| 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 | Spain |
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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 gut microbiota is key to human health and disease. Metagenome-wide association studies (MGWAS) that search for disease markers in the gut microbiota, species identification according to metagenomic linkage groups (MLGs) or metagenomic clusters (MGCs), and metatranscriptomics or metaproteomics studies, all depend on a reference gene catalog, which has only been available for individual cohorts or based on reference genome or protein sequences. Here we report a high-quality integrated reference gene catalog consisting 9,879,896 genes, using 6.4 TB sequencing data derived from 1267 published and unpublished human gut metagenomes from three continents. The catalog represents a comprehensive collection of common and rare species, genes and genetic variants, and suggests individuality in the human gut microbiota. Analyses of a group of Chinese and Danish samples using the catalog revealed country-specific signatures in nutrient and xenobiotic metabolism. Our data suggest that interventions on nutrition, pollution and epidemiology should be tailored to the gut microbiota of a given population or even personalized for an individual. |
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| sample name | ERR414465_bin.31_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 | SAMEA14084394 |
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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 | 2023-01-03T00:33:09Z |
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| INSDC last update | 2023-01-03T00:33:09Z |
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| INSDC status | public |
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| Submitter Id | ERR414465_bin.31_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 | spades_v3.11.1 |
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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 | 93.16 |
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| completeness software | CheckM |
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| contamination score | 0.0 |
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| geographic location (latitude) | 40.416634 |
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| geographic location (longitude) | -3.7037659 |
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| metagenomic source | human gut metagenome |
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| sample derived from | SAMEA2338835 |
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| scientific_name | uncultured Akkermansia sp. |
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| sequencing method | Illumina HiSeq 2000 |
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| taxonomic identity marker | multi-marker approach |
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