text: Faculty of Medicine, TU Dresden

text: public

text: Recombinase library evolved for loxX-6 target site

text: Escherichia coli

text: Escherichia coli

text: loxX-6 Recombinase library


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oxford

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: NATURAL HISTORY MUSEUM

characteristic: barcoding center

text: COPO

characteristic: broker name

text: Liam Crowley

text: University of Oxford

characteristic: collecting institution

characteristic: collection date

unit: m

characteristic: elevation

text: United Kingdom

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: West Midlands | Olton

characteristic: geographic location (region and locality)

text: Buildings

characteristic: habitat

text: Liam Crowley

text: University of Oxford

text: adult

characteristic: lifestage

text: Lepisma saccharina

characteristic: organism

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

characteristic: project name

text: Potted

characteristic: sample collection device or method

text: Lepisma saccharina

text: NOT COLLECTED

characteristic: sex

text: 7695c769-0789-4ebc-b27a-4128ff5d43d4-DTOL-specimen

characteristic: title

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oxford

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: NATURAL HISTORY MUSEUM

characteristic: barcoding center

text: COPO

characteristic: broker name

text: Liam Crowley

text: University of Oxford

text: United Kingdom

text: Berkshire | Wytham Woods

text: Woodland

text: Liam Crowley

text: University of Oxford

text: adult

text: Eudonia lacustrata

text: WHOLE ORGANISM

text: DTOL

text: Light trap

text: Eudonia lacustrata

text: NOT COLLECTED

text: 40ea4fec-6010-4879-933d-8692d44d847a-DTOL-specimen


text: University of Oxford

text: NOT PROVIDED

text: EarlhamInstitute

text: public

text: NATURAL HISTORY MUSEUM

text: COPO

text: Alex McDermott-Roberts | Liam Crowley

text: University of Oxford

characteristic: collecting institution

characteristic: collection date

characteristic: elevation

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Oxfordshire | Trap grounds

characteristic: geographic location (region and locality)

text: Wetland

characteristic: habitat

text: Liam Crowley

text: University of Oxford

text: adult

characteristic: lifestage

text: Neria commutata

characteristic: organism

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

characteristic: project name

text: Netted

characteristic: sample collection device or method

text: Neria commutata

text: NOT COLLECTED

text: bef990aa-ae4f-4e58-92d6-eff227578936-DTOL-specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oxford

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: NATURAL HISTORY MUSEUM

text: COPO

text: Liam Crowley

text: University of Oxford

text: United Kingdom

text: Oxfordshire | Trap grounds

text: Wetland

text: Liam Crowley

text: University of Oxford

text: adult

text: Leptopterna dolabrata

text: WHOLE ORGANISM

text: DTOL

text: Sweep net

text: Leptopterna dolabrata

text: MALE

characteristic: sex

text: f6868dbb-3d7b-4f32-b16f-5286ee35b9f8-DTOL-specimen

characteristic: title

characteristic: tolid


text: University of Oxford

text: NOT PROVIDED

text: EarlhamInstitute

text: public

characteristic: Submitter Id

text: NATURAL HISTORY MUSEUM

characteristic: barcoding center

text: COPO

characteristic: broker name

text: Liam Crowley

text: University of Oxford

characteristic: collecting institution

characteristic: collection date

characteristic: elevation

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Oxfordshire | Trap grounds

characteristic: geographic location (region and locality)

text: Wetland

characteristic: habitat

text: Liam Crowley

text: University of Oxford

text: adult

characteristic: lifestage

text: Coleophora deauratella

characteristic: organism

text: WHOLE ORGANISM

text: DTOL

text: Potted

text: Coleophora deauratella

text: NOT COLLECTED

text: 2ae36778-3e6e-4461-84e4-6d4bbbec424a-DTOL-specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oxford

