| collection date | 2008-01-01 |
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| broad-scale environmental context | Host-associated |
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| local-scale environmental context | Human |
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| environmental medium | Digestive system |
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| geographic location | Denmark |
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| investigation type | metagenome-assembled genome |
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| isolation source | human gut metagenome |
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| project name | 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 |
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| sample name | ERR209456_bin.21_CONCOCT_v1.1_MAG |
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| ENA-CHECKLIST | ERC000047 |
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| ENA-FIRST-PUBLIC | 2023-01-03 |
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| ENA-LAST-UPDATE | 2023-01-03 |
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| External Id | SAMEA14083900 |
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| INSDC center alias | EBI |
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| INSDC center name | European Bioinformatics Institute |
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| INSDC first public | 2023-01-03T00:33:44Z |
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| INSDC last update | 2023-01-03T00:33:44Z |
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| INSDC status | public |
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| Submitter Id | ERR209456_bin.21_CONCOCT_v1.1_MAG |
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| assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics |
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| assembly software | metaspadesv3.11.1 |
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| binning parameters | Default |
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| binning software | CONCOCT v1.1 |
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| broker name | EMG broker account, EMBL-EBI |
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| completeness score | 96.63 |
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| completeness software | CheckM |
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| contamination score | 1.12 |
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| geographic location (latitude) | 55.676098 |
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| geographic location (longitude) | 12.568337 |
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| metagenomic source | human gut metagenome |
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| sample derived from | SAMEA2042605 |
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| scientific_name | uncultured Mollicutes bacterium |
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| sequencing method | Illumina Genome Analyzer IIx |
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| taxonomic identity marker | multi-marker approach |
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