ERC000047
ENA-CHECKLIST
2022-08-15T16:14:16Z
ENA-FIRST-PUBLIC
2022-08-15T16:14:16Z
ENA-LAST-UPDATE
SAMEA110653515
External Id
EMG
INSDC center name
2022-08-15T16:14:16Z
INSDC first public
2022-08-15T16:14:16Z
INSDC last update
public
INSDC status
ERS12751097
SRA accession
SRR14812339_bin.4_metaWRAP_v1.3_MAG
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaSPAdes v3.15.3
assembly software
MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning parameters
metaWRAP v1.3
binning software
Pig digestive system
broad-scale environmental context
EBI-EMG
broker name
not provided
collection date
74.23
%
completeness score
CheckM
completeness software
0.94
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR14812339 of study SRP324051.
description
Feces
environmental medium
not provided
geographic location (country and/or sea)
not provided
DD
geographic location (latitude)
not provided
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
pig gut metagenome
isolation_source
Intestine
local environmental context
pig gut metagenome
metagenomic source
uncultured Prevotellaceae bacterium
organism
In response to new stringent regulations in Canada on the use of antibiotics in animal production, many farms implemented practices to produce animals that are Raised Without Antibiotics (RWA) from birth to slaughter. This study aimed to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance monitoring of farms that adopted the RWA program and conventional farms using antibiotics as per the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week old pigs and composite ma-nure from the barn over 6 time points and applying whole genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced frequency of AMR genes in piglet feces and in barn manure. However, metagenomic analyses showed that RWA barns had significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.
project name
SAMN19686885
sample derived from
uncultured Prevotellaceae bacterium
scientific_name
Illumina HiSeq 4000
sequencing method
The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__;s__
taxonomic classification
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: SRR14812339_bin.4_metaWRAP_v1.3_MAG
title