characteristics.text: ERC000047
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-01-18T16:18:32Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-01-18T16:18:32Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112227858
characteristics.characteristic: External Id
characteristics.text: EMG
characteristics.characteristic: INSDC center name
characteristics.text: 2023-01-18T16:18:32Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-01-18T16:18:32Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14338761
characteristics.characteristic: SRA accession
characteristics.text: SRR13428087_bin.27_metawrap_v1.3_MAG
characteristics.characteristic: Submitter Id
characteristics.text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
characteristics.characteristic: assembly quality
characteristics.text: metaSPAdes v3.15.3
characteristics.characteristic: assembly software
characteristics.text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
characteristics.characteristic: binning parameters
characteristics.text: metawrap v1.3
characteristics.characteristic: binning software
characteristics.text: mouse digestive system
characteristics.characteristic: broad-scale environmental context
characteristics.text: EBI-EMG
characteristics.characteristic: broker name
characteristics.text: 2019-09-09
characteristics.characteristic: collection date
characteristics.text: 59.54
characteristics.unit: %
characteristics.characteristic: completeness score
characteristics.text: CheckM
characteristics.characteristic: completeness software
characteristics.text: 0.86
characteristics.unit: %
characteristics.characteristic: contamination score
characteristics.text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428087 of study SRP301591.
characteristics.characteristic: description
characteristics.text: feces
characteristics.characteristic: environmental medium
characteristics.text: Luxembourg
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not provided
characteristics.unit: DD
characteristics.characteristic: geographic location (latitude)
characteristics.text: not provided
characteristics.unit: DD
characteristics.characteristic: geographic location (longitude)
characteristics.text: metagenome-assembled genome
characteristics.characteristic: investigation type
characteristics.text: mouse gut metagenome
characteristics.characteristic: isolation_source
characteristics.text: digestive tube
characteristics.characteristic: local environmental context
characteristics.text: mouse gut metagenome
characteristics.characteristic: metagenomic source
characteristics.text: uncultured Lachnospiraceae bacterium
characteristics.characteristic: organism
characteristics.text: The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale.
characteristics.characteristic: project name
characteristics.text: SAMN17307571
characteristics.characteristic: sample derived from
characteristics.text: uncultured Lachnospiraceae bacterium
characteristics.characteristic: scientific_name
characteristics.text: NextSeq 500
characteristics.characteristic: sequencing method
characteristics.text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__
characteristics.characteristic: taxonomic classification
characteristics.text: multi-marker approach
characteristics.characteristic: taxonomic identity marker
characteristics.text: Metagenome-assembled genome: SRR13428087_bin.27_metawrap_v1.3_MAG
characteristics.characteristic: title