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text: UNIVERSITY OF OXFORD

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tag: Namespace:UNIVERSITY OF OXFORD

text: Ecoli CFT073 isolate sequenced with Ilumina miseq

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tag: Namespace:INSERM U1301 CNRS 5070 EFS/Univ Paul Sabatier

text: 18 to 20

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Liver biopsies were harvested from control flox and Hmgb1 liver knockout mice in chow diet or after fasting/refeeding challenge Flash-frozen liver biopsies were sent to Active Motif to perform the ATAC-seq assay. The tissue was manually dissociated, isolated nuclei were quantified using a hemocytometer, and 100,000 nuclei were tagmented as previously described (58), with some modifications based on (59) using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).

text: adult

characteristic: developmental stage

text: chow

characteristic: diet

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

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text: male

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characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 18 to 20

text: ArrayExpress

text: house mouse

characteristic: description

text: adult

text: fast for 6 hours and refeed for 8 hours

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: male


text: public

tag: Namespace:INSERM U1301 CNRS U5070 EFS/Univ Paul Sabatier

text: 18 to 20

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Liver from control (flox) or Hmgb1 liver knockout mice after a metabolic stress either induced by a 12-week high fat diet consumption or a fasting (6hours)-refeeding (8hours) challenge. Briefly, frozen liver biopsies (100-200 mg) harvested from HMGB1fl/fl and HMGB1ΔHep mice under CD, upon HFD60% or after F/R, were minced and fixed at room temperature in PBS-1% formaldehyde (Sigma-Aldrich, 47608, Saint Louis, MO, USA) for 20 minutes. After sonication, chromatin immunoprecipitation was performed using anti-HMGB1 antibody (Abcam, ab18256, Cambridge, UK). Immunoprecipitated DNA was subjected to library preparation using NEBNext DNA Ultra II kit.

text: adult

characteristic: developmental stage

text: fast for 6 hours and refeed for 8 hours

characteristic: diet

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INSERM U1301 CNRS U5070 EFS/Univ Paul Sabatier

text: public

text: 18 to 20

text: ArrayExpress

text: house mouse

text: adult

text: high fat diet

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 18 to 20

text: ArrayExpress

text: house mouse

text: adult

text: chow

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 18 to 20

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: description

text: adult

text: chow

text: HMGB1 fl/fl

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: 18 to 20

text: ArrayExpress

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

text: fast for 6 hours and refeed for 8 hours

characteristic: diet

text: HMGB1 fl/fl

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: 18 to 20

text: ArrayExpress

text: house mouse

text: adult

text: high fat diet

text: HMGB1 fl/fl

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


text: UNIVERSITY OF OXFORD

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Ecoli CFT073 isolate ONT multiplex sequenced with r10.4

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF OXFORD

text: public

text: Klebsiella pneumoniae MGH 78578 isolate ONT multiplex sequenced with r10.4

characteristic: description

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae


text: UNIVERSITY OF OXFORD

text: public

text: MRSA 252 isolate ONT multiplex sequenced with r10.4

text: Staphylococcus aureus

text: Staphylococcus aureus

characteristic: title


characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF OXFORD

text: public

text: Pseudomonas aeruginosa PAO1 isolate ONT multiplex sequenced with r10.4

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


characteristic: External Id

text: INRAE

text: public

characteristic: collection date

text: cow teat skin

characteristic: environment (biome)

text: cow teat skin

characteristic: environment (feature)

text: cow teat skin

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: skin metagenome

text: MSQ-16SV3F (5′- TACGGRAGGCWGCAG-3) and PCR1R-460 (5′- TTACCAGGGTATCTAATCCT-3)

characteristic: pcr primers

text: Actrade

characteristic: project name

text: skin metagenome

text: Illumina

characteristic: sequencing method

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text: teat_skin sample j1 C


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

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text: public

characteristic: INSDC status

characteristic: SRA accession

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text: milk

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text: cow milk

text: cow milk

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text: milk metagenome

characteristic: organism

text: Actrade

text: milk metagenome

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

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text: cow teat skin

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text: cow teat skin

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text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin metagenome

text: Actrade

text: skin metagenome

text: Illumina

text: pool sample j1 C

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characteristic: ENA-CHECKLIST

