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text: hCoV-19/Switzerland/SZ-Risch-20220809R13064/2022

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Dr. Risch

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: AG

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/AG-Risch-20220810R13063/2022


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: GISAID Accession ID

text: Dr. Risch

characteristic: INSDC center name

text: public

text: SIB

text: Switzerland

characteristic: geographic location (country and/or sea)

text: GR

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

text: hCoV-19/Switzerland/GR-Risch-20220802R13006/2022


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Dr. Risch

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SIB

text: Switzerland

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/VD-Risch-20220808R13033/2022

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: GISAID Accession ID

text: Dr. Risch

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Liechtenstein

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Liechtenstein/FL-Risch-20220809R13066/2022

text: active surveillance in response to outbreak


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Dr. Risch

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: SIB

text: Dr. Risch Ostschweiz AG, Lagerstrasse 30, 9470 Buchs

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

text: hCoV-19/Switzerland/LU-Risch-20220803R13083/2022


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: GISAID Accession ID

text: Dr. Risch

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: SIB

text: Switzerland

text: SO

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/SO-Risch-20220807R13046/2022

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Dr. Risch

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: SG

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/SG-Risch-20220802R13013/2022


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: GISAID Accession ID

text: Dr. Risch

characteristic: INSDC center name

text: public

text: SIB

text: Switzerland

characteristic: geographic location (country and/or sea)

text: AG

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

text: hCoV-19/Switzerland/AG-Risch-20220808R13071/2022


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Dr. Risch

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SIB

text: Nadia Wohlwend, Faina Wehrli, Dominique Fabien Hilti, Sinem Kas, Martin Risch, Thomas Bodmer, Lorenz Risch

text: Switzerland

text: TG

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/TG-Risch-20220802R13009/2022

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: GISAID Accession ID

text: Dr. Risch

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Liechtenstein

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Liechtenstein/FL-Risch-20220805R13056/2022


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Dr. Risch

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: SIB

text: Switzerland

characteristic: geographic location (country and/or sea)

text: JU

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

text: hCoV-19/Switzerland/JU-Risch-20220808R13031/2022

text: active surveillance not initiated by an outbreak


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Canterbury

characteristic: INSDC center name

text: public

characteristic: INSDC status

tag: Namespace:University of Canterbury

text: Raw fastq files from genome sequencing of V.stagnispumantis type strain CP.B2

characteristic: description

text: New Zealand

text: Waiotapu geothermal field, Taupo Volcanic Zone

text: Venenivibrio stagnispumantis

characteristic: isolate

text: Champagne Pool

text: Venenivibrio stagnispumantis

characteristic: organism

text: Venenivibrio stagnispumantis

characteristic: strain

text: Whole genome shotgun sequence of V. stagnispumantis CP.B2

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

characteristic: INSDC first public

text: public

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 v3.15.3

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 v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

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 SRR7986790 of study SRP164743.

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: Frischella perrara

text: The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of Apicystis bombi, a parasitic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota.

characteristic: project name

characteristic: sample derived from

text: Frischella perrara

text: Illumina HiSeq 2500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Orbales;f__Orbaceae;g__Frischella;s__Frischella perrara

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986790_bin.1_metawrap_v1.3.0_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 v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: Snodgrassella alvi

characteristic: organism

text: Snodgrassella alvi

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae;g__Snodgrassella;s__Snodgrassella alvi

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986790_bin.3_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

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 SRR7986792 of study SRP164743.

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: uncultured Lactobacillus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Lactobacillus sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus bombi

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986792_bin.2_metawrap_v1.3.0_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 v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR7986793 of study SRP164743.

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: uncultured Commensalibacter sp.

characteristic: organism

text: uncultured Commensalibacter sp.

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Acetobacteraceae;g__Commensalibacter;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986793_bin.7_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

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 SRR7986796 of study SRP164743.

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: Serratia fonticola

characteristic: project name

characteristic: sample derived from

text: Serratia fonticola

text: Illumina HiSeq 2500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Yersiniaceae;g__Serratia;s__Serratia fonticola

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986796_bin.1_metawrap_v1.3.0_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 v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: uncultured Bartonella sp.

characteristic: organism

text: uncultured Bartonella sp.

