weinstock⁸, George M Garrity⁹, Jeremy A Dodsworth¹⁰, Shibu Yooseph¹¹, Granger Sutton¹², Frank O Glöckner¹³, Jack A Gilbert^{14

15}, William C Nelson¹⁶, Steven J Hallam¹⁷, Sean P Jungbluth^{1

18}, Thijs J G Ettema¹⁹, Scott Tighe²⁰, Konstantinos T Konstantinidis²¹, Wen-Tso Liu²², Brett J Baker²³, Thomas Rattei²⁴, Jonathan A Eisen²⁵, Brian Hedlund^{26

27}, Katherine D McMahon^{28

29}, Noah Fierer^{30

31}, Rob Knight³², Rob Finn³³, Guy Cochrane³³, Ilene Karsch-Mizrachi³⁴, Gene W Tyson³⁵, Christian Rinke³⁵; Genome Standards Consortium; Alla Lapidus³⁶, Folker Meyer¹⁴, Pelin Yilmaz¹³, Donovan H Parks³⁵, A M Eren³⁷, Lynn Schriml³⁸, Jillian F Banfield³⁹, Philip Hugenholtz³⁵, Tanja Woyke^{1

4}

Collaborators, Affiliations

Collaborators

Genome Standards Consortium:
Nikos C Kyrpides, Lynn Schriml, George M Garrity, Philip Hugenholtz, Granger Sutton, Pelin Yilmaz, Folker Meyer, Frank O Glöckner, Jack A Gilbert, Rob Knight, Rob Finn, Guy Cochrane, Ilene Karsch-Mizrachi

Affiliations

¹ Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
² Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA.
³ United States Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Gainesville, Florida, USA.
⁴ School of Natural Sciences, University of California Merced, Merced, California, USA.
⁵ Broad Institute, Cambridge, Massachusetts, USA.
⁶ Biosciences Division, Oak Ridge National Laboratory, Oakridge Tennessee, USA.
⁷ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
⁸ The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
⁹ Department of Microbiology &Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan, USA.
¹⁰ Department of Biology, California State University, San Bernardino, California, USA.
¹¹ J. Craig Venter Institute, San Diego, California, USA.
¹² J. Craig Venter Institute, Rockville, Maryland, USA.
¹³ Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
¹⁴ Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.
¹⁵ Department of Surgery, University of Chicago, Chicago, Illinois, USA.
¹⁶ Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
¹⁷ Department of Microbiology &Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
¹⁸ Center for Dark Energy Biosphere Investigation, University of Southern California, Los Angeles, California, USA.
¹⁹ Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
²⁰ Advanced Genomics Lab, University of Vermont Cancer Center, Burlington Vermont, USA.
²¹ Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, Georgia, USA.
²² Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
²³ Department of Marine Science, University of Texas-Austin, Marine Science Institute, Austin, Texas, USA.
²⁴ Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
²⁵ Genome Center, University of California, Davis, California, USA.
²⁶ School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA.
²⁷ Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA.
²⁸ Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.
²⁹ Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
³⁰ Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.
³¹ Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.
³² Center for Microbiome Innovation, and Departments of Pediatrics and Computer Science &Engineering, University of California San Diego, La Jolla, California, USA.
³³ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Trust Genome Campus, Hinxton, Cambridge, UK.
³⁴ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
³⁵ Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
³⁶ Centre for Algorithmic Biotechnology, ITBM, St. Petersburg State University, St. Petersburg, Russia.
³⁷ Knapp Center for Biomedical Discovery, Chicago, Illinois, USA.
³⁸ National Cancer Institute, Frederick, Maryland, USA.
³⁹ Department of Earth and Planetary Science, University of California, Berkeley, California, USA.

PMID: 28787424
PMCID: PMC6436528
DOI: 10.1038/nbt.3893

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

Robert M Bowers et al. Nat Biotechnol. 2017.

. 2017 Aug 8;35(8):725-731.

doi: 10.1038/nbt.3893.