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text: INRAE

characteristic: INSDC center name

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text: skin metagenome

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text: teat_skin sample j2 C


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characteristic: SRA accession

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text: milk

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text: cow milk

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characteristic: organism

text: Actrade

text: milk metagenome

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text: milk sample j2 C


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

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characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin metagenome

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characteristic: INSDC center name

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characteristic: SRA accession

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text: cow milk

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characteristic: organism

text: Actrade

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characteristic: ENA-LAST-UPDATE

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text: INRAE

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text: cow teat skin

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text: France

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characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin metagenome

text: Actrade

text: skin metagenome

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characteristic: ENA-CHECKLIST

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text: INRAE

characteristic: INSDC center name

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text: skin metagenome

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text: Actrade

characteristic: project name

text: skin metagenome

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text: teat_skin sample j1 N


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text: cow milk

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text: Actrade

text: milk metagenome

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characteristic: ENA-CHECKLIST

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text: INRAE

characteristic: INSDC center name

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text: cow teat skin

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text: France

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characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin metagenome

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text: skin metagenome

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characteristic: ENA-LAST-UPDATE

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text: INRAE

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characteristic: SRA accession

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text: cow milk

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characteristic: ENA-LAST-UPDATE

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text: INRAE

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text: cow teat skin

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text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

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text: skin metagenome

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text: skin metagenome

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characteristic: ENA-CHECKLIST

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text: INRAE

characteristic: INSDC center name

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text: Actrade

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text: skin metagenome

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characteristic: ENA-LAST-UPDATE

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text: INRAE

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text: milk

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text: cow milk

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text: cow milk

text: cow milk

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text: milk metagenome

characteristic: organism

text: Actrade

text: milk metagenome

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text: milk sample j3 N


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

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text: public

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characteristic: environment (feature)

text: cow teat skin

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text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin metagenome

text: Actrade

text: skin metagenome

text: Illumina

text: pool sample j3 N

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

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text: cow teat skin

text: cow teat skin

text: cow teat skin

text: France

characteristic: investigation type

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text: skin metagenome

characteristic: pcr primers

text: Actrade

characteristic: project name

text: skin metagenome

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characteristic: sequencing method

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text: teat_skin sample j1 A


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

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text: public

characteristic: SRA accession

characteristic: Submitter Id

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text: milk

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text: cow milk

characteristic: environment (biome)

text: cow milk

text: cow milk

text: France

text: milk metagenome

characteristic: organism

text: Actrade

text: milk metagenome

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text: milk sample j1 A


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

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text: cow teat skin

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characteristic: environment (feature)

text: cow teat skin

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characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin metagenome

text: Actrade

text: skin metagenome

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text: pool sample j1 A

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

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text: public

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characteristic: investigation type

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text: Actrade

characteristic: project name

text: skin metagenome

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characteristic: sequencing method

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text: teat_skin sample j2 A


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

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text: milk

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text: cow milk

characteristic: environment (biome)

text: cow milk

text: cow milk

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text: milk metagenome

characteristic: organism

text: Actrade

text: milk metagenome

text: Illumina

text: milk sample j2 A


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

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text: public

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characteristic: environment (feature)

text: cow teat skin

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text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin metagenome

text: Actrade

text: skin metagenome

text: Illumina

text: pool sample j2 A

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

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text: cow teat skin

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text: skin metagenome

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characteristic: sequencing method

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text: teat_skin sample j3 A


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

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text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: milk

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text: cow milk

characteristic: environment (biome)

text: cow milk

text: cow milk

text: France

text: milk metagenome

characteristic: organism

text: Actrade

text: milk metagenome

text: Illumina

text: milk sample j3 A


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

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text: pool

text: cow teat skin

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characteristic: environment (feature)

text: cow teat skin

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text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin metagenome

text: Actrade

text: skin metagenome

text: Illumina

text: pool sample j3 A

characteristic: title


characteristic: ENA-CHECKLIST

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text: INRAE

characteristic: INSDC center name

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text: public

text: milk

text: cow milk

text: cow milk

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text: France

characteristic: investigation type

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text: milk metagenome

characteristic: pcr primers

text: Actrade

characteristic: project name

text: milk metagenome

text: Illumina

characteristic: sequencing method

characteristic: target gene

text: milk control


TnL

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: TnL

characteristic: Submitter Id

characteristic: collection date

text: milk

characteristic: description

text: cow milk

characteristic: environment (biome)

text: cow milk

text: cow milk

text: France

text: milk metagenome

characteristic: organism

text: Actrade

text: milk metagenome

text: Illumina

text: milk control


TnP

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: TnP

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text: cow teat skin

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characteristic: environment (feature)

text: cow teat skin

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text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin metagenome

text: Actrade

text: skin metagenome

text: Illumina

text: pool control

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

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text: cow teat skin

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text: France

characteristic: investigation type

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characteristic: project name

text: skin metagenome

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characteristic: sequencing method

