Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

Abstract

BackgroundProkaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.ResultsWe compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77–99.84%) across overlapping regions (30–80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.ConclusionsThe strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0550-0) contains supplementary material, which is available to authorized users.

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity

“…high strain variation, and/or sequences with insufficient compositional or coding signal. Recent work has particularly focused on the problem of strain confusion, in which high strain variation results in considerable fragmentation of assembled content in mock or synthetic communities [11,12]; the extent and impact of strain confusion in real metagenomes is still unknown but potentially significant-metagenome-assembled genomes may be missing 20-40% of true content [13][14][15].…”

Metagenomic Association Analysis of Gut Symbiont Lactobacillus Reuteri Without Host-Specific Genome Isolation

“…Nonetheless, the analysis based on read-mapping has advantages over the MAG placement based one. First, obtaining high-quality MAGs requires a large number of samples [23]. In this study, we obtained 85 medium-to-high quality MAGs from 148 metagenomic samples.…”

“…In this study, we obtained 85 medium-to-high quality MAGs from 148 metagenomic samples. Since the quality of MAGs depends on the quality of assembly [23,24], the phylogenetic placement would be inaccurate if the assembled contigs contain too much noise or have low coverages. Additionally, the MAG often represents multiple strains rather than an individual so that it could cause a bias in the strain-level analysis [23,24].…”

A lab in the field: applications of real-time, in situ metagenomic sequencing

“…Long-scale studies like the Earth Microbiome Project have led to the massive characterization of microbial populations inhabiting different environments on our planet [ 30 ]. Moreover, metagenomic sequencing has proved to be very useful for a wide range of applications such as recovering new genomes from unculturable organisms, mining microbial enzymes with potential applications in the industry, or discovering new biosynthetic gene clusters [ 31–33 ]. These studies have typically relied on next-generation sequencing platforms like Illumina, which usually requires shipping samples to a centralized sequencing facility.…”