| broad-scale environmental context | Pig digestive system |
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| collection date | not provided |
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| environmental medium | Feces |
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| geographic location | not provided |
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| investigation type | metagenome-assembled genome |
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| isolation source | pig gut metagenome |
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| project name | 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. |
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| sample name | SRR14812340_bin.37_metaWRAP_v1.3_MAG |
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| ENA-CHECKLIST | ERC000047 |
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| ENA-FIRST-PUBLIC | 2022-08-15 |
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| ENA-LAST-UPDATE | 2022-08-15 |
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| External Id | SAMEA110653532 |
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| INSDC center alias | EMG |
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| INSDC center name | EMG |
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| INSDC first public | 2022-08-15T16:14:16Z |
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| INSDC last update | 2022-08-15T16:14:16Z |
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| INSDC status | public |
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| Submitter Id | SRR14812340_bin.37_metaWRAP_v1.3_MAG |
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| assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics |
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| assembly software | metaSPAdes v3.15.3 |
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| binning parameters | MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. |
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| binning software | metaWRAP v1.3 |
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| broker name | EMG broker account, EMBL-EBI |
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| completeness score | 93.66 |
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| completeness software | CheckM |
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| contamination score | 0.87 |
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| geographic location (latitude) | not provided |
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| geographic location (longitude) | not provided |
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| local environmental context | Intestine |
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| metagenomic source | pig gut metagenome |
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| sample derived from | SAMN19686884 |
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| sequencing method | Illumina HiSeq 4000 |
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| taxonomic classification | 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 johnsonii |
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| taxonomic identity marker | multi-marker approach |
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