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text: teat_skin control


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: pool

characteristic: description

text: cow teat skin

characteristic: environment (biome)

text: cow teat skin

text: cow teat skin

text: France

text: skin metagenome

characteristic: organism

text: Actrade

text: skin metagenome

text: Illumina

text: pool control


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: milk

text: cow milk

text: cow milk

characteristic: environment (feature)

text: cow milk

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: eukaryote

text: milk metagenome

text: ITS3f (5′-GCATCGATGAAGAACGCAGC-3′) and ITS4_KYO1 (5′-TCCTCCGCTTWTTGWTWTGC-3′)

text: Actrade

text: milk metagenome

text: Illumina

text: ITS

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INRAE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: pool

text: cow teat skin

text: cow teat skin

text: cow teat skin

text: France

text: eukaryote

characteristic: investigation type

characteristic: miscellaneous environmental package

text: skin metagenome

characteristic: pcr primers

text: Actrade

characteristic: project name

text: skin metagenome

text: Illumina

characteristic: sequencing method

text: ITS

characteristic: target gene


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: cow teat skin

characteristic: environment (biome)

text: cow teat skin

text: cow teat skin

text: France

text: eukaryote

text: skin metagenome

characteristic: organism

text: Actrade

text: skin metagenome

text: Illumina

text: ITS


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CNAP

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Assembled and Annotated Reference Genome for P. putredinis NO1

text: Parascedosporium putredinis

text: Parascedosporium putredinis

text: P. putredinis NO1 Genome Assembly

characteristic: title


text: CNAP

text: public

text: Nanopore DNA Reads of P. putredinis NO1 Genome

text: Parascedosporium putredinis

text: Parascedosporium putredinis

text: P. putredinis NO1 Genome Nanopore Reads


text: CNAP

text: public

text: Illumina DNA Reads of P. putredinis NO1 Genome

text: Parascedosporium putredinis

text: Parascedosporium putredinis

text: P. putredinis NO1 Genome Illumina Reads


text: CNAP

text: public

text: Illumina RNA reads of P. putredinis grown on Wheat Straw

text: Parascedosporium putredinis

text: Parascedosporium putredinis

text: P. putredinis NO1 Wheat Straw RNA


text: CNAP

text: public

text: Illumina RNA reads of P. putredinis grown on Rice Straw

text: Parascedosporium putredinis

text: Parascedosporium putredinis

text: P. putredinis NO1 Rice Straw RNA


text: CNAP

text: public

text: Illumina RNA reads of P. putredinis grown on Sugar Cane

text: Parascedosporium putredinis

text: Parascedosporium putredinis

text: P. putredinis NO1 Sugar Cane RNA


text: CNAP

text: public

text: Illumina RNA reads of P. putredinis grown on Wheat Bran

text: Parascedosporium putredinis

text: Parascedosporium putredinis

text: P. putredinis NO1 Wheat Bran RNA


text: CNAP

text: public

text: Illumina RNA reads of P. putredinis grown on Empty Fruit Bunch

text: Parascedosporium putredinis

text: Parascedosporium putredinis

text: P. putredinis NO1 Empty Fruit Bunch RNA


text: CNAP

text: public

text: Illumina RNA reads of P. putredinis grown on Kraft Lignin

text: Parascedosporium putredinis

text: Parascedosporium putredinis

text: P. putredinis NO1 Kraft Lignin RNA


text: public

tag: Namespace:Max Planck Institute for Evolutionary Anthropology

text: human

characteristic: common name

text: Hungary

characteristic: geographic location (country and/or sea)

text: Danube-Tisza Interfluve

characteristic: geographic location (region and locality)

