Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Dylan Chivian, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Benjamin H. Allen, Mikayla M. Clark, Tianhao Gu, Miriam L. Land, Gavin A. Price, William J. Riehl, Michael W. Sneddon, Roman Sutormin, Qizhi Zhang, Robert W. Cottingham, Chris S. Henry, Adam P. Arkin

Research output: Contribution to journalArticlepeer-review

39 Scopus citations

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. 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).

Original languageEnglish
Pages (from-to)208-238
Number of pages31
JournalNature Protocols
Volume18
Issue number1
DOIs
StatePublished - Jan 2023

Funding

The authors thank S. Singer for the use of the Compost sequence data and T. Northen for the Desert Crust sequence data. We thank U. Karaoz and E.L. Brodie for the use of the MicroTrait HMMs. We thank K. Wrighton, M. Shaffer and M. Borton for the use of their DRAM app and P. Chain, M. Flynn and C. Lo for the use of their GOTTCHA2 app. We thank D. Parks and G. Tyson for the use of CheckM and P.-A. Chaumeil, D. Parks, A. J. Mussig and P. Hugenholtz for the use of GTDB-Tk. KBase especially thanks all primary developers whose tools have been wrapped as apps in KBase; please make sure to cite their primary publications if you use any of those apps. KBase greatly appreciates funding by the Genomic Science program within the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award nos. DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725 and DE-AC02-98CH10886.

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