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Related Experiment Video

Updated: Oct 8, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.

Derek M Bickhart¹, Mikhail Kolmogorov², Elizabeth Tseng³

¹USDA Dairy Forage Research Center, Madison, WI, USA.

Nature Biotechnology

|January 4, 2022

Summary

Deep sequencing with long reads and Hi-C binning, plus the new MAGPhase tool, successfully resolved closely related microbial lineages in complex communities, enabling better genome assembly and gene discovery.

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Last Updated: Oct 8, 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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Published on: August 20, 2021

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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Metagenomic assembly is often hindered by closely related microbial lineages.
Generating complete, high-quality metagenome-assembled genomes (MAGs) from complex communities remains challenging.

Purpose of the Study:

To develop and apply methods for resolving closely related microbial lineages within complex communities.
To improve the completeness and accuracy of metagenome-assembled genomes (MAGs).

Main Methods:

Deep sequencing utilizing long (HiFi) reads.
Hi-C proximity ligation for genome binning.
Development and application of MAGPhase for lineage resolution.

Main Results:

Successfully generated 428 MAGs (>90% complete), with 44 in single circular contigs.
MAGPhase identified 220 lineage-resolved MAGs from the sheep fecal metagenome.
Improved identification of novel biosynthetic gene clusters and host-mobile genetic element associations.

Conclusions:

Combining long-read sequencing, Hi-C binning, and MAGPhase effectively resolves closely related microbes in complex communities.
This approach enhances genomic analysis, facilitating the discovery of novel functional elements and host-pathogen/symbiont relationships.