Metagenome-assembled genome: SRR17257134_bin.20_metawrap_v1.3_MAG
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR17257134 of study SRP301591.
ENA-FIRST-PUBLIC
2022-12-15
ENA-LAST-UPDATE
2022-12-15
External Id
SAMEA112227924
INSDC center alias
EMG
INSDC center name
EMG
INSDC first public
2022-12-15T16:21:26Z
INSDC last update
2022-12-15T16:21:26Z
INSDC status
public
Submitter Id
SRR17257134_bin.20_metawrap_v1.3_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaSPAdes v3.15.3
binning parameters
MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning software
metawrap v1.3
broad-scale environmental context
mouse digestive system
broker name
EMG broker account, EMBL-EBI
collection date
2020-09-12
completeness score
97.47
completeness software
CheckM
contamination score
1.58
environmental medium
feces
geographic location (country and/or sea)
Luxembourg
geographic location (latitude)
not provided
geographic location (longitude)
not provided
investigation type
metagenome-assembled genome
isolation_source
mouse gut metagenome
local environmental context
digestive tube
metagenomic source
mouse gut metagenome
project name
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.
sample derived from
SAMN24154457
sample name
SRR17257134_bin.20_metawrap_v1.3_MAG
sequencing method
NextSeq 550
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__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__
taxonomic identity marker
multi-marker approach