Metagenome-assembled genome: ERR1995237_bin.21_CON... - BioSample

Metagenome-assembled genome: ERR1995237_bin.21_CONCOCT_v1.1_MAG

Identifiers: BioSample: SAMEA14083869; SRA: ERS11687003

Organism: Haemophilus influenzae
cellular organisms; Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Haemophilus

Attributes

collection date	2012-05-07
broad-scale environmental context	Host-associated
local-scale environmental context	Human
environmental medium	Digestive system
geographic location	Denmark
investigation type	metagenome-assembled genome
isolation source	human gut metagenome
project name	Antibiotics 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 name	ERR1995237_bin.21_CONCOCT_v1.1_MAG
ENA-CHECKLIST	ERC000047
ENA-FIRST-PUBLIC	2023-01-03
ENA-LAST-UPDATE	2023-01-03
External Id	SAMEA14083869
INSDC center alias	EBI
INSDC center name	European Bioinformatics Institute
INSDC first public	2023-01-03T00:33:22Z
INSDC last update	2023-01-03T00:33:22Z
INSDC status	public
Submitter Id	ERR1995237_bin.21_CONCOCT_v1.1_MAG
assembly quality	Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software	spadesv3.13.0
binning parameters	Default
binning software	CONCOCT v1.1
broker name	EMG broker account, EMBL-EBI
completeness score	99.89
completeness software	CheckM
contamination score	0.08
geographic location (latitude)	55.65
geographic location (longitude)	12.47
metagenomic source	human gut metagenome
sample derived from	SAMEA104062409
scientific_name	Haemophilus influenzae
sequencing method	Illumina HiSeq 2000
taxonomic identity marker	multi-marker approach

Description: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1995237 of study ERP022986.

BioProject: PRJEB51075 Large-scale analysis of novel cellular microbes from the human gut biome
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Submission: EBI; 2023-01-04

Accession:: SAMEA14083869
ID:: 32560498

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Metagenome-assembled genome: ERR1995237_bin.21_CONCOCT_v1.1_MAG

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