Genome-resolved metagenomics using environmental and clinical samples

Abstract

Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.

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

Figure 1

Schematic representation of the workflow for genome-resolved metagenomics analysis. The typical genome-resolved analysis of metagenomes, obtained through any source, typically involves four steps i.e. (1) read preprocessing, (2) metagenome assembly and QC, (3) genome binning and refinement and (4) taxonomic and functional annotation of the recovered MAGs. In the figure, examples of several tools for each of the steps is also provided (names italicized).