Introduction to the principles and methods underlying the recovery of metagenome‐assembled genomes from metagenomic data

Abstract

The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it represents a relatively new discipline with various levels of complexity and demands on bioinformatics. The underlying principles and methods used in metagenomics are often seen as common knowledge and often not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes, that is, metagenome‐assembled genomes, integrating DNA sequencing, assembly, binning, identification and annotation.

The under-recognized dominance of magnetosome gene cluster-containing bacteria in oxygen-stratified freshwater ecosystems

“…During the magnetic enrichment step, fast-swimming cells with more efficient magnetotactic behavior, such as magnetotactic cocci within the Magnetococcia, are more preferentially enriched compared to those slow swimming populations with less efficient magnetotaxis 33 . Apart from magnetic cell enrichment, bias could also be introduced during the following 16S rRNA gene amplification or whole genomic DNA amplification processes [66][67][68] .…”

Hybrid sequence-based analysis reveals the distribution of bacterial species and genes in the oral microbiome at a high resolution

“…Traditionally, metagenomic shotgun sequencing has been used to study gene functions in the bacterial ora. However, metagenome shotgun analysis involves binning to identify bacterial species and then constructing a metagenome-assembled genome to search for gene distribution [44]. Although the binning technology has improved and contributed to the identi cation of many bacteria, the high homology of essential genes among species makes complete classi cation extremely di cult.…”

Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-Producing Escherichia coli in Presence of Commensal E. coli

“…Despite the possible influence of the enrichment conditions on the growth of the two strains, the limits that were determined in this study are more related to the post-enrichment steps, including DNA extraction, library preparation, data acquisition, and data processing [ 29 ]. It has been shown that the DNA extraction procedure can affect the structure of the population, especially in these particular conditions where high quantities of high-molecular-weight DNA are required (MinION sequencing from complex matrices) [ 30 ]. Similarly, according to the properties of the DNA (for example, GC content), the library preparation step performs differently [ 31 , 32 , 33 ].…”