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Metagenome-assembled genome: ERR1995250_bin.62_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14083874; SRA: ERS11687008
Organism
uncultured Alphaproteobacteria bacterium
cellular organisms; Bacteria; Pseudomonadota; Alphaproteobacteria; environmental samples
Attributes
collection date2013-03-06
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationDenmark
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project nameAntibiotics have profound impacts on the microbial communities living in the human gut, where bacterial species harbor and exchange antibiotic resistance genes collectively called resistome. Human population surveys have demonstrated that gut microbial resistomes reflect local antibiotics usage patterns, while previous small cohort studies based on single antibiotic exposures have shown varying degrees of antibiotic impact on the gut microbiota and their associated resistome. However, the role of resistomes of particular gut species in their ability to persist in the face of antibiotic treatment has not been systematically studied.Applying shotgun sequencing and quantitative metagenomics, we analyzed the partial eradication and subsequent regrowth of gut microbiota in 12 healthy young men over a 6 month period following a 4-day intervention with three broad-spectrum antibiotics. The gut microbial communities of the study subjects underwent profound compositional changes due to the treatment but slowly recovered to near-baseline compositions. Immediately after the treatment, the gut microbiota featured an increased relative abundance of opportunistic and proinflammatory bacterial species, and a decreased relative abundance of short chain fatty acid producers, while exhibiting an increased functional potential for multidrug efflux pumps and virulence factors. These enrichment trends were weaker after 8 days and mostly cleared out after 42 days. However, 9 common intestinal commensal species found at baseline and associated with short chain fatty production or efficient digestion of polysaccharides remained undetectable in most of the subjects even after 180 days.Carrying genes that confer resistance to the antibiotics used in this multidrug study had specific consequences for the survival and de novo colonization potential of microbial species. While species harboring beta-lactam resistance genes were positively selected during and after the intervention, those harboring glycopeptide or aminoglycoside resistance exhibited increased odds of de novo colonization but decreased odds of survival. Despite a mild long-lasting imprint following exposure to three antibiotics, the gut microbiota of healthy young adults are resilient to a broad-spectrum antibiotic intervention, and their recovery process is modulated by antibiotic resistance gene carriage.
sample nameERR1995250_bin.62_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14083874
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:33:27Z
INSDC last update2023-01-03T00:33:27Z
INSDC statuspublic
Submitter IdERR1995250_bin.62_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwarespadesv3.13.0
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score96.7
completeness softwareCheckM
contamination score2.2
geographic location (latitude)55.65
geographic location (longitude)12.47
metagenomic sourcehuman gut metagenome
sample derived fromSAMEA104062423
scientific_nameuncultured Alphaproteobacteria bacterium
sequencing methodIllumina HiSeq 2000
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1995250 of study ERP022986.

BioProject
PRJEB51075 Large-scale analysis of novel cellular microbes from the human gut biome
Retrieve all samples from this project

Submission
EBI; 2023-01-04
Accession:
SAMEA14083874
ID:
32560503

BioProject Nucleotide

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