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Genome-resolved metagenomics using environmental and clinical samples.

Masood Ur Rehman Kayani¹, Wanqiu Huang², Ru Feng¹

¹Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China.

Briefings in Bioinformatics

|March 24, 2021

Summary

Genome-resolved metagenomics enables recovery of microbial genomes from complex samples. This review guides researchers through essential steps and tools for analyzing metagenomic data, facilitating discovery of novel species.

Keywords:

MAG annotation MAG refinement MAG taxonomic classification de novo assembly genome binning metagenome assembly validation metagenome-assembled genomes read preprocessing

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Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

High-throughput sequencing and computational advances have enabled genome-resolved metagenomics.
This approach allows for the recovery, classification, and functional annotation of microbial genomes from complex samples.
Previous studies have successfully identified novel microbial species using this methodology.

Purpose of the Study:

To provide a comprehensive review of genome-resolved metagenome analysis.
To guide researchers in selecting appropriate tools and pipelines for each step of the analysis.
To highlight resources for automating analysis and validating genome quality.

Main Methods:

The review outlines four key steps: read preprocessing, de novo assembly, genome binning, and taxonomic/functional analysis.
It discusses commonly used tools and available pipelines for each step.
Methods for assembly quality validation and genome quality improvement are also covered.

Main Results:

Identification of previously unknown microbial species from human and environmental samples.
A detailed overview of current bioinformatics tools and pipelines for genome-resolved metagenomics.
Guidance on selecting widely adapted and actively maintained tools for decision-making.

Conclusions:

Genome-resolved metagenomics is a powerful approach for microbial genome recovery and analysis.
This review serves as a practical guide for researchers, offering tool recommendations and pipeline insights.
The discussed resources aim to empower scientists, even those without extensive bioinformatics expertise, to analyze metagenomic data effectively.