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Metagenome-assembled genome: ERR11768867_binner12_Refined_9

Identifiers
BioSample: SAMEA117401634; SRA: ERS22469221
Organism
Lactobacillus johnsonii
cellular organisms; Bacteria; Bacillati; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus
Attributes
broad-scale environmental contextpoultry
collection date2019-10
environmental mediumpoultry litter
geographic locationItaly
investigation typemetagenome-assembled genome
isolation sourcechicken gut metagenome
project namePoultry 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 nameERR11768867_binner12_Refined_9
ENA first public2024-11-29
ENA-CHECKLISTERC000047
INSDC center nameEMG
INSDC statuspublic
Submitter IdERR11768867_binner12_Refined_9
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwareMetaSPAdes_v3.15.5
binning parametersdefault
binning softwareMGnify-genomes-generation-pipeline_v1.0.0
broker nameEBI-EMG
completeness score95.83
completeness softwareCheckM2_v1.0.1
contamination score0.33
geographic location (latitude)missing: third party data
geographic location (longitude)missing: third party data
local environmental contextchicken
metagenomic sourcechicken gut metagenome
sample derived fromSAMEA113907112
scientific_nameLactobacillus johnsonii
sequencing methodNextSeq 500
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic run ERR11768867 of study ERP148522.

BioProject
PRJEB82468
Retrieve all samples from this project

Submission
EBI; 2024-11-30
Accession:
SAMEA117401634
ID:
45111978

Nucleotide

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