Animal models play a critical role in establishing causal relationships between gut microbiota and disease. The laboratory mouse is widely used to study the role of microbes in various disorders; however, differences between mouse vendors, genetic lineages and husbandry protocols have been shown to contribute to variation in phenotypes and to non-reproducibility of experimental results. We sought to understand how gut microbiome profiles of mice vary by vendor, vendor production facility and health status upon receipt into an academic facility and how they change over 12 weeks in the new environment. C57BL/6 mice were sourced from two different production sites for each of three different vendors. Mice were shipped to an academic research vivarium, and fresh-catch stool samples were collected from mice immediately from the shipping box upon receipt, and again after 2, 6 and 12 weeks in the new facility. Substantial variation in bacterial proportional abundance was observed among mice from each vendor at the time of receipt, but shared microbes accounted for most sequence reads. Vendor-specific microbes were generally of low abundance. Microbial profiles of mice from all vendors exhibited shifts over time, highlighting the importance of environmental conditions on microbial dynamics. Our results emphasize the need for continued efforts to account for sources of variation in animal models and understand how they contribute to experimental reproducibility.

动物模型在建立肠道微生物群与疾病之间的因果关系方面发挥着关键作用。实验室小鼠广泛用于研究微生物在各种疾病中的作用；然而，小鼠供应商、遗传谱系和饲养方案之间的差异已被证明会导致表型变异和实验结果的不可重复性。我们试图了解小鼠肠道微生物组谱如何因供应商、供应商生产设施和健康状况而变化，并在接收到学术设施后，以及它们在新环境中的 12 周内如何变化。C57BL/6 小鼠来自三个不同供应商的两个不同生产基地。老鼠被运送到一个学术研究动物饲养室，收到后立即从装运箱中收集新鲜捕获的小鼠粪便样本，并在新设施中的 2、6 和 12 周后再次收集。在收到时，在每个供应商的小鼠中观察到细菌比例丰度的显着变化，但共享微生物占大多数序列读数。供应商特定微生物的丰度通常较低。所有供应商的小鼠微生物特征都随着时间的推移而发生变化，突出了环境条件对微生物动力学的重要性。我们的研究结果强调需要继续努力解释动物模型中的变异来源，并了解它们如何促进实验可重复性。在收到时，在每个供应商的小鼠中观察到细菌比例丰度的显着变化，但共享微生物占大多数序列读数。供应商特定微生物的丰度通常较低。所有供应商的小鼠微生物特征都随着时间的推移而发生变化，突出了环境条件对微生物动力学的重要性。我们的研究结果强调需要继续努力解释动物模型中的变异来源，并了解它们如何促进实验可重复性。在收到时，在每个供应商的小鼠中观察到细菌比例丰度的显着变化，但共享微生物占大多数序列读数。供应商特定微生物的丰度通常较低。所有供应商的小鼠微生物特征都随着时间的推移而发生变化，突出了环境条件对微生物动力学的重要性。我们的研究结果强调需要继续努力解释动物模型中的变异来源，并了解它们如何促进实验可重复性。强调环境条件对微生物动力学的重要性。我们的研究结果强调需要继续努力解释动物模型中的变异来源，并了解它们如何促进实验可重复性。强调环境条件对微生物动力学的重要性。我们的研究结果强调需要继续努力解释动物模型中的变异来源，并了解它们如何促进实验可重复性。