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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Accurate and complete genomes from metagenomes.

Lin-Xing Chen¹, Karthik Anantharaman¹, Alon Shaiber^2,3

¹Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA.

Genome Research

|March 20, 2020

Summary

Achieving complete bacterial genomes from complex microbial communities is now possible. This study introduces genome curation methods to enhance metagenome-assembled genomes (MAGs) into complete MAGs (CMAGs) for accurate analysis.

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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

Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Historically, microbial genomes were obtained from isolated cultures, limiting insights into unculturable majority.
Genome-resolved metagenomics enables the assembly of metagenome-assembled genomes (MAGs) from environmental DNA.
MAGs often suffer from incompleteness, errors, and contamination, restricting their utility.

Purpose of the Study:

To discuss genome curation strategies for improving MAGs.
To achieve complete MAGs (CMAGs) from complex microbial samples.
To validate methods for assessing bacterial genome accuracy.

Main Methods:

Analysis of approximately 7000 published bacterial isolate genomes.
Utilizing cumulative GC skew and other metrics to evaluate genome accuracy.
Identifying misassemblies and repeat sequences in bacterial genomes.

Main Results:

Cumulative GC skew is a valuable metric for assessing bacterial genome sequence accuracy.
Potential misassemblies and causative repeat sequences were identified in reference genomes.
Few CMAGs have been generated, including from challenging environments like soil and sediment.

Conclusions:

Genome curation is essential for producing high-quality MAGs.
Accurate CMAGs are crucial for reliable metabolic and evolutionary analyses.
Bioinformatic approaches can be implemented to improve genome curation pipelines.