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text: hCoV-19/Switzerland/TI-EOC-26552823/2022

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status: PUBLIC

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characteristic: GISAID Accession ID

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text: public

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tag: Namespace:Laboratorio di Microbiologia, Dipartimento di Medicina di Laboratorio EOLAB, Ente Ospedaliero Cantonale, Bellinzona, Switzerland

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text: SIB

text: Laboratorio di Microbiologia, Istituto di Medicina di Laboratorio EOLAB, Ente Ospedaliero Cantonale, Bellinzona, Switzerland

characteristic: collection date

text: Martinetti Lucchini Gladys, Valeria Spina

characteristic: collector name

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characteristic: isolate

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: Laboratorio di Microbiologia, Dipartimento di Medicina di Laboratorio EOLAB, Ente Ospedaliero Cantonale, Bellinzona, Switzerland

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characteristic: ENA-CHECKLIST

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characteristic: External Id

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characteristic: isolate

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characteristic: GISAID Accession ID

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text: public

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characteristic: organism

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

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characteristic: collection date

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characteristic: geographic location (country and/or sea)

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characteristic: GISAID Accession ID

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

text: SIB

text: Switzerland

text: TI

characteristic: geographic location (region and locality)

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characteristic: isolate

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: public

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characteristic: broker name

characteristic: collecting institution

text: Switzerland

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text: Human

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text: restricted access

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text: hCoV-19/Switzerland/TI-EOC-26539601/2022

characteristic: organism

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characteristic: GISAID Accession ID

characteristic: INSDC center name

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: TI

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text: restricted access

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text: hCoV-19/Switzerland/TI-EOC-26539666/2022


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2245331 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Prevotellaceae bacterium

text: Antimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://www.effort-against-amr.eu/), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 Gigabases of DNA sequence, using shotgun metagenomics. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.

characteristic: project name

characteristic: sample derived from

text: uncultured Prevotellaceae bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2245331_bin.30_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2244943 of study ERP024389.

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2244943_bin.46_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

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text: metaSPAdes v3.14.1

text: metaWRAP v1.1

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characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2241627 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2241627_bin.6_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Prevotella sp.

characteristic: organism

text: uncultured Prevotella sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2244943_bin.42_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

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characteristic: completeness score

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characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: Lactobacillus johnsonii

characteristic: project name

characteristic: sample derived from

text: Lactobacillus johnsonii

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2241627_bin.21_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

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characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

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characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

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text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2245331_bin.13_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

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text: metaSPAdes v3.14.1

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characteristic: completeness score

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characteristic: completeness software

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text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

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text: chicken gut metagenome

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text: uncultured Prevotella sp.

characteristic: project name

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text: uncultured Prevotella sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2245331_bin.1_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.35_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2241627_bin.31_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Lactobacillus sp.

characteristic: organism

text: uncultured Lactobacillus sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.50_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2241627_bin.2_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured bacterium

characteristic: organism

text: uncultured bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2244943_bin.3_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2245331 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Veillonellaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Veillonellaceae bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2245331_bin.33_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Bacteroides sp.

characteristic: organism

text: Antimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://www.effort-against-amr.eu/), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 Gigabases of DNA sequence, using shotgun metagenomics. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.

text: uncultured Bacteroides sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2245331_bin.18_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2244943 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Treponema sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Treponema sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.40_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2241627 of study ERP024389.

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Prevotella sp.

characteristic: organism

text: uncultured Prevotella sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.15_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.52_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.14_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.14_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2244943_bin.49_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.58_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Treponema sp.

characteristic: organism

text: uncultured Treponema sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2244943_bin.22_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Prevotella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Prevotella sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.59_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured bacterium

characteristic: organism

text: uncultured bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.36_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.15_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured bacterium

characteristic: organism

text: Antimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://www.effort-against-amr.eu/), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 Gigabases of DNA sequence, using shotgun metagenomics. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.

text: uncultured bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2244943_bin.38_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2244943 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.30_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2241627 of study ERP024389.

