| broad-scale environmental context | human digestive system |
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| collection date | 2014-04-14 |
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| environmental medium | plaque biofilm |
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| geographic location | Australia |
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| investigation type | metagenome-assembled genome |
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| isolation source | oral metagenome |
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| project name | Antibiotic overuse has promoted the spread of antimicrobial resistance (AMR) with significant health and economic consequences. Surveillance of resistance reservoirs, like the rarely explored oral microbiome, is necessary to combat AMR. We characterised the development of the paediatric oral resistome and investigated its role in dental caries in 221 twin children sampled over the first decade of life. From 535 oral metagenomes, we identified 309 antimicrobial resistance genes (ARGs), which significantly clustered by age, with the influence of host genetics on antimicrobial resistance increasing over time. Our results suggest the mobilisation potential of ARGs increased with age as Tn916 transposase was co-located with more species and ARGs as children grew. Dental caries compared to health was associated with a depletion of ARGs and species, which was reversed when restored. Our results highlight the dynamic nature of the paediatric oral resistome, and its potential role in transmission of AMR and dysbiosis. |
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| sample name | ERR9968772_bin.23_MetaWRAP_v1.3_MAG |
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| ENA-CHECKLIST | ERC000047 |
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| INSDC center name | EMG |
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| Submitter Id | ERR9968772_bin.23_MetaWRAP_v1.3_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 | metaspades v3.15.3 |
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| binning parameters | MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. |
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| binning software | MetaWRAP v1.3 |
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| broker name | EBI-EMG |
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| completeness score | 96.55 |
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| completeness software | CheckM |
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| contamination score | 1.09 |
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| geographic location (latitude) | 33.8688 |
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| geographic location (longitude) | 151.2093 |
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| local environmental context | oral cavity |
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| metagenomic source | oral metagenome |
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| sample derived from | SAMEA110373439 |
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| scientific_name | Granulicatella elegans |
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| sequencing method | Illumina NovaSeq 6000 |
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| taxonomic classification | The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Granulicatella;s__Granulicatella elegans |
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| taxonomic identity marker | multi-marker approach |
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