Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

Assembling microbial and phage genomes from metagenomes is a powerful and appealing method to understand structure-function relationships in complex environments that are dominated by uncultured and/or under-studied groups. This study aimed to investigate the impact of incorporating long-read data into the process of reconstructing metagenome-assembled genomes (MAGs) from a complex groundwater aquifer. We generated shotgun metagenomes with traditional Illumina sequencing accompanied by long reads derived from the Oxford Nanopore sequencing platform. This work provides quantitative data to inform a cost-benefit analysis on the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups. Groundwater was collected from the Hainich Critical Zone Exploratory, a near-surface aquifer transect that is established in NW Thuringia, Germany. This data set is part of the DFG-funded CRC AquaDiva (https://www.aquadiva.uni-jena.de/) of the Friedrich Schiller University Jena.