2024-11-29
ENA first public
ERC000047
ENA-CHECKLIST
EMG
INSDC center name
public
INSDC status
ERS22469175
SRA accession
ERR11768915_binner123_Refined_8
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
MetaSPAdes_v3.15.5
assembly software
default
binning parameters
MGnify-genomes-generation-pipeline_v1.0.0
binning software
poultry
broad-scale environmental context
EBI-EMG
broker name
2019-10
collection date
98.73
%
completeness score
CheckM2_v1.0.1
completeness software
1.09
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic run ERR11768915 of study ERP148522.
description
poultry litter
environmental medium
Italy
geographic location (country and/or sea)
missing: third party data
DD
geographic location (latitude)
missing: third party data
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
chicken gut metagenome
isolation_source
chicken
local environmental context
chicken gut metagenome
metagenomic source
Candidatus Eisenbergiella merdigallinarum
organism
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.
project name
SAMEA113907160
sample derived from
Candidatus Eisenbergiella merdigallinarum
scientific_name
NextSeq 500
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: ERR11768915_binner123_Refined_8
title