Recovering metagenome-assembled genomes from shotgun metagenomic sequencing data: Methods, applications, challenges, and opportunities

Reference genomes are essential for analyzing the metabolic and functional potentials of microbiomes. However, microbial genome resources are limited because most of microorganisms are difficult to culture. Genome binning is a culture-independent approach that can recover a vast number of microbial genomes from short-read high throughput shotgun metagenomic sequencing data. In this review, we summarize methods commonly used for reconstructing metagenome-assembled genomes (MAGs) to provide a reference for researchers to choose propriate software programs among the numerous and complicated tools and pipelines that are available for these analyses. In addition, we discuss application prospects, challenges, and opportunities for recovering MAGs from metagenomic sequencing data.

Automated summary

Reference genomes are crucial for analyzing the metabolic and functional potentials of microbiomes. However, limited microbial genome resources are available due to the difficulty of culturing microorganisms. Genome binning is a culture-independent method that can recover a large number of microbial genomes from short-read high throughput shotgun metagenomic sequencing data. In this review, commonly used methods for reconstructing metagenome-assembled genomes (MAGs) are summarized to assist researchers in selecting appropriate software programs for these analyses. Additionally, the application prospects, challenges, and opportunities for recovering MAGs from metagenomic sequencing data are discussed.