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

Anders F. Andersson,Felix Homa,Johannes Alneberg,Christofer M. G. Karlsson,Claudia Bergin,Stefan Bertilsson,Markus V. Lindh,Jarone Pinhassi,Luisa W. Hugerth,Anna-Maria Divne,Thijs J. G. Ettema

doi:10.1186/s40168-018-0550-0

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.

Highlights

Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life
We obtained 16 single-amplified genome (SAG) of a variety of taxa including Bacteroidetes, Cyanobacteria, Alphaproteobacteria, and Gammaproteobacteria (Additional file 1: Table S1). These were compared to 83 Metagenome-assembled genome (MAG) from 30 phylogenetically distinct Baltic Sea clusters (BACLs) [23] (Additional file 2: Figure S1; Additional file 1: Table S1)
The SAGs ranged in size from 0.14 to 2.15 Million base pairs (Mbp) and MAGs from 0.59 to 2.98 Mbp (Additional file 1: Table S1)

Summary

Introduction

Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Molecular techniques allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating indepth analyses that may improve our understanding of these key organisms. Prokaryotes dominate the biosphere in the context of abundance and diversity [12] and hold key roles in biogeochemical processes essential to all life [13]. In the single-amplified genome (SAG) strategy, genomes of individual cells are sequenced. The step involves cell lysis and whole-genome amplification (WGA) for which three methods are most commonly used: PCR-based (e.g., degenerate oligonucleotide-primed PCR (DOP-PCR)), isothermal (e.g., multiple displacement amplification (MDA)), or hybrid methods (e.g., multiple annealing and looping-based amplification cycles (MALBAC)) [21] before applying shotgun sequencing and genome assembly [20, 22]

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