Improving recovery of member genomes from enrichment reactor microbial communities using MinION--based long read metagenomics

Abstract

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes. While much progress has been made on cultured isolates, the ability of these methods to recover genomes of member taxa in complex microbial communities is less clear. Here we examine the ability of long read data to recover genomes from enrichment reactor metagenomes. Such modified communities offer a moderate level of complexity compared to the source communities and so are realistic, yet tractable, systems to use for this problem. We sampled an enrichment bioreactor designed to target anaerobic ammonium-oxidising bacteria (AnAOB) and sequenced genomic DNA using both short read (Illumina 301bp PE) and long read data (MinION Mk1B) from the same extraction aliquot. The community contained 23 members, of which 16 had genome bins defined from an assembly of the short read data. Two distinct AnAOB species from genus Candidatus Brocadia were present and had complete genomes, of which one was the most abundant member species in the community. We can recover a 4Mb genome, in 2 contigs, of long read assembled sequence that is unambiguously associated with the most abundant AnAOB member genome. We conclude that obtaining near closed, complete genomes of members of low-medium microbial communities using MinION long read sequence is feasible.