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: NATURAL HISTORY MUSEUM

text: COPO

text: Will Langdon

text: University of Oxford

text: United Kingdom

text: Berkshire | Wytham Woods

text: Woodland

text: Will Langdon

text: University of Oxford

text: adult

text: Nemapogon ruricolella

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

characteristic: project name

text: Pheromone lure

characteristic: sample collection device or method

text: Nemapogon ruricolella

text: NOT COLLECTED

text: 215573ff-dfaa-4545-99ea-a7af5d80d4aa-DTOL-specimen


text: UNIVERSITY OF OXFORD

text: public

tag: Namespace:UNIVERSITY OF OXFORD

characteristic: Submitter Id

text: University of Oxford

characteristic: collecting institution

characteristic: collection date

text: Modernising Medical Microbiology

characteristic: collector name

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: human

characteristic: host common name

text: not collected

characteristic: host health state

text: Homo sapien

characteristic: host scientific name

text: not collected

characteristic: host sex

text: not collected

characteristic: host subject id

text: RT-PCR

characteristic: influenza test method

text: P

characteristic: influenza test result

text: Influenza A virus

text: Influenza A virus

text: Influenza genome sequencing

characteristic: title


text: female

characteristic: ArrayExpress-SEX

text: Sphaerularia bombi

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Female

characteristic: GENDER

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Sphaerularia bombi

characteristic: common name

text: Sphaerularia bombi

characteristic: organism

text: Sphaerularia bombi


text: female

text: Crenosoma striatum

text: Female

text: SC

text: public

characteristic: Submitter Id

text: Crenosoma striatum

text: Crenosoma striatum

text: Crenosoma striatum


text: University of Ostrava

text: public

tag: Namespace:University of Ostrava

text: human

text: Ancient DNA from Bronze Age Iran

characteristic: description

text: Iran

characteristic: geographic location (country and/or sea)

text: Seistan, Shahr-i Sokhta site

characteristic: geographic location (region and locality)

text: human petrous

text: 30.649857, 61.400311

text: Homo sapiens

text: Homo sapiens

text: Bronze Age Iranian


text: Wageningen University & Research

text: public

tag: Namespace:Wageningen University & Research

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Rhizosphere sample from two-week-old B. oleracea plant

text: rhizosphere [ENVO:00005801]|soil [ENVO:00001998]

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Control sample 1

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Control sample 2


text: Wageningen University & Research

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Control sample 3


text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Control sample 4


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 1

characteristic: title


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 2


text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 1


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 2

characteristic: title


text: Wageningen University & Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 4


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 1


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 2

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 3


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 4


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 5


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Rhizosphere sample from four-week-old B. oleracea plant

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Control sample 5

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Control sample 6


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Control sample 7


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 4


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 5

characteristic: title


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 6


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: rhizosphere [ENVO:00005801]|soil [ENVO:00001998]

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 7


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 8


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 5

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 6


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 7


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 8


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 9

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 6


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 7


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 8


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 9

characteristic: title


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 10


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

text: Rhizosphere sample from eight-week-old B. oleracea plant

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Control sample 8


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Control sample 9


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Control sample 10

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Control sample 11


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Control sample 12


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 9


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 10

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 11


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: rhizosphere [ENVO:00005801]|soil [ENVO:00001998]

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 12


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with black soldier fly exuviae sample 13


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 10

characteristic: title


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 11


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 12


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 13


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with house cricket exuviae sample 14

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 11


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: common name

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 12


text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

characteristic: environmental medium

text: Netherlands

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Plant [ENVO:01001001]

characteristic: local environmental context

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 13


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wageningen University & Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: greenhouse [AGRO:00000363]

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

characteristic: project name

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 14

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wageningen University & Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: greenhouse [AGRO:00000363]

characteristic: broad-scale environmental context

characteristic: collection date

text: Brussels sprouts

text: Netherlands

text: Plant [ENVO:01001001]

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Soil amended with mealworm exuviae sample 15


characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Max Planck Institute for Evolutionary Anthropology

text: human

characteristic: common name

text: tooth/bone powder from human remains

characteristic: description

text: Greece, Corinthia - Peloponnese

characteristic: geographic location (region and locality)

