Complete and validated genomes from a metagenome

The assembly and binning of metagenomically-assembled genomes (MAGs) using Illumina sequencing has improved the genomic characterization of unculturable communities. However, short-read-only metagenomic assemblies rarely result in completed genomes because of the difficulty assembling repetitive regions.

Here, we present a strategy to complete and validate multiple MAGs from a bacterial community using a combination of short and ultra long reads (N50 > 25 kb).

Our strategy is to perform an initial long read-only metagenomic assembly using metaFlye, followed by multiple rounds of polishing using both long and short reads. To validate the genomes, we verified that longs reads spanned the regions that were not supported by uniquely mapped paired-end Illumina sequences. We obtained multiple complete genomes from a naphthenic acid-degrading community, including one from the recently proposed Candidate Phyla Radiation. The majority of the population is represented by the assembled genomes; recruiting 63.77 % of Nanopore reads, and 64.38 % of Illumina reads.

The pipeline we developed will enable researchers to validate genomes from metagenomic assemblies, increasing the quality of metagenomically assembled genomes through additional scrutiny.