Highly simplified model of a mammalian intestinal community

人类胃肠道(GI)是一个极其复杂的细菌群落的家园 对宿主的重要作用，包括代谢产物的转化和分解，免疫系统的发展 以及对微生物病原体的保护。这些社区是高度动态的-它们的组成和 代谢活动可以通过哺乳动物宿主的变化而显著改变，包括饮食、抗生素、 疾病和衰老。值得注意的是，胃肠道微生物区系的变化(生物失调)通常与人类 炎症性疾病，包括克罗恩病和溃疡性结肠炎、传染病和结直肠疾病 癌症。这些疾病影响着数百万人，每年给美国经济造成近400亿美元的损失。这个 GI微生物群落的复杂性极大地增加了其研究的复杂性，并使其难以分配 生物学功能(S)对特定的细菌属，更不用说物种。因此，缺乏敏感度。 用于胃肠道疾病早期检测和监测的生物标志物。为了解决这些知识上的差距，我们 建议采用一种高度简化的小鼠模型，其胃肠道只有8种细菌定植 种，改变的Schaedler植物群(ASF)。总的来说，ASF促进了正常的生理功能和 小鼠胃肠系统的健康状况。与大多数由传统微生物群组成的细菌不同，每个ASF 成员可以在体外培养。我们是美国少数几个有经验使用这一技术的研究团队之一 评估胃肠道粘膜健康和疾病的宿主-微生物群落模型。我们的中心假设是 宿主遗传学和微生物激发剂介导的扰动推动代谢适应， 是健康和疾病的独特标志。我们将使用深度转录组测序以及 定量聚合酶链式反应分析整个GI群体基因表达和丰度的变化以评估 个体物种对疾病状态的反应的代谢状态。ASF模型将允许我们 通过GI环境的变化，确定对维护社区非常重要的适应 用传统的小鼠模型或用一种细菌定植的小鼠是不可能达到的水平 物种。这些研究的成功完成将产生一部关于个人如何 GI社区的成员对免疫(即内在的)和细菌驱动的(即外在的)做出反应 微扰。这项研究将有助于个性化医疗的未来，包括识别 预测疾病易感性和严重程度的新生物标志物，以及缓解 生物失调对宿主造成的后果。

The human gastrointestinal (GI) tract is home to an extremely complex bacterial community that plays essential roles for the host, including conversion and breakdown of metabolites, immune system development and protection against microbial pathogens. These communities are highly dynamic-their composition and metabolic activity can be altered dramatically by changes in their mammalian host, including diet, antibiotics, disease and aging. Significantly, changes in the GI microbiota (dysbiosis) are often associated with human inflammatory diseases, including Crohn's disease and ulcerative colitis, infectious diseases and colorectal cancer. These disorders affect millions of people and cost the US economy nearly $40 billion each year. The sheer complexity of the GI microbial community greatly complicates its study and makes it difficult to assign biological function(s) to specific bacterial genera, much less species. Consequently, there is a lack of sensitive biomarkers for early detection and monitoring of GI diseases. To address these gaps in knowledge, we propose to employ a highly simplified mouse model whose GI tract is colonized with only eight bacterial species, the altered Schaedler flora (ASF). Collectively, the ASF facilitates normal physiological function and health of the mouse GI system. In contrast to most bacteria comprising a conventional microbiota, each ASF member can be cultured in vitro. We are one of the few research teams in the US experienced in using this host-microbial community model to evaluate GI mucosal health and disease. Our central hypothesis is that perturbations mediated by host genetics and microbial provocateurs drive metabolic adaptations that are unique signatures of health and disease. We will use deep transcriptome sequencing along with quantitative PCR to profile changes in gene expression and abundance of the entire GI community to assess the metabolic states of the individual species in response to disease states. The ASF model will allow us to identify adaptations important for maintenance of the community through changes in the GI environment at a level not possible with a conventional mouse models, or by using mice colonized with a single bacterial species. The successful completion of these studies will yield a detailed "documentary" of how individual members of the GI community respond to immune- (i.e., intrinsic) and bacterial-driven (i.e., extrinsic) perturbations. This research will contribute to the future of personalized medicine, including identification of new biomarkers that predict predisposition and severity of disease, as well as new strategies to mitigate the consequences of dysbiosis on the host.