description: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR14812369 of study SRP324051.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2022-08-15
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2022-08-15
attributes.tag: External Id
attributes.value: SAMEA110653612
attributes.tag: INSDC center alias
attributes.value: EMG
attributes.tag: INSDC center name
attributes.value: EMG
attributes.tag: INSDC first public
attributes.value: 2022-08-15T16:14:15Z
attributes.tag: INSDC last update
attributes.value: 2022-08-15T16:14:15Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: SRR14812369_bin.11_metaWRAP_v1.3_MAG
attributes.tag: assembly quality
attributes.value: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
attributes.tag: assembly software
attributes.value: metaSPAdes v3.15.3
attributes.tag: binning parameters
attributes.value: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
attributes.tag: binning software
attributes.value: metaWRAP v1.3
attributes.tag: broad-scale environmental context
attributes.value: Pig digestive system
attributes.tag: broker name
attributes.value: EMG broker account, EMBL-EBI
attributes.tag: collection date
attributes.value: not provided
attributes.tag: completeness score
attributes.value: 98.3
attributes.tag: completeness software
attributes.value: CheckM
attributes.tag: contamination score
attributes.value: 0.0
attributes.tag: environmental medium
attributes.value: Feces
attributes.tag: geographic location (country and/or sea)
attributes.value: not provided
attributes.tag: geographic location (latitude)
attributes.value: not provided
attributes.tag: geographic location (longitude)
attributes.value: not provided
attributes.tag: investigation type
attributes.value: metagenome-assembled genome
attributes.tag: isolation_source
attributes.value: pig gut metagenome
attributes.tag: local environmental context
attributes.value: Intestine
attributes.tag: metagenomic source
attributes.value: pig gut metagenome
attributes.tag: project name
attributes.value: 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.
attributes.tag: sample derived from
attributes.value: SAMN19686893
attributes.tag: sample name
attributes.value: SRR14812369_bin.11_metaWRAP_v1.3_MAG
attributes.tag: sequencing method
attributes.value: Illumina HiSeq 4000
attributes.tag: taxonomic classification
attributes.value: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus amylovorus
attributes.tag: taxonomic identity marker
attributes.value: multi-marker approach