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max Planck Institute for Evolutionary Anthropology

text: public

text: human

text: Hungary

text: Danube-Tisza Interfluve

text: Homo sapiens

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: Hungary

text: Transtisza region

text: Homo sapiens

text: Homo sapiens


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Hungary

text: South Transdanubia

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Hungary

text: Tisza region

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Hungary

text: North-Central Hungary, North Hungarian Mountains

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Hungary

text: South-East Hungary, Transtisza/Maros region

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Hungary

text: North Transdanubia

text: Homo sapiens

text: Homo sapiens


text: public

tag: Namespace:Berlin Institute for Medical Systems Biology

text: ArrayExpress

characteristic: broker name

text: neuron of cerebral cortex

characteristic: cell type

text: neurite

characteristic: cellular component

text: house mouse

text: Protocols: Primary neuron cultures were prepared from C57B/6 wild type mice (P0) pups and cultured as previously described (Kaech and Banker, 2006). RNA was extracted from Trifast lysate using Directzol column purification kit (zymo) including DNaseI treatment procedure; RNA samples were quantified and analysed for integrity by Bioanalyser; Good separation was verified by RT-qPCR. (2.5-3.7 cycles difference in Taglin between soma/neurite samples) Stranded mRNA Library kit; 1ul of 1:100 ERCC1 spike-in was added to 49ul initial solution with 400ng total RNA.; Final PCR was done with 10-15 cycles’ reaction.

characteristic: description

text: neonate

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: brain

characteristic: organism part

text: Mus musculus

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Berlin Institute for Medical Systems Biology

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: neuron of cerebral cortex

text: neurite

text: house mouse

characteristic: common name

text: neonate

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: brain

text: Mus musculus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: neuron of cerebral cortex

text: soma

text: house mouse

text: neonate

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

text: d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__UBA1609;g__;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

text: public

characteristic: MAG coverage depth

text: Reads (ERR7738460) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567617) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_J_17_RAJ1013YZ.12

tag: Namespace:Stanford University School of Medicine

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;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738460 were assembled into contigs (ERZ4567617). The following read sets from this study were the most similar to ERR7738460 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738460,ERR7745346,ERR7745755,ERR7738229,ERR7738144,ERR7745769,ERR7738619,ERR7738258,ERR7738621,ERR7738529. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4567617. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: CheckM marker lineage: k__Bacteria (UID3187)

characteristic: completeness approach

characteristic: completeness score

characteristic: completeness software

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738460 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Bdellovibrionales bacterium MAG assembled and binned from ERR7738460.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Nepal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

text: uncultured Bdellovibrionales bacterium

text: Metagenome sequencing of Nepali gut microbiome

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Bdellovibrionales bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13868;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746773) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560047) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_N_21_2138.117

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7746773 were assembled into contigs (ERZ4560047). The following read sets from this study were the most similar to ERR7746773 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746773,ERR7738190,ERR7738192,ERR7738599,ERR7738604,ERR7738661,ERR7746144,ERR7745783,ERR7738271,ERR7738247. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4560047. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: CheckM marker lineage: k__Bacteria (UID2329)

characteristic: completeness approach

characteristic: completeness score

characteristic: completeness software

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7746773 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7746773.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: most complete 5S rRNA recovered

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

text: uncultured Bacilli bacterium

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738223) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560427) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_A_8_1817.114

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738223 were assembled into contigs (ERZ4560427). The following read sets from this study were the most similar to ERR7738223 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738223,ERR7747140,ERR7745994,ERR7738936,ERR7738598,ERR7738595,ERR7738607,ERR7738567,ERR7747324,ERR7745335. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4560427. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: reads

text: All reads in ERR7738223 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7738223.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (longitude)

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

text: uncultured Bacilli bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__ML615J-28;f__CAG-698;g__Tener-01;s__Tener-01 sp001940985

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738268) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561917) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_E_19_1056.40

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738268 were assembled into contigs (ERZ4561917). The following read sets from this study were the most similar to ERR7738268 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738268,ERR7738190,ERR7745759,ERR7745990,ERR7738624,ERR7745845,ERR7746101,ERR7738192,ERR7738581,ERR7746094. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561917. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: k__Bacteria (UID2328)

characteristic: completeness approach

characteristic: completeness score

characteristic: completeness software

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738268 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7738268.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

text: uncultured Bacilli bacterium

characteristic: organism

text: No

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: TRUE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1000;s__CAG-1000 sp000436975

