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"data": {
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"key": "project name",
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"value": "Germany",
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"value": "2013/2016",
"unit": null
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"key": "environment (feature)",
"value": "Feces",
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},
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"value": "stool",
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"key": "sequencing method",
"value": "Illumina HiSeq",
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],
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"sample-desc": "Altered gut microbiome composition has been associated with many human diseases. However, microbiome-disease association studies have not always reported consistent results, creating an increasing need for cross-study comparisons. Here we present a meta-analysis of five faecal shotgun metagenomic studies of colorectal cancer (CRC) that are diverse in geographic sampling range and metagenomic data generation. We find a core of 30 species to be differentially abundant in CRC metagenomes (stringent FDR of 1E-05) including 8 species without genomic reference. Metagenomic classification models trained to detect CRC on one study generally maintained similar accuracy when applied to other studies. When combining training data across four studies, average accuracy on the fifth, held-out study was 0.83 (area under the receiver operating characteristic curve). These classifiers were CRC-specific as they maintained the expected false positive rate on other diseases. Functional metagenomic analysis uncovered an enrichment of amino acid and mucin degradation pathways in CRC metagenomes concomitant with a depletion of carbohydrate degradation, in line with established dietary CRC risk factors. We moreover found a strong enrichment of secondary bile acid conversion genes in CRC metagenomes suggesting a metabolic link between CRC-associated gut microbes and a high-risk diet rich in fat and red meat. Taken together, our meta-analysis establishes predictive taxonomic and functional metagenomic signatures for CRC that are robust to technical and biological variation providing further support for the development of microbiome-based diagnostic tests.",
"environment-biome": "Feces",
"environment-feature": "Feces",
"environment-material": "stool",
"sample-name": "CCMD35633353ST-11-0",
"sample-alias": "CCMD35633353ST-11-0",
"host-tax-id": 9606,
"species": "Homo sapiens",
"last-update": "2024-01-09T03:23:50"
},
"relationships": {
"biome": {
"data": {
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Large intestine:Fecal"
},
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Large%20intestine:Fecal?format=api"
}
},
"studies": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/ERS2637811/studies?format=api"
},
"data": [
{
"type": "studies",
"id": "MGYS00006553",
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},
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"related": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/ERS2637811/runs?format=api"
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},
"links": {
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}
}