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Bacteroides sp.

characteristic: organism

text: uncultured Bacteroides sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.11_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Ruminococcus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Ruminococcus sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.20_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Treponema sp.

characteristic: organism

text: uncultured Treponema sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.17_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.36_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2245331 of study ERP024389.

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Prevotella sp.

characteristic: organism

text: uncultured Prevotella sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2245331_bin.21_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.24_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.34_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.37_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: Lactobacillus amylovorus

characteristic: organism

text: Lactobacillus amylovorus

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.1_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured bacterium

text: Antimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://www.effort-against-amr.eu/), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 Gigabases of DNA sequence, using shotgun metagenomics. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.

characteristic: project name

characteristic: sample derived from

text: uncultured bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2241627_bin.45_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2245331_bin.57_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2244943 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Streptococcus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Streptococcus sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.41_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Prevotellaceae bacterium

characteristic: organism

text: uncultured Prevotellaceae bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2245331_bin.23_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2241627 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2241627_bin.44_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.10_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Prevotella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Prevotella sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2241627_bin.20_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Prevotellaceae bacterium

characteristic: organism

text: uncultured Prevotellaceae bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2244943_bin.13_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.51_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2245331 of study ERP024389.

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2245331_bin.46_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Prevotella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Prevotella sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.12_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Lachnobacterium sp.

characteristic: organism

text: Antimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://www.effort-against-amr.eu/), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 Gigabases of DNA sequence, using shotgun metagenomics. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.

text: uncultured Lachnobacterium sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2245331_bin.34_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2245331_bin.36_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Prevotella sp.

characteristic: organism

text: uncultured Prevotella sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2245331_bin.26_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2244943 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.6_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2244943_bin.56_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2241627 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2241627_bin.40_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Parabacteroides sp.

characteristic: organism

text: uncultured Parabacteroides sp.

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.29_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Prevotella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Prevotella sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2244943_bin.39_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2241627_bin.56_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes v3.14.1

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2245331_bin.28_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

characteristic: collection date

text: CheckM

text: Chicken digestive system

text: Digestive tube

text: Fecal

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: chicken gut metagenome

text: chicken gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: Illumina HiSeq 2500

text: multi-marker approach

text: Metagenome-assembled genome: ERR2244943_bin.55_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.14.1

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: metaWRAP v1.1

text: EBI-EMG

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2245331 of study ERP024389.

characteristic: description

text: Chicken digestive system

characteristic: environment (biome)

text: Digestive tube

characteristic: environment (feature)

text: Fecal

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

characteristic: isolation source

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Treponema sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Treponema sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR2245331_bin.51_metaWRAP_v1.1_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: Medisupport

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: Bioanalytika AG, Luzern, Switzerland

characteristic: collecting institution

characteristic: collection date

text: Tanguy ARAUD, Geraldine Jost, Katia Jaton, Nadia Liassine

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: LU

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/LU-DIA-011438291501/2022

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: active surveillance in response to outbreak

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

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characteristic: External Id

characteristic: GISAID Accession ID

text: Medisupport

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Bioanalytika AG, Luzern, Switzerland

text: Switzerland

text: LU

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/LU-DIA-011438292201/2022


text: Medisupport

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: Bioanalytika AG, Luzern, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

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text: LU

characteristic: geographic location (region and locality)

text: Human

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text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/LU-DIA-011438292301/2022


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: Medisupport

text: public

text: SIB

text: Bioanalytika AG, Luzern, Switzerland

text: Switzerland

text: LU

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/LU-DIA-011438292401/2022

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: GISAID Accession ID

text: Medisupport

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: Bioanalytika AG, Luzern, Switzerland

characteristic: collecting institution

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text: Switzerland

text: LU

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/LU-DIA-011438292501/2022


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Medisupport

text: public

text: SIB

text: Bioanalytika AG, Luzern, Switzerland

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: LU

characteristic: geographic location (region and locality)

text: Human

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text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/LU-DIA-011438292601/2022


text: CNRS

characteristic: INSDC center name

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text: public

text: This is the genome sequence of a thermophilic species of the recently discovered cyanobacterial order Gloeomargaritales

characteristic: description

text: Temperate rainforest

characteristic: environment (biome)

