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text: The emergence and description of Klebsiella pneumoniae subspecies pneumoniae (Kpp) sequence type 25 (ST25) as a novel cause of septicaemia in preweaned pigs in England


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text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

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text: Klebsiella pneumoniae

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text: J-Line Breast Muscle RNAseq Data


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text: Genome sequence of Phialocephala subalpina

text: Phialocephala subalpina

text: Phialocephala subalpina

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text: Insight in the genome structure and lifestyle of a globally distributed root endophyte


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text: whole-genome shotgun sequencing of four representative MRSA strains positive for the presence of the tirS gene.

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text: Dictyostelium discoideum AX4

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text: The intestinal microbiota is involved in many physiological processes, and it is increasingly recognized that differences in community composition can influence the outcome of a variety of murine models used in biomedical research. In an effort to describe and account for the variation in intestinal microbiota composition across the animal facilities of participating members of the DFG Priority Program 1656 “Intestinal Microbiota”, we performed a survey of C57BL/6J mice from 21 different mouse rooms/facilities located at 13 different institutions across Germany. Fresh feces was sampled from five mice per room/facility using standardized procedures, followed by extraction and 16S rRNA gene profiling (V1-V2 region, Illumina MiSeq) at both the DNA and RNA (reverse transcribed to cDNA) level. In order to determine the variables contributing to bacterial community differences, we collected detailed questionnaires of animal husbandry practices and incorporated this information into our analyses. We identified considerable variation in a number of descriptive aspects including the proportions of major phyla, alpha- and beta diversity, all of which displayed significant associations to specific aspects of husbandry. Salient findings include a reduction in alpha diversity with the use of irradiated chow, an increase in inter-individual variability (beta diversity) with respect to barrier access and open cages and an increase in bacterial community divergence with time since importing from a vendor. We further observe a high degree of facility-level individuality, which is likely due to each facility harboring its own unique combination of multiple varying attributes of animal husbandry. While it is important to account and control for such differences between facilities, the documentation of such diversity may also serve as a valuable future resource for investigating the origins of microbial-driven host phenotypes.

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characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: RNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: open

characteristic: barrier access

text: untreated

characteristic: bedding treatment

text: Altromin

characteristic: chow provider

text: irradiated

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: L

text: Germany

text: colon

text: feces

text: house mouse

text: Altromin

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: open

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Jackson

characteristic: mouse provider

characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

characteristic: pcr primers

characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: DNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: open

characteristic: barrier access

text: untreated

characteristic: bedding treatment

text: Altromin

characteristic: chow provider

text: irradiated

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: L

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Altromin

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: open

text: metagenome

text: no medication

text: Jackson

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: RNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: irradiated

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Germany

text: colon

text: feces

text: house mouse

text: Ssniff

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: IVC

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Jackson

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characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

characteristic: pcr primers

characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: DNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: irradiated

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Ssniff

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: IVC

text: metagenome

text: no medication

text: Jackson

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: RNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Altromin

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: P

text: Germany

text: colon

text: feces

text: house mouse

text: Altromin

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: IVC

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Charles River

characteristic: mouse provider

characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

characteristic: pcr primers

characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: DNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Altromin

characteristic: chow provider

text: autoclave

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: P

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Altromin

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: IVC

text: metagenome

text: no medication

text: Charles River

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: RNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: autoclave


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: open

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text: untreated

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text: Altromin

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text: untreated

characteristic: chow treatment

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text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: P

text: Germany

text: colon

text: feces

text: house mouse

text: Altromin

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: open

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

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text: Charles River

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text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

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text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: DNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: open

characteristic: barrier access

text: untreated

characteristic: bedding treatment

text: Altromin

characteristic: chow provider

text: untreated

characteristic: chow treatment

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text: house mouse

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characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: P

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Altromin

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: open

text: metagenome

text: no medication

text: Charles River

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: RNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

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characteristic: SRA accession

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text: restricted

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text: autoclave

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text: Ssniff

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text: autoclave

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characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: H

text: Germany

text: colon

text: feces

text: house mouse

text: Ssniff

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text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: open

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Central Animal facility (ZTL) Isolator unit

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characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

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characteristic: project name

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characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: no


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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

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text: autoclave

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text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: H

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Ssniff

characteristic: host diet

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characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

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text: metagenome

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text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: RNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

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characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

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text: Ssniff

characteristic: chow provider

text: irradiated

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characteristic: collection date

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characteristic: common name

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characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: H

text: Germany

text: colon

text: feces

text: house mouse

text: Ssniff

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: IVC

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: Jackson

characteristic: mouse provider

characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

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characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: DNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

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characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: restricted

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Ssniff

characteristic: chow provider

text: irradiated

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: H

characteristic: facility

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: colon

characteristic: host body habitat

text: feces

characteristic: host body product

text: house mouse

characteristic: host common name

text: Ssniff

characteristic: host diet

text: healthy

characteristic: host disease status

text: adult

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

text: IVC

text: metagenome

text: no medication

text: Jackson

text: Qiagen AllPrep DNA/RNA

text: Mus musculus

characteristic: organism

text: Variation in C57BL/6J mouse microbiota

text: Mus musculus

text: RNA

text: Illumina Miseq

text: fecal sample

text: 16S rRNA

text: Variation in C57BL/6J mouse microbiota

characteristic: title

text: no


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: open

characteristic: barrier access

text: autoclave

characteristic: bedding treatment

text: Altromin

characteristic: chow provider

text: irradiated

characteristic: chow treatment

characteristic: collection date

text: house mouse

characteristic: common name

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text: host associated

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: H

text: Germany

text: colon

text: feces

text: house mouse

text: Altromin

text: healthy

text: adult

text: male

characteristic: host total mass

text: host-associated

characteristic: host-associated environmental package

text: IVC

characteristic: housing condition

text: metagenome

characteristic: investigation type

text: no medication

characteristic: medication

text: ZTL Quarantine unit

characteristic: mouse provider

characteristic: multiplex identifiers

text: Qiagen AllPrep DNA/RNA

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

characteristic: pcr primers

characteristic: presence of other strains

text: Variation in C57BL/6J mouse microbiota

characteristic: project name

text: Mus musculus

text: DNA

characteristic: sequence type

text: Illumina Miseq

characteristic: sequencing method

text: fecal sample

characteristic: source material identifiers

text: 16S rRNA

characteristic: target gene

text: Variation in C57BL/6J mouse microbiota

text: autoclave