Metagenome-assembled genome extraction and analysis from microbiomes using KBase
Abstract
Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computationalmore »
- Authors:
-
[1];
[1];
[1];
[2];
[3];
[2];
[2];
[1]
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Argonne National Lab. (ANL), Lemont, IL (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Predicine, Inc., Hayward, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Google, Inc., San Francisco, CA (United States)
- Univ. of Tennessee, Knoxville, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1899026
- Grant/Contract Number:
- AC05-00OR22725; AC02-05CH11231; AC02-06CH11357; AC02-98CH10886
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Protocols
- Additional Journal Information:
- Journal Volume: 18; Journal Issue: 11; Journal ID: ISSN 1754-2189
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; bioinformatics; genome assembly algorithms; metagenomics; microbial ecology; microbiology techniques
Citation Formats
Chivian, Dylan, Jungbluth, Sean P., Dehal, Paramvir S., Wood-Charlson, Elisha M., Canon, Richard S., Allen, Benjamin H., Clark, Mikayla M., Gu, Tianhao, Land, Miriam L., Price, Gavin A., Riehl, William J., Sneddon, Michael W., Sutormin, Roman, Zhang, Qizhi, Cottingham, Jr., Robert W., Henry, Chris S., and Arkin, Adam P. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. United States: N. p., 2022.
Web. doi:10.1038/s41596-022-00747-x.
Chivian, Dylan, Jungbluth, Sean P., Dehal, Paramvir S., Wood-Charlson, Elisha M., Canon, Richard S., Allen, Benjamin H., Clark, Mikayla M., Gu, Tianhao, Land, Miriam L., Price, Gavin A., Riehl, William J., Sneddon, Michael W., Sutormin, Roman, Zhang, Qizhi, Cottingham, Jr., Robert W., Henry, Chris S., & Arkin, Adam P. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. United States. https://doi.org/10.1038/s41596-022-00747-x
Chivian, Dylan, Jungbluth, Sean P., Dehal, Paramvir S., Wood-Charlson, Elisha M., Canon, Richard S., Allen, Benjamin H., Clark, Mikayla M., Gu, Tianhao, Land, Miriam L., Price, Gavin A., Riehl, William J., Sneddon, Michael W., Sutormin, Roman, Zhang, Qizhi, Cottingham, Jr., Robert W., Henry, Chris S., and Arkin, Adam P. Mon .
"Metagenome-assembled genome extraction and analysis from microbiomes using KBase". United States. https://doi.org/10.1038/s41596-022-00747-x. https://www.osti.gov/servlets/purl/1899026.
@article{osti_1899026,
title = {Metagenome-assembled genome extraction and analysis from microbiomes using KBase},
author = {Chivian, Dylan and Jungbluth, Sean P. and Dehal, Paramvir S. and Wood-Charlson, Elisha M. and Canon, Richard S. and Allen, Benjamin H. and Clark, Mikayla M. and Gu, Tianhao and Land, Miriam L. and Price, Gavin A. and Riehl, William J. and Sneddon, Michael W. and Sutormin, Roman and Zhang, Qizhi and Cottingham, Jr., Robert W. and Henry, Chris S. and Arkin, Adam P.},
abstractNote = {Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).},
doi = {10.1038/s41596-022-00747-x},
journal = {Nature Protocols},
number = 11,
volume = 18,
place = {United States},
year = {Mon Nov 14 00:00:00 EST 2022},
month = {Mon Nov 14 00:00:00 EST 2022}
}
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