1 Department of Chemistry and Bioscience, The Faculty of Engineering and Science (ENG), Aalborg University, VBN2 Section of Biotechnology, The Faculty of Engineering and Science (ENG), Aalborg University, VBN3 The Faculty of Engineering and Science (ENG), Aalborg University, VBN4 EcoDesign, The Faculty of Engineering and Science (ENG), Aalborg University, VBN5 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Australia
Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition–independent approach to recover high-quality microbial genomes from deeply sequenced metagenomes. Multiple metagenomes of the same community, which differ in relative population abundances, were used to assemble 31 bacterial genomes, including rare (<1% relative abundance) species, from an activated sludge bioreactor. Twelve genomes were assembled into complete or near-complete chromosomes. Four belong to the candidate bacterial phylum TM7 and represent the most complete genomes for this phylum to date (relative abundances, 0.06–1.58%). Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than other currently used methods, which are primarily based on sequence composition. This approach will be an important addition to the standard metagenome toolbox and greatly improve access to genomes of uncultured microorganisms.