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
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.
Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
Int J Med Microbiol. 2016 Aug;306(5):343-355. doi: 10.1016/j.ijmm.2016.03.004. Epub 2016 Mar 15.
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.
肠道微生物群参与许多生理过程，并且人们越来越认识到群落组成的差异会影响生物医学研究中使用的各种小鼠模型的结果。为了描述和解释德国研究基金会优先项目1656“肠道微生物群”参与成员的动物设施中肠道微生物群组成的差异，我们对来自德国13个不同机构的21个不同小鼠房/设施的C57BL/6J小鼠进行了调查。使用标准化程序从每个房间/设施的五只小鼠中采集新鲜粪便，随后在DNA和RNA（逆转录为cDNA）水平上进行提取和16S rRNA基因分析（V1-V2区域，Illumina MiSeq）。为了确定导致细菌群落差异的变量，我们收集了详细的动物饲养管理调查问卷，并将这些信息纳入我们的分析中。我们在许多描述性方面发现了相当大的差异，包括主要门类的比例、α和β多样性，所有这些都与饲养管理的特定方面显示出显著关联。显著的发现包括使用辐照饲料会降低α多样性，屏障进入和开放式笼子会增加个体间变异性（β多样性），以及自从供应商处进口后，细菌群落差异会随着时间增加。我们进一步观察到高度的设施水平个体性，这可能是由于每个设施都有其独特的多种不同饲养管理属性的组合。虽然考虑和控制设施之间的这种差异很重要，但记录这种多样性也可能成为未来研究微生物驱动的宿主表型起源的宝贵资源。
