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

Alneberg J, Karlsson CMG, Divne AM, Bergin C, Homa F, Lindh MV, Hugerth LW, Ettema TJG, Bertilsson S, Andersson AF, Pinhassi J

Microbiome 6 (1) - [2018-12-00; online 2018-09-28]

Prokaryotes 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. We 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. The 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.

Bioinformatics Compute and Storage [Service]

Microbial Single Cell Genomics [Collaborative]

NGI Stockholm (Genomics Applications) [Service]

NGI Stockholm (Genomics Production) [Service]

NGI Uppsala (SNP&SEQ Technology Platform) [Service]

National Genomics Infrastructure [Service]

QC bibliography QC xrefs

PubMed 30266101

DOI 10.1186/s40168-018-0550-0

Crossref 10.1186/s40168-018-0550-0

BioProject: PRJNA273799 Baltic Sea Surface Water Metagenome
SRA: SRP058493 Baltic Sea Surface Water Metagenome