title: Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities.
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.
authors.affiliation: Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, August-Thienemann-Str. 2, 24306, Plön, Germany; Institute for Experimental Medicine, Evolutionary Genomics, Christian-Albrechts-University of Kiel, Arnold-Heller-Str. 3, Haus 17, 24105 Kiel, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Rausch
authors.affiliation: Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
authors.forename: Marijana
authors.initials: M
authors.lastname: Basic
authors.affiliation: Charité-Universitätsklinikum Berlin, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Hindenburgdamm 30, 12203 Berlin, Germany.
authors.forename: Arvind
authors.initials: A
authors.lastname: Batra
authors.affiliation: Department of Nutritional Medicine, University of Hohenheim, Fruwirthstr. 12, 70593 Stuttgart, Germany.
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Bischoff
authors.affiliation: Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Blaut
authors.affiliation: ZIEL Institute for Food and Health, Technische Universität München, Gregor-Mendel-Str. 2, 85354, Freising-Weihenstephan, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Clavel
authors.affiliation: Institute for Medical Microbiology and Hygiene, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany.
authors.forename: Joachim
authors.initials: J
authors.lastname: Gläsner
authors.affiliation: Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany.
authors.forename: Shreya
authors.initials: S
authors.lastname: Gopalakrishnan
authors.affiliation: German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Carl-Neuberg-Str. 1, 30625 Hannover, Germany; Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany; Research Center Borstel, Parkallee 1-40, 23845, Borstel, Germany.
authors.forename: Guntram A
authors.initials: GA
authors.lastname: Grassl
authors.affiliation: Medical Clinic 1, Friedrich Alexander University, Ulmenweg 18, 91054 Erlangen, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Günther
authors.affiliation: ZIEL Institute for Food and Health, Technische Universität München, Gregor-Mendel-Str. 2, 85354, Freising-Weihenstephan, Germany; Chair of Nutrition and Immunology, Technische Universität München, Gregor-Mendel-Str. 2, 85354 Freising-Weihenstephan, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Haller
authors.affiliation: Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany.
authors.forename: Misa
authors.initials: M
authors.lastname: Hirose
authors.affiliation: Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany.
authors.forename: Saleh
authors.initials: S
authors.lastname: Ibrahim
authors.affiliation: Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Loh
authors.affiliation: Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Lehrstuhl für Mikrobiologie und Infektionsimmunologie, Wasserturmstr. 3/5, 91054 Erlangen, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Mattner
authors.affiliation: Charité - Universitätsklinikum Berlin, Research Institutes for Experimental Medicine, Krahmerstr. 6-10, 12207 Berlin, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Nagel
authors.affiliation: Institute of Molecular Medicine, RWTH University, Pauwelsstraße 30, 52074, Aachen, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Pabst
authors.affiliation: Charité-Universitätsklinikum Berlin, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Hindenburgdamm 30, 12203 Berlin, Germany.
authors.forename: Franziska
authors.initials: F
authors.lastname: Schmidt
authors.affiliation: Charité-Universitätsklinikum Berlin, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Hindenburgdamm 30, 12203 Berlin, Germany.
authors.forename: Britta
authors.initials: B
authors.lastname: Siegmund
authors.affiliation: Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
authors.forename: Till
authors.initials: T
authors.lastname: Strowig
authors.affiliation: Department of Nutritional Medicine, University of Hohenheim, Fruwirthstr. 12, 70593 Stuttgart, Germany.
authors.forename: Valentina
authors.initials: V
authors.lastname: Volynets
authors.affiliation: Medical Clinic 1, Friedrich Alexander University, Ulmenweg 18, 91054 Erlangen, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wirtz
authors.affiliation: Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany; Department of Medicine I, University Medical Center Dresden and Center for Regenerative Therapies, Technical University Dresden, 01307 Dresden, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Zeissig
authors.affiliation: Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany; Department of General Pediatrics, University Medical Center Dresden, Technical University Dresden, 01307 Dresden, Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Zeissig
authors.affiliation: Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
authors.forename: André
authors.initials: A
authors.lastname: Bleich
authors.affiliation: Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, August-Thienemann-Str. 2, 24306, Plön, Germany; Institute for Experimental Medicine, Evolutionary Genomics, Christian-Albrechts-University of Kiel, Arnold-Heller-Str. 3, Haus 17, 24105 Kiel, Germany. Electronic address: baines@evolbio.mpg.de.
authors.forename: John F
authors.initials: JF
authors.lastname: Baines
mesh_terms: D000822:Animal Husbandry / Q000379:methods*; D000818:Animals; D016000:Cluster Analysis; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D005858:Germany; D008297:Male; D008810:Mice, Inbred C57BL; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D011795:Surveys and Questionnaires
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA gene; C57BL/6J; Gut microbiota; Mouse husbandry