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

Abstract

The number of genomes from uncultivated microbes will soon surpass the number of isolate genomes in public databases (Hugenholtz, Skarshewski, & Parks, 2016). Technological advancements in high-throughput sequencing and assembly, including single-cell genomics and the computational extraction of genomes from metagenomes (GFMs), are largely responsible. Here we propose community standards for reporting the Minimum Information about a Single-Cell Genome (MIxS-SCG) and Minimum Information about Genomes extracted From Metagenomes (MIxS-GFM) specific for Bacteria and Archaea. The standards have been developed in the context of the International Genomics Standards Consortium (GSC) community (Field et al., 2014) and can be viewed as a supplement to other GSC checklists including the Minimum Information about a Genome Sequence (MIGS), Minimum information about a Metagenomic Sequence(s) (MIMS) (Field et al., 2008) and Minimum Information about a Marker Gene Sequence (MIMARKS) (P. Yilmaz et al., 2011). Community-wide acceptance of MIxS-SCG and MIxS-GFM for Bacteria and Archaea will enable broad comparative analyses of genomes from the majority of taxa that remain uncultivated, improving our understanding of microbial function, ecology, and evolution.

Authors:
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Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1414520
Report Number(s):
PNNL-SA-125978
Journal ID: ISSN 1087-0156; KP1702030
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nature Biotechnology; Journal Volume: 35; Journal Issue: 8
Country of Publication:
United States
Language:
English

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, Glöckner, 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, Glöckner, 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.
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, Glöckner, 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, Glöckner, 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. doi:10.1038/nbt.3893.
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, Glöckner, 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, Glöckner, 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. doi:10.1038/nbt.3893.
@article{osti_1414520,
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 Glöckner, 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 Glöckner, 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 = {The number of genomes from uncultivated microbes will soon surpass the number of isolate genomes in public databases (Hugenholtz, Skarshewski, & Parks, 2016). Technological advancements in high-throughput sequencing and assembly, including single-cell genomics and the computational extraction of genomes from metagenomes (GFMs), are largely responsible. Here we propose community standards for reporting the Minimum Information about a Single-Cell Genome (MIxS-SCG) and Minimum Information about Genomes extracted From Metagenomes (MIxS-GFM) specific for Bacteria and Archaea. The standards have been developed in the context of the International Genomics Standards Consortium (GSC) community (Field et al., 2014) and can be viewed as a supplement to other GSC checklists including the Minimum Information about a Genome Sequence (MIGS), Minimum information about a Metagenomic Sequence(s) (MIMS) (Field et al., 2008) and Minimum Information about a Marker Gene Sequence (MIMARKS) (P. Yilmaz et al., 2011). Community-wide acceptance of MIxS-SCG and MIxS-GFM for Bacteria and Archaea will enable broad comparative analyses of genomes from the majority of taxa that remain uncultivated, improving our understanding of microbial function, ecology, and evolution.},
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}
}