Metagenome-assembled genome: ERR11768849_concoct_18

Identifiers: BioSample: SAMEA117401579; SRA: ERS22469166

Organism: uncultured Oscillospiraceae bacterium
cellular organisms; Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales; Oscillospiraceae; environmental samples

Attributes

broad-scale environmental context	poultry
collection date	2019-10
environmental medium	poultry litter
geographic location	Italy
investigation type	metagenome-assembled genome
isolation source	chicken gut metagenome
project name	Poultry farms are hotspots for the development and spread of antibiotic resistance genes (ARGs), due to high stocking densities and extensive use of antibiotics, posing a threat of spread and contagion to workers and the external environment. Here, we applied shotgun metagenome sequencing to characterize the gut microbiome and resistome of poultry, workers and their households - also including microbiomes from the internal and external farm environment – in three different farms in Italy during a complete rearing cycle. Our results highlighted a relevant overlap among the microbiomes of poultry, workers, and their families (gut and skin), with clinically relevant ARGs and associated mobile elements shared in both poultry and human samples. On a finer scale, the reconstruction of species-level genome bins (SGBs) allowed us to delineate the dynamics of microorganism and ARGs dispersion from farm systems. We found the associations with worker microbiomes representing the main route of ARGs dispersion from poultry to human populations. Collectively, our findings clearly demonstrate the urgent need to implement more effective procedures to counteract ARGs dispersion from poultry food systems and the relevance of metagenomics-based metacommunity approaches to monitor the ARGs dispersion process for the safety of the working environment on farms.
sample name	ERR11768849_concoct_18
ENA first public	2024-11-29
ENA-CHECKLIST	ERC000047
INSDC center name	EMG
INSDC status	public
Submitter Id	ERR11768849_concoct_18
assembly quality	Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software	MetaSPAdes_v3.15.5
binning parameters	default
binning software	MGnify-genomes-generation-pipeline_v1.0.0
broker name	EBI-EMG
completeness score	93.04
completeness software	CheckM2_v1.0.1
contamination score	2.35
geographic location (latitude)	missing: third party data
geographic location (longitude)	missing: third party data
local environmental context	chicken
metagenomic source	chicken gut metagenome
sample derived from	SAMEA113907094
scientific_name	uncultured Oscillospiraceae bacterium
sequencing method	NextSeq 500
taxonomic identity marker	multi-marker approach

Description: This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic run ERR11768849 of study ERP148522.

Submission: EBI; 2024-11-30

Accession:: SAMEA117401579
ID:: 45113246

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Metagenome-assembled genome: ERR11768849_concoct_18

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