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_A_22_1120.300

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738447 were assembled into contigs (ERZ4561837). The following read sets from this study were the most similar to ERR7738447 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738447,ERR7745759,ERR7738177,ERR7738624,ERR7738581,ERR7746748,ERR7746094,ERR7745990,ERR7745890,ERR7738604. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561837. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: k__Bacteria (UID2329)

text: reads

text: All reads in ERR7738447 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7738447.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (longitude)

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: most complete 16S rRNA recovered

characteristic: most complete 23S rRNA recovered

characteristic: most complete 5S rRNA recovered

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

text: uncultured Bacilli bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

text: GTDB-TK v1.7.0, r202 database, default parameters

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1000;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738170) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_B_5_2673.98

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738170 were assembled into contigs (ERZ4559535). The following read sets from this study were the most similar to ERR7738170 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738170,ERR7738231,ERR7738612,ERR7738593,ERR7738611,ERR7738271,ERR7738552,ERR7738162,ERR7747255,ERR7738604. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4559535. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

characteristic: completeness approach

characteristic: completeness score

characteristic: completeness software

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738170 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7738170.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

text: uncultured Bacilli bacterium

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: TRUE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1000;s__CAG-1000 sp000434555

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ.170

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7739005 were assembled into contigs (ERZ4567239). The following read sets from this study were the most similar to ERR7739005 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7739005,ERR7745858,ERR7745346,ERR7745755,ERR7738572,ERR7738575,ERR7738662,ERR7745760,ERR7738535,ERR7738529. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4567239. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

characteristic: completeness approach

text: reads

text: All reads in ERR7739005 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7739005.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Nepal

characteristic: geographic location (longitude)

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: most complete 16S rRNA recovered

characteristic: most complete 23S rRNA recovered

characteristic: most complete 5S rRNA recovered

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

text: uncultured Bacilli bacterium

text: Metagenome sequencing of Nepali gut microbiome

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: TRUE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_K_14_2624.34

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745990 were assembled into contigs (ERZ4559405). The following read sets from this study were the most similar to ERR7745990 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745990,ERR7745845,ERR7747255,ERR7745823,ERR7738959,ERR7738588,ERR7747394,ERR7745335,ERR7746217,ERR7738569. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4559405. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: CheckM marker lineage: k__Bacteria (UID2329)

characteristic: completeness approach

characteristic: completeness score

characteristic: completeness software

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7745990 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7745990.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

text: uncultured Bacilli bacterium

characteristic: organism

text: No

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: GTDB-TK v1.7.0, r202 database, default parameters

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: TRUE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1000;s__CAG-1000 sp900761555

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745408) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561111) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_B_17_1592.217

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745408 were assembled into contigs (ERZ4561111). The following read sets from this study were the most similar to ERR7745408 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745408,ERR7745881,ERR7745743,ERR7738168,ERR7745563,ERR7738266,ERR7745914,ERR7745759,ERR7746411,ERR7738264. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561111. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: reads

text: All reads in ERR7745408 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7745408.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (longitude)

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: most complete 16S rRNA recovered

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

text: uncultured Bacilli bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_N_3_1523.68

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7746785 were assembled into contigs (ERZ4561612). The following read sets from this study were the most similar to ERR7746785 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746785,ERR7738176,ERR7738184,ERR7745362,ERR7738251,ERR7746184,ERR7745937,ERR7738660,ERR7738586,ERR7738569. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561612. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: completeness approach

characteristic: completeness score

characteristic: completeness software

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7746785 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7746785.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: most complete 5S rRNA recovered

text: uncultured Bacilli bacterium

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1000;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_E_2_1148.59

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738254 were assembled into contigs (ERZ4561852). The following read sets from this study were the most similar to ERR7738254 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738254,ERR7738271,ERR7738177,ERR7738594,ERR7746101,ERR7738588,ERR7745582,ERR7745432,ERR7747084,ERR7746440. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561852. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: CheckM marker lineage: k__Bacteria (UID2329)

characteristic: completeness approach

text: reads

text: All reads in ERR7738254 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Bacilli bacterium MAG assembled and binned from ERR7738254.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (longitude)

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

text: uncultured Bacilli bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Bacilli bacterium

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach