Highly simplified model of a mammalian intestinal community

人类胃肠道是一个极其复杂的细菌群落的家园， 对宿主的重要作用，包括代谢物的转化和分解，免疫系统的发育 和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 代谢活性可以通过哺乳动物宿主的改变而显著改变，包括饮食，抗生素， 疾病和衰老。值得注意的是，胃肠道微生物群的变化（生态失调）通常与人类疾病有关。 炎性疾病，包括克罗恩病和溃疡性结肠炎，传染病和结肠直肠炎， 癌这些疾病影响了数百万人，每年给美国经济造成近400亿美元的损失。的 GI微生物群落的复杂性使其研究变得非常复杂， 生物学功能对特定细菌属，更不用说物种。因此，缺乏敏感的 用于早期检测和监测GI疾病的生物标志物。为了填补这些知识空白，我们 我建议采用一种高度简化的小鼠模型，其胃肠道仅定植有八种细菌， 改变的Schaedler植物群（ASF）。总的来说，ASF促进正常的生理功能， 小鼠GI系统的健康。与包含常规微生物群的大多数细菌相比，每种ASF 可以在体外培养。我们是美国少数几个有经验的研究团队之一 宿主-微生物群落模型，以评估GI粘膜健康和疾病。我们的核心假设是， 由宿主遗传学和微生物代谢介导的扰动驱动代谢适应， 是健康和疾病的独特标志。我们将使用深度转录组测序沿着 定量PCR分析整个GI群落的基因表达和丰度变化， 个体物种对疾病状态的代谢状态。ASF模型将允许我们 通过GI环境的变化，确定对维持社区重要的适应措施， 水平不可能与传统的小鼠模型，或通过使用小鼠与单一的细菌定殖 物种这些研究的成功完成将产生一个详细的“纪录片”， GI群体的成员对免疫应答（即，内在的）和细菌驱动的（即，外在的） 扰动这项研究将有助于未来的个性化医疗，包括识别 新的生物标志物，预测疾病的易感性和严重程度，以及新的战略，以减轻 生态失调对宿主的影响

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.