Authors

Collaborators

Genome Standards Consortium:
Nikos C Kyrpides, Lynn Schriml, George M Garrity, Philip Hugenholtz, Granger Sutton, Pelin Yilmaz, Folker Meyer, Frank O Glöckner, Jack A Gilbert, Rob Knight, Rob Finn, Guy Cochrane, Ilene Karsch-Mizrachi

Affiliations

¹ Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
² Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA.
³ United States Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Gainesville, Florida, USA.
⁴ School of Natural Sciences, University of California Merced, Merced, California, USA.
⁵ Broad Institute, Cambridge, Massachusetts, USA.
⁶ Biosciences Division, Oak Ridge National Laboratory, Oakridge Tennessee, USA.
⁷ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
⁸ The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
⁹ Department of Microbiology &Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan, USA.
¹⁰ Department of Biology, California State University, San Bernardino, California, USA.
¹¹ J. Craig Venter Institute, San Diego, California, USA.
¹² J. Craig Venter Institute, Rockville, Maryland, USA.
¹³ Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
¹⁴ Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.
¹⁵ Department of Surgery, University of Chicago, Chicago, Illinois, USA.
¹⁶ Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
¹⁷ Department of Microbiology &Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
¹⁸ Center for Dark Energy Biosphere Investigation, University of Southern California, Los Angeles, California, USA.
¹⁹ Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
²⁰ Advanced Genomics Lab, University of Vermont Cancer Center, Burlington Vermont, USA.
²¹ Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, Georgia, USA.
²² Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
²³ Department of Marine Science, University of Texas-Austin, Marine Science Institute, Austin, Texas, USA.
²⁴ Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
²⁵ Genome Center, University of California, Davis, California, USA.
²⁶ School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA.
²⁷ Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA.
²⁸ Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.
²⁹ Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
³⁰ Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.
³¹ Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.
³² Center for Microbiome Innovation, and Departments of Pediatrics and Computer Science &Engineering, University of California San Diego, La Jolla, California, USA.
³³ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Trust Genome Campus, Hinxton, Cambridge, UK.
³⁴ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
³⁵ Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
³⁶ Centre for Algorithmic Biotechnology, ITBM, St. Petersburg State University, St. Petersburg, Russia.
³⁷ Knapp Center for Biomedical Discovery, Chicago, Illinois, USA.
³⁸ National Cancer Institute, Frederick, Maryland, USA.
³⁹ Department of Earth and Planetary Science, University of California, Berkeley, California, USA.

PMID: 28787424
PMCID: PMC6436528
DOI: 10.1038/nbt.3893

Erratum in

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium; Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Bowers RM, et al. Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. Nat Biotechnol. 2018. PMID: 29406516 Free PMC article. No abstract available.
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium; Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Bowers RM, et al. Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. Nat Biotechnol. 2018. PMID: 29979671 Free PMC article. No abstract available.

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.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing financial interests.

Figures

**Figure 1. Sequencing of bacterial and archaeal genomes^,,,,,,,,,.**
Increase in the number of SAGs and MAGs over time. Inset displays the number of isolate genomes over time for comparison. Data for figure were taken from IMG/GOLD in January 2017.

**Figure 2. Generation of SAGs and MAGs.**
Flow diagram outlining the typical pipeline for the production of both SAGs and MAGs.

See this image and copyright information in PMC

References

1. Amann, R.I., Ludwig, W. & Schleifer, K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev.59, 143–169 (1995). - PMC - PubMed
1. Rappé, M.S. & Giovannoni, S.J. The uncultured microbial majority. Annu. Rev. Microbiol.57, 369–394 (2003). - PubMed
1. Tyson, G.W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature428, 37–43 (2004). - PubMed
1. Venter, J.C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science304, 66–74 (2004). - PubMed
1. Lasken, R.S. Single-cell sequencing in its prime. Nat. Biotechnol.31, 211–212 (2013). - PubMed

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

Collaborators

Affiliations

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

Authors

Collaborators

Affiliations

Erratum in

Abstract

Conflict of interest statement

Figures

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Research Materials