text: Hot spring

characteristic: environment (feature)

text: Microbial mat

characteristic: environment (material)

text: Canada

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: Gloeomargaritales cyanobacterium VI4D9

characteristic: organism

text: Exploring genome diversity of Gloeomargaritales, the closest relatives of plastids

characteristic: project name

text: Gloeomargaritales cyanobacterium VI4D9

text: Illumina HiSeq + Oxford Nanopore MinION

characteristic: sequencing method

text: Thermomargarita ahousahtiae VI4D9

characteristic: title


characteristic: ENA-CHECKLIST

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characteristic: External Id

characteristic: GISAID Accession ID

text: Medisupport

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text: Bioanalytika AG, Luzern, Switzerland

characteristic: collecting institution

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text: Switzerland

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text: LU

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text: Human

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text: restricted access

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text: Homo sapiens

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text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/LU-DIA-011438292701/2022

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-CHECKLIST

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characteristic: External Id

characteristic: GISAID Accession ID

text: Medisupport

characteristic: INSDC center name

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text: public

text: SIB

text: Bioanalytika AG, Luzern, Switzerland

text: Switzerland

text: LU

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/LU-DIA-011438292801/2022

characteristic: organism

characteristic: title


text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:INSTITUTE OF APPLIED BIOSCIENCES - CERTH

characteristic: Submitter Id

text: General Hospital of Kavala

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

characteristic: common name

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Kavala

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

text: Homo sapiens

text: male

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUTE OF APPLIED BIOSCIENCES - CERTH

text: public

text: General Hospital of Kavala

text: not provided

text: Greece

text: Kavala

text: human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

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text: RNA

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characteristic: INSDC center name

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text: public

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characteristic: SRA accession

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text: General Hospital of Kavala

characteristic: collecting institution

characteristic: collection date

text: not provided

text: Greece

text: Kavala

text: human

text: not provided

text: Homo sapiens

text: male

text: RNA

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: General Hospital of Drama

text: not provided

characteristic: collector name

characteristic: common name

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Drama

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

text: Homo sapiens

text: female

text: RNA


characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

text: General Hospital of Drama

text: not provided

text: Greece

text: Drama

text: human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

characteristic: host subject id

text: RNA

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: General Hospital of Drama

characteristic: collecting institution

text: not provided

characteristic: collection date

text: not provided

text: Greece

text: Xanthi

text: human

text: not provided

text: Homo sapiens

text: not provided

text: RNA

characteristic: organism

characteristic: title


characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: General Hospital of Serres

text: not provided

characteristic: collector name

characteristic: common name

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Serres

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: General Hospital of Katerini

text: not provided

text: Greece

text: Katerini

text: human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

characteristic: host subject id

text: RNA

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characteristic: INSDC center name

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text: public

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characteristic: SRA accession

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text: General Hospital of Katerini

characteristic: collecting institution

characteristic: collection date

text: not provided

text: Greece

text: Katerini

text: human

text: not provided

text: Homo sapiens

text: female

text: RNA

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: General Hospital of Halkidiki

text: not provided

characteristic: collector name

characteristic: common name

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Chalkidiki

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

text: Homo sapiens

text: male

text: RNA


characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: General Hospital of Halkidiki

text: not provided

text: Greece

text: Chalkidiki

text: human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: RNA

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: University General Hospital of Thessaloniki, AHEPA

characteristic: collecting institution

characteristic: collection date

text: not provided

text: Greece

text: Mitilini

text: human

text: not provided

text: Homo sapiens

text: male

text: RNA

characteristic: organism

characteristic: title


characteristic: INSDC center name

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text: public

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text: not provided

characteristic: collector name

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text: Greece

characteristic: geographic location (country and/or sea)

text: Kavala

characteristic: geographic location (region and locality)

text: human

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text: not provided

text: Homo sapiens

text: female

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: not provided

text: Greece

text: Thessaloniki

text: human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

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characteristic: INSDC center name

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: not provided

text: Greece

text: Thessaloniki

text: human

text: not provided

text: Homo sapiens

text: male

text: RNA

characteristic: organism

characteristic: title