2024-12-11
ENA first public
ERC000047
ENA-CHECKLIST
CMR
INSDC center name
public
INSDC status
ERS22187503
SRA accession
ERP122455_co4_33
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaSPAdes;3.15.4;default
assembly software
coverage and kmer
binning parameters
MetaBAT2;2.15;default
binning software
engineered
broad-scale environmental context
2017-06-07
collection date
95.15
%
completeness score
CheckM2;1.0.2;default
completeness software
0.12
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic run ERR5295732 of study ERP122455.
description
engineered
environmental medium
United Kingdom
geographic location (country and/or sea)
52.83877326
DD
geographic location (latitude)
-1.24955258
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
metagenome
isolation_source
metagenome
local environmental context
metagenome
metagenomic source
uncultured Lachnospiraceae bacterium
organism
Our vision is to establish a strategic research programme in antimicrobial resistance (AMR) in waste from agricultural farm environments. Our aim is to quantify and mitigate the risks of emergence of resistant pathogens and AMR gene reservoirs associated with mixing antimicrobials with waste matter in these environments.The project is focussed on the University of Nottingham’s (UoN) dairy and arable farm, which is typical of high performance UK dairy production, with ~200 high yielding cows. Slurry is stored in a 3M L slurry tank and subsequently spread on surrounding fields. We hypothesise that conditions in the slurry tank environment drive the evolution and acquisition of antimicrobial resistance, and the slurry acts as a reservoir for AMR that is regularly distributed into the environmentThe project consists of six integrated Research Questions:RQ1: What are the levels and nature of antimicrobial and virulence genes present in the slurry tank, their prevalence, carriage, and bacterial hosts?RQ2: What are the chemical agents in the tank? What is their persistence?RQ3: To what extent is resistance maintained after slurry application to soil?RQ4: How can we elicit culturally embedded ways in which scientists and stakeholders know AMR risks? How can we use narrative and visual methods of engaging across these ways of knowing to develop resources for deliberation on AMR risk management?RQ5: To what extent can we reduce resistance profiles through changes in slurry tank composition?RQ6: Can we quantify the risk of emergence of AMR pathogens and what factors are predicted to control this risk best?
project name
SAMEA8023930
sample derived from
uncultured Lachnospiraceae bacterium
scientific_name
Illumina NovaSeq 6000
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: ERP122455_co4_33
title