SAMEA14083917 ERS11687051 Faecalibacterium prausnitzii This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR209721 of study ERP002061. EBI Generic Generic.1.0 ERC000047 2023-01-03 2023-01-03 SAMEA14083917 EBI European Bioinformatics Institute 2023-01-03T00:33:12Z 2023-01-03T00:33:12Z public ERR209721_bin.0_CONCOCT_v1.1_MAG Many fragments with little to no review of assembly other than reporting of standard assembly statistics metaspadesv3.11.1 Default CONCOCT v1.1 EMG broker account, EMBL-EBI 2008-01-01 92.04 CheckM 1.54 Host-associated Human Digestive system Spain 40.416634 -3.7037659 metagenome-assembled genome human gut metagenome human gut metagenome The microbial diversity of environments like the human gut extends far beyond what is covered by reference genomes. Here we present a method for exhaustive and unsupervised co-abundance gene binning across a series of highly complex metagenomic samples. As the method does not rely on previously sequenced reference genomes it allows for discovery of new species, viruses and clonal heterogeneity. We demonstrate the method on human gut microbiome data and identify 7,381 co-abundance gene groups (CAGs) ranging in size from 3 to 6,319 genes. The CAGs represent a wide variety of biological entities including microbial genomes, phages and clonal differences. We name the 741 largest of these metagenomic species (MGS), because they correspond to microbial species. In addition, we establish microbial host affiliations by dependency-associations for many small CAGs. Longitudinal sampling in the same individuals indicates that some of these dependency-associations are important for the persistence of their microbial host SAMEA2042219 ERR209721_bin.0_CONCOCT_v1.1_MAG Faecalibacterium prausnitzii Illumina Genome Analyzer IIx multi-marker approach