SAMEA112227948 ERS14338851 uncultured bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257141 of study SRP301591. EBI Generic Generic.1.0 ERC000047 2022-12-15 2022-12-15 SAMEA112227948 EMG EMG 2022-12-15T16:21:26Z 2022-12-15T16:21:26Z public SRR17257141_bin.15_metawrap_v1.3_MAG Many fragments with little to no review of assembly other than reporting of standard assembly statistics metaSPAdes v3.15.3 MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. metawrap v1.3 mouse digestive system EMG broker account, EMBL-EBI 2020-09-12 93.69 CheckM 1.58 feces Luxembourg not provided not provided metagenome-assembled genome mouse gut metagenome digestive tube mouse gut metagenome 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. SAMN24154415 SRR17257141_bin.15_metawrap_v1.3_MAG NextSeq 550 The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__ multi-marker approach