organism: Stenotrophomonas maltophilia
description: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run ERR9968950 of study ERP139515.
attributes.tag: INSDC center name
attributes.value: EMG
attributes.tag: Submitter Id
attributes.value: ERR9968950_bin.7_MetaWRAP_v1.3_MAG
attributes.tag: assembly quality
attributes.value: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
attributes.tag: assembly software
attributes.value: metaspades v3.15.3
attributes.tag: binning parameters
attributes.value: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
attributes.tag: binning software
attributes.value: MetaWRAP v1.3
attributes.tag: broad-scale environmental context
attributes.value: human digestive system
attributes.tag: broker name
attributes.value: EBI-EMG
attributes.tag: collection date
attributes.value: 2008-01-21
attributes.tag: completeness score
attributes.value: 97.59
attributes.tag: completeness software
attributes.value: CheckM
attributes.tag: contamination score
attributes.value: 0.34
attributes.tag: environmental medium
attributes.value: plaque biofilm
attributes.tag: geographic location (country and/or sea)
attributes.value: Australia
attributes.tag: geographic location (latitude)
attributes.value: 33.8688
attributes.tag: geographic location (longitude)
attributes.value: 151.2093
attributes.tag: investigation type
attributes.value: metagenome-assembled genome
attributes.tag: isolation_source
attributes.value: oral metagenome
attributes.tag: local environmental context
attributes.value: oral cavity
attributes.tag: metagenomic source
attributes.value: oral metagenome
attributes.tag: project name
attributes.value: 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.
attributes.tag: sample derived from
attributes.value: SAMEA110373618
attributes.tag: sample name
attributes.value: ERR9968950_bin.7_MetaWRAP_v1.3_MAG
attributes.tag: scientific_name
attributes.value: Stenotrophomonas maltophilia
attributes.tag: sequencing method
attributes.value: Illumina NovaSeq 6000
attributes.tag: taxonomic classification
attributes.value: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas;s__Stenotrophomonas maltophilia
attributes.tag: taxonomic identity marker
attributes.value: multi-marker approach