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Max Planck Institute for Evolutionary Anthropology

text: public

text: human

text: tooth/bone powder from human remains

text: Greece, Corinthia - Peloponnese

text: Homo sapiens

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: tooth/bone powder from human remains

text: Greece, Heraklion - Crete

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: tooth/bone powder from human remains

text: Greece, Attica

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

text: human

text: tooth/bone powder from human remains

text: Greece, Lasithi - Crete

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: public

text: human

text: tooth/bone powder from human remains

text: Greece, Cyclades - South Aegean Islands

text: Homo sapiens

text: Homo sapiens


text: public

characteristic: SRA accession

text: human

text: tooth/bone powder from human remains

text: Greece, Aegina - Attica

text: Homo sapiens

text: Homo sapiens


text: public

characteristic: Submitter Id

text: human

text: tooth/bone powder from human remains

text: Creece, Achaea - Western Greece/ Peloponnese

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: tooth/bone powder from human remains

text: Greece, Euboea - Central Greece

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: tooth/bone powder from human remains

text: Greece, Argolis - Peloponnese

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: tooth/bone powder from human remains

text: Greece, Chania - Crete

text: Homo sapiens

text: Homo sapiens


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 v3.15.3

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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

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 ERR346579 of study ERP003648.

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Bacteroides cellulosilyticus

text: The microbial diversity, interpersonal variation and dynamism of the human gut microbiota make the task of identifying the factors that define community configurations, both structural and functional, extremely challenging. Bacterial viruses (phage) are the most abundant biological group on Earth and are more genetically diverse than their bacterial prey/hosts. To characterize their role as agents shaping gut community structure, adult germ-free mice were colonized with a consortium of 15 sequenced human bacterial symbionts, 13 of which harbored one or more predicted prophage in their genomes. One member, Bacteroides cellulosilyticus WH2, was represented by a library of isogenic transposon mutants covering 90% of its genes. Once assembled, the community was subjected to a staged phage attack with a pool of live or heat-killed virus-like particles (VLPs) purified from the fecal microbiota of five healthy humans. Shotgun sequencing of DNA from the input pooled human VLP preparation plus shotgun sequencing of gut microbiota samples, and purified fecal VLPs, from the gnotobiotic mice revealed a reproducible non-simultaneous pattern of attack extending over a 25 day period and involving five phage, none described previously. This system allowed us to (i) correlate increases in abundances of specific phage present in the input VLP preparation with reductions in the representation of particular bacterial hosts, (ii) provide evidence that phage resistance occurred because of ecological or epigenetic factors, (ii) track the origin of each of the five phages among the five human donors plus the extent of their genome variation between and within recipient mice, and (iv) establish the dramatic in vivo fitness advantage that a locus within a B. cellulosilyticus prophage confers upon its host bacterium. Together, these results provide a defined community-wide view of phage-bacterial host dynamics in the gut ecosystem.

characteristic: project name

characteristic: sample derived from

text: Bacteroides cellulosilyticus

text: Illumina HiSeq 1000

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__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides cellulosilyticus

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR346579_bin.1_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: USA

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Bacteroides sp.

characteristic: organism

text: uncultured Bacteroides sp.

text: Illumina HiSeq 1000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides vulgatus

text: multi-marker approach

text: Metagenome-assembled genome: ERR346579_bin.2_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

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 ERR346580 of study ERP003648.

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Bacteroides ovatus

characteristic: project name

characteristic: sample derived from

text: Bacteroides ovatus

text: Illumina HiSeq 1000

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__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides ovatus

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR346580_bin.2_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR346593 of study ERP003648.

characteristic: description

text: feces

text: USA

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: Bacteroides cellulosilyticus

characteristic: organism

text: Bacteroides cellulosilyticus

text: Illumina HiSeq 1000

text: multi-marker approach

text: Metagenome-assembled genome: ERR346593_bin.1_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

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 SRR13428081 of study SRP301591.

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

text: The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale.

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: NextSeq 500

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__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428081_bin.15_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Porphyromonadaceae bacterium

characteristic: organism

text: uncultured Porphyromonadaceae bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428081_bin.25_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Roseburia sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Roseburia sp.

text: NextSeq 500

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__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428081_bin.28_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428082 of study SRP301591.

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Desulfovibrio sp.

characteristic: organism

text: uncultured Desulfovibrio sp.

