characteristics.text: ERC000013
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2016-09-29T17:01:44Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2016-10-21T09:40:08Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA3883489
characteristics.characteristic: External Id
characteristics.text: MPIEVB
characteristics.characteristic: INSDC center name
characteristics.text: 2016-09-29T17:01:44Z
characteristics.characteristic: INSDC first public
characteristics.text: 2016-10-21T09:40:08Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1070623
characteristics.characteristic: SRA accession
characteristics.text: 21_3RNA_1
characteristics.characteristic: Submitter Id
characteristics.text: R1-TATGGTAATTGTAGAGTTTGATCCTGGCTCAG;R2-AGTCAGTCAGCCTGCTGCCTCCCGTAGGAGT
characteristics.characteristic: adapters
characteristics.text: open
characteristics.characteristic: barrier access
characteristics.text: autoclave
characteristics.characteristic: bedding treatment
characteristics.text: Altromin
characteristics.characteristic: chow provider
characteristics.text: autoclave
characteristics.characteristic: chow treatment
characteristics.text: 2014-11-10
characteristics.characteristic: collection date
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.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.
characteristics.characteristic: description
characteristics.text: host associated
characteristics.characteristic: environment (biome)
characteristics.text: feces
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCIT_C13234
characteristics.characteristic: environment (feature)
characteristics.text: feces
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCIT_C13234
characteristics.characteristic: environment (material)
characteristics.text: P
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0002099
characteristics.characteristic: facility
characteristics.text: Germany
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: 54�09'35.1N
characteristics.unit: DD
characteristics.characteristic: geographic location (latitude)
characteristics.text: 10�26'00.3E
characteristics.unit: DD
characteristics.characteristic: geographic location (longitude)
characteristics.text: 95
characteristics.unit: day
characteristics.characteristic: host age
characteristics.text: colon
characteristics.characteristic: host body habitat
characteristics.text: feces
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCIT_C13234
characteristics.characteristic: host body product
characteristics.text: house mouse
characteristics.characteristic: host common name
characteristics.text: Altromin
characteristics.characteristic: host diet
characteristics.text: healthy
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000461
characteristics.characteristic: host disease status
characteristics.text: adult
characteristics.characteristic: host life stage
characteristics.text: male
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000384
characteristics.characteristic: host sex
characteristics.text: 21_3
characteristics.characteristic: host subject id
characteristics.text: 10090
characteristics.characteristic: host taxid
characteristics.text: 26,29
characteristics.unit: g
characteristics.characteristic: host total mass
characteristics.text: host-associated
characteristics.characteristic: host-associated environmental package
characteristics.text: IVC
characteristics.characteristic: housing condition
characteristics.text: metagenome
characteristics.characteristic: investigation type
characteristics.text: no medication
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0004285
characteristics.characteristic: medication
characteristics.text: Charles River
characteristics.characteristic: mouse provider
characteristics.text: R1-CTAGTCGA;R2-CGTTCCTA
characteristics.characteristic: multiplex identifiers
characteristics.text: Qiagen AllPrep DNA/RNA
characteristics.characteristic: nucleic acid extraction
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: 98�C-30s, 30 � [98�C-9s, 55�C-60s, 72�C-90s], 72�C-10 min
characteristics.characteristic: pcr conditions
characteristics.text: 27F-338R
characteristics.characteristic: pcr primers
characteristics.text: 1
characteristics.characteristic: presence of other strains
characteristics.text: Variation in C57BL/6J mouse microbiota
characteristics.characteristic: project name
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: RNA
characteristics.characteristic: sequence type
characteristics.text: Illumina Miseq
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0004205
characteristics.characteristic: sequencing method
characteristics.text: fecal sample
characteristics.characteristic: source material identifiers
characteristics.text: 16S rRNA
characteristics.characteristic: target gene
characteristics.text: Variation in C57BL/6J mouse microbiota
characteristics.characteristic: title
characteristics.text: autoclave
characteristics.characteristic: water treatment