Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities.

2.50
Hdl Handle:
http://hdl.handle.net/10033/620903
Title:
Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities.
Authors:
Rausch, Philipp; Basic, Marijana; Batra, Arvind; Bischoff, Stephan C; Blaut, Michael; Clavel, Thomas; Gläsner, Joachim; Gopalakrishnan, Shreya; Grassl, Guntram A; Günther, Claudia; Haller, Dirk; Hirose, Misa; Ibrahim, Saleh; Loh, Gunnar; Mattner, Jochen; Nagel, Stefan; Pabst, Oliver; Schmidt, Franziska; Siegmund, Britta; Strowig, Till; Volynets, Valentina; Wirtz, Stefan; Zeissig, Sebastian; Zeissig, Yvonne; Bleich, André; Baines, John F
Abstract:
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.
Affiliation:
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Citation:
Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities. 2016, 306 (5):343-55 Int. J. Med. Microbiol.
Journal:
International journal of medical microbiology : IJMM
Issue Date:
Aug-2016
URI:
http://hdl.handle.net/10033/620903
DOI:
10.1016/j.ijmm.2016.03.004
PubMed ID:
27053239
Type:
Article
Language:
en
ISSN:
1618-0607
Appears in Collections:
publications of the research group microbial immune regulation (MIKI)

Full metadata record

DC FieldValue Language
dc.contributor.authorRausch, Philippen
dc.contributor.authorBasic, Marijanaen
dc.contributor.authorBatra, Arvinden
dc.contributor.authorBischoff, Stephan Cen
dc.contributor.authorBlaut, Michaelen
dc.contributor.authorClavel, Thomasen
dc.contributor.authorGläsner, Joachimen
dc.contributor.authorGopalakrishnan, Shreyaen
dc.contributor.authorGrassl, Guntram Aen
dc.contributor.authorGünther, Claudiaen
dc.contributor.authorHaller, Dirken
dc.contributor.authorHirose, Misaen
dc.contributor.authorIbrahim, Salehen
dc.contributor.authorLoh, Gunnaren
dc.contributor.authorMattner, Jochenen
dc.contributor.authorNagel, Stefanen
dc.contributor.authorPabst, Oliveren
dc.contributor.authorSchmidt, Franziskaen
dc.contributor.authorSiegmund, Brittaen
dc.contributor.authorStrowig, Tillen
dc.contributor.authorVolynets, Valentinaen
dc.contributor.authorWirtz, Stefanen
dc.contributor.authorZeissig, Sebastianen
dc.contributor.authorZeissig, Yvonneen
dc.contributor.authorBleich, Andréen
dc.contributor.authorBaines, John Fen
dc.date.accessioned2017-04-21T10:47:31Z-
dc.date.available2017-04-21T10:47:31Z-
dc.date.issued2016-08-
dc.identifier.citationAnalysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities. 2016, 306 (5):343-55 Int. J. Med. Microbiol.en
dc.identifier.issn1618-0607-
dc.identifier.pmid27053239-
dc.identifier.doi10.1016/j.ijmm.2016.03.004-
dc.identifier.urihttp://hdl.handle.net/10033/620903-
dc.description.abstractThe 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.en
dc.language.isoenen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subject.meshAnimal Husbandryen
dc.subject.meshAnimalsen
dc.subject.meshCluster Analysisen
dc.subject.meshDNA, Ribosomalen
dc.subject.meshFecesen
dc.subject.meshGastrointestinal Microbiomeen
dc.subject.meshGermanyen
dc.subject.meshMaleen
dc.subject.meshMice, Inbred C57BLen
dc.subject.meshPhylogenyen
dc.subject.meshRNA, Ribosomal, 16Sen
dc.subject.meshSequence Analysis, DNAen
dc.subject.meshSurveys and Questionnairesen
dc.titleAnalysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities.en
dc.typeArticleen
dc.contributor.departmentHelmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.en
dc.identifier.journalInternational journal of medical microbiology : IJMMen

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