Our bodies and those of our animal research subjects are colonized by bacterial communities that occupy virtually every organ system, including many previously considered sterile. These bacteria reside as complex communities that are collectively referred to as microbiota. Prior to the turn of the century, characterization of these communities was limited by a reliance on culture of organisms on a battery of selective media. It was recognized that the vast majority of microbes, especially those occupying unique niches of the body such as the anaerobic environment of the intestinal tract, were uncultivatable. However, with the onset and advancement of next-generation sequencing technology, we are now capable of characterizing these complex communities without the need to cultivate, and this has resulted in an explosion of information and new challenges in interpreting data generated about, and in the context of, these complex communities. We have long known that these microbial communities often exist in an intricate balance that, if disrupted (ie, dysbiosis), can lead to disease or increased susceptibility to disease. Because of many functional redundancies, the makeup of these colonies can vary dramatically within healthy individuals [1]. However, there is growing evidence that subtle differences can alter the phenotype of various animal models, which may translate to the varying susceptibility to disease seen in the human population. In this manuscript, we discuss how to include complex microbiota as a consideration in experimental design and model reproducibility and how to exploit the extensive variation that exists in contemporary rodent research colonies. Our focus will be the intestinal or gut microbiota (GM), but it should be recognized that microbial communities exist in many other body compartments and these too likely influence health and disease [2, 3]. Much like host genetics, can we one day harness the vast genetic capacity of the microbes we live with in ways that will benefit human and animal health?

中文翻译：

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实验室啮齿动物中的复杂微生物群：管理注意事项。

我们的身体和我们的动物研究对象的身体被细菌群落定植，这些群落几乎占据了每个器官系统，包括许多以前被认为是无菌的。这些细菌作为复杂的群落存在，统称为微生物群。在世纪之交之前，这些群落的特征受到依赖于一系列选择性培养基上的生物体培养的限制。人们认识到绝大多数微生物，尤其是那些占据身体独特生态位的微生物，例如肠道的厌氧环境，是不可培养的。然而，随着新一代测序技术的出现和进步，我们现在能够表征这些复杂的社区，而无需培养，这导致信息爆炸式增长，并在解释这些复杂社区及其背景下产生的数据时面临新的挑战。我们早就知道，这些微生物群落通常以错综复杂的平衡存在，如果被破坏（即生态失调），可能会导致疾病或增加对疾病的易感性。由于许多功能冗余，这些菌落的组成在健康个体中可能会有很大差异。1]。然而，越来越多的证据表明，细微的差异可以改变各种动物模型的表型，这可能会转化为人类对疾病的不同易感性。在这份手稿中，我们讨论了如何将复杂的微生物群作为实验设计和模型再现性的考虑因素，以及如何利用当代啮齿动物研究群体中存在的广泛变异。我们的重点将是肠道或肠道微生物群 (GM)，但应该认识到微生物群落存在于许多其他身体部位，这些也很可能影响健康和疾病。2、 3]。就像宿主遗传学一样，有朝一日我们能否以有益于人类和动物健康的方式利用与我们一起生活的微生物的巨大遗传能力？