title: Metagenome-assembled genome: SRR13428087_bin.27_metawrap_v1.3_MAG
organism: uncultured Lachnospiraceae bacterium
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2023-01-18
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2023-01-18
attributes.tag: External Id
attributes.value: SAMEA112227858
attributes.tag: INSDC center alias
attributes.value: EMG
attributes.tag: INSDC center name
attributes.value: EMG
attributes.tag: INSDC first public
attributes.value: 2023-01-18T16:18:32Z
attributes.tag: INSDC last update
attributes.value: 2023-01-18T16:18:32Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: SRR13428087_bin.27_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: mouse digestive system
attributes.tag: broker name
attributes.value: EMG broker account, EMBL-EBI
attributes.tag: collection date
attributes.value: 2019-09-09
attributes.tag: completeness score
attributes.value: 59.54
attributes.tag: completeness software
attributes.value: CheckM
attributes.tag: contamination score
attributes.value: 0.86
attributes.tag: environmental medium
attributes.value: feces
attributes.tag: geographic location (country and/or sea)
attributes.value: Luxembourg
attributes.tag: geographic location (latitude)
attributes.value: not provided
attributes.tag: geographic location (longitude)
attributes.value: not provided
attributes.tag: investigation type
attributes.value: metagenome-assembled genome
attributes.tag: isolation_source
attributes.value: mouse gut metagenome
attributes.tag: local environmental context
attributes.value: digestive tube
attributes.tag: metagenomic source
attributes.value: mouse gut metagenome
attributes.tag: project name
attributes.value: 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.
attributes.tag: sample derived from
attributes.value: SAMN17307571
attributes.tag: sample name
attributes.value: SRR13428087_bin.27_metawrap_v1.3_MAG
attributes.tag: sequencing method
attributes.value: NextSeq 500
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__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__
attributes.tag: taxonomic identity marker
attributes.value: multi-marker approach