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Bartonellaceae;g__Bartonella;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986796_bin.5_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

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

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

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 SRR7986799 of study SRP164743.

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: Bartonella apis

text: The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of Apicystis bombi, a parasitic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota.

characteristic: project name

characteristic: sample derived from

text: Bartonella apis

text: Illumina HiSeq 2500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Bartonellaceae;g__Bartonella;s__Bartonella apis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986799_bin.1_metawrap_v1.3.0_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 v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR7986800 of study SRP164743.

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: Gilliamella apicola

characteristic: organism

text: Gilliamella apicola

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Orbales;f__Orbaceae;g__Gilliamella;s__Gilliamella apicola

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986800_bin.1_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

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 SRR7986801 of study SRP164743.

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: uncultured Apibacter sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Apibacter sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Flavobacteriaceae;g__Apibacter;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986801_bin.1_metawrap_v1.3.0_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 v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: uncultured Lactobacillus sp.

characteristic: organism

text: uncultured Lactobacillus sp.

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus mellifer

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986801_bin.2_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: Bifidobacterium asteroides

characteristic: project name

characteristic: sample derived from

text: Bifidobacterium asteroides

text: Illumina HiSeq 2500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium asteroides

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986801_bin.4_metawrap_v1.3.0_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 v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR7986802 of study SRP164743.

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: uncultured Lactobacillus sp.

characteristic: organism

text: uncultured Lactobacillus sp.

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus kunkeei

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986802_bin.5_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

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

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

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 SRR7986804 of study SRP164743.

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: uncultured Lactobacillus sp.

text: The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of Apicystis bombi, a parasitic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota.

characteristic: project name

characteristic: sample derived from

text: uncultured Lactobacillus sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986804_bin.1_metawrap_v1.3.0_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 v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: uncultured Commensalibacter sp.

characteristic: organism

text: uncultured Commensalibacter sp.

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Acetobacteraceae;g__Commensalibacter;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986804_bin.4_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

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 SRR7986807 of study SRP164743.

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: Lactobacillus apis

characteristic: project name

characteristic: sample derived from

text: Lactobacillus apis

text: Illumina HiSeq 2500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus apis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986807_bin.3_metawrap_v1.3.0_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 v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: Bartonella apis

characteristic: organism

text: Bartonella apis

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Bartonellaceae;g__Bartonella;s__Bartonella apis

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986807_bin.4_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

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 SRR7986808 of study SRP164743.

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: Bartonella apis

characteristic: project name

characteristic: sample derived from

text: Bartonella apis

text: Illumina HiSeq 2500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986808_bin.11_metawrap_v1.3.0_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 v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: uncultured Lactobacillus sp.

characteristic: organism

text: uncultured Lactobacillus sp.

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986808_bin.4_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: uncultured Lactobacillus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Lactobacillus sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986808_bin.8_metawrap_v1.3.0_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 v3.15.3

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 v1.3.0

characteristic: binning software

text: insect

characteristic: broad-scale environmental context

text: EBI-EMG

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR7986811 of study SRP164743.

characteristic: description

text: thorax and abdomen

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: honeybee metagenome

text: honeybee

text: honeybee metagenome

text: Cedecea davisae

characteristic: organism

text: Cedecea davisae

text: Illumina HiSeq 2500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea;s__Cedecea davisae

text: multi-marker approach

text: Metagenome-assembled genome: SRR7986811_bin.1_metawrap_v1.3.0_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3.0

text: insect

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: thorax and abdomen

characteristic: environmental medium

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: honeybee metagenome

text: honeybee

characteristic: local environmental context

text: honeybee metagenome

characteristic: metagenomic source

text: uncultured Commensalibacter sp.

text: The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of Apicystis bombi, a parasitic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota.

characteristic: project name

characteristic: sample derived from

text: uncultured Commensalibacter sp.

text: Illumina HiSeq 2500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Acetobacteraceae;g__Commensalibacter;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR7986811_bin.4_metawrap_v1.3.0_MAG