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Related Concept Videos

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Related Experiment Video

Updated: Aug 22, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Metagenome-assembled genome extraction and analysis from microbiomes using KBase.

Dylan Chivian1, Sean P Jungbluth2, Paramvir S Dehal2

  • 1Lawrence Berkeley National Laboratory, Berkeley, CA, USA. DCChivian@lbl.gov.

Nature Protocols
|November 14, 2022
PubMed
Summary

This study introduces a streamlined workflow for extracting high-quality metagenome-assembled genomes (MAGs) from environmental samples. The U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform accelerates the recovery of microbial genomes for ecosystem research.

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Area of Science:

  • Microbial genomics
  • Bioinformatics
  • Environmental metagenomics

Background:

  • Uncultivated Bacteria and Archaea represent the majority of Earth's species, but their genomes are difficult to access.
  • Environmental shotgun sequencing has recently enabled direct genome recovery from microbial communities.
  • Accelerated recovery of high-quality genomes is crucial for understanding microbial roles in ecosystems.

Purpose of the Study:

  • To present analysis steps and data products for extracting high-quality metagenome-assembled genomes (MAGs).
  • To leverage the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform for MAG recovery.
  • To facilitate the investigation of functional roles of specific microbial lineages within ecosystems.

Main Methods:

  • Utilized a series of analysis steps and data products within the KBase platform.
  • Employed shotgun sequencing data from environmental microbiomes.
  • Integrated end-to-end processing from raw sequencing reads to MAGs.

Main Results:

  • Developed a workflow for extracting high-quality MAGs from microbiomes.
  • Achieved genome extraction in approximately one day for smaller libraries and up to a week for larger ones.
  • KBase platform provides integrated tools for MAG analysis, including phylogenetic placement and functional assignment.

Conclusions:

  • The KBase platform offers an intuitive, interoperable, and integrated resource for MAG recovery.
  • This workflow accelerates the process of obtaining and analyzing microbial genomes from environmental samples.
  • The platform serves as a extensible scaffold for future MAG recovery and analysis tool development.