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428082_bin.17_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Hungatella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Hungatella sp.

text: NextSeq 500

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__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hungatella;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428082_bin.21_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured bacterium

characteristic: organism

text: uncultured bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428082_bin.6_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428082_bin.7_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428083 of study SRP301591.

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale.

text: uncultured Lachnospiraceae bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428083_bin.10_metawrap_v1.3_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 v3.15.3

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Prevotella sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Prevotella sp.

text: NextSeq 500

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__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428083_bin.2_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Muribaculaceae bacterium

characteristic: organism

text: uncultured Muribaculaceae bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428083_bin.37_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Porphyromonadaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Porphyromonadaceae bacterium

text: NextSeq 500

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__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428083_bin.40_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428083_bin.43_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Firmicutes bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Firmicutes bacterium

text: NextSeq 500

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__;o__;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428083_bin.8_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428084 of study SRP301591.

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Clostridium sp.

characteristic: organism

text: uncultured Clostridium sp.

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428084_bin.10_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured bacterium

text: The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale.

characteristic: project name

characteristic: sample derived from

text: uncultured bacterium

text: NextSeq 500

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__;c__;o__;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428084_bin.16_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Alistipes sp.

characteristic: organism

text: uncultured Alistipes sp.

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428084_bin.25_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Faecalibaculum sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Faecalibaculum sp.

text: NextSeq 500

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__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalibaculum;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428084_bin.30_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13428085 of study SRP301591.

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Porphyromonadaceae bacterium

characteristic: organism

text: uncultured Porphyromonadaceae bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428085_bin.12_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: NextSeq 500

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__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428085_bin.2_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Muribaculaceae bacterium

characteristic: organism

text: uncultured Muribaculaceae bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428085_bin.26_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

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 SRR13428086 of study SRP301591.

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: NextSeq 500

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__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428086_bin.20_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Porphyromonadaceae bacterium

characteristic: organism

text: The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale.

text: uncultured Porphyromonadaceae bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428086_bin.35_metawrap_v1.3_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 v3.15.3

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

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 SRR13428087 of study SRP301591.

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured bacterium

text: NextSeq 500

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__;c__;o__;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428087_bin.10_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured bacterium

characteristic: organism

text: uncultured bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428087_bin.13_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Odoribacter sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Odoribacter sp.

text: NextSeq 500

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__Bacteroidia;o__Bacteroidales;f__Odoribacteraceae;g__Odoribacter;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428087_bin.31_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Porphyromonadaceae bacterium

characteristic: organism

text: uncultured Porphyromonadaceae bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428087_bin.32_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Porphyromonadaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Porphyromonadaceae bacterium

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428087_bin.37_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Muribaculaceae bacterium

characteristic: organism

text: uncultured Muribaculaceae bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428087_bin.47_metawrap_v1.3_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

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Lactobacillus taiwanensis

characteristic: project name

characteristic: sample derived from

text: Lactobacillus taiwanensis

text: NextSeq 500

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 taiwanensis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428087_bin.48_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and time-scales shaping this resistome remain elusive. Here, using a cocktail of antibiotics administered to a murine model over a single generation along with a detailed, longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire AMR within a single generation. While the majority of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Lachnospiraceae family develop resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotic cocktail in the corresponding metagenome-assembled genomes (MAGs), and trace their origins within each genome. While mobile genetic elements (MGEs), including plasmids and phages, contribute to the spread of AMR, we observe that integrons represent the primary factors mediating AMR in the antibiotic-treated mice. Our findings suggest that antibiotic treatment alone may act as the selective pressure driving AMR acquisition and incidence in gut commensals on a generational timescale.

text: uncultured Lachnospiraceae bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428087_bin.9_metawrap_v1.3_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 v3.15.3

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

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 SRR13428088 of study SRP301591.

text: feces

characteristic: environmental medium

text: Luxembourg

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Muribaculaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Muribaculaceae bacterium

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13428088_bin.1_metawrap_v1.3_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

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: collection date

text: CheckM

characteristic: description

text: feces

text: Luxembourg

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Muribaculaceae bacterium

characteristic: organism

text: uncultured Muribaculaceae bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: SRR13428088_bin.13_metawrap_v1.3_MAG

characteristic: title