Spatial Organization of the Microbiota - Impact of Direct Bacterial Interaction with the Colonic Crypt Epithelium and Long-lived Stem Cells

我们的微生物群是一个复杂的社区，近年来，我们对其组成的理解有了显着提高。炎症、饮食和恶性疾病与肠道微生物组成的数量变化有关。虽然这些数量上的差异已经很好地建立起来，但对微生物群空间组织的确切分布和变化知之甚少。最近的工作表明，饮食和炎症的变化可能与管腔细菌向肠道上皮细胞的易位有关，但这种易位的确切条件和影响尚不清楚。我们假设，肠道慢性病理状态的发展是由管腔细菌向肠道上皮细胞的病理性易位促进的。肠腔细菌直接附着于隐窝中的特化上皮肠细胞，特别是隐窝基底中的干细胞，可能导致直接上皮损伤，以及通过诱导严重的免疫反应而导致的间接损伤。我们将应用可视化技术以及新的计算分析系统来研究健康肠组织和样品中细菌与宿主上皮解剖结构的关系炎症性肠病和结直肠恶性肿瘤患者的血液样本。为了揭示促进细菌向上皮易位的条件，并研究某些细菌菌株与上皮干细胞直接相互作用的影响，我们将使用干细胞报告小鼠以及新的原代上皮培养系统。在小鼠中，将研究炎症和饮食变化对微生物群空间重组的影响和由干细胞特异性介导的反应。此外，将用能够附着于肠道上皮的特定细菌菌株对小鼠进行定殖。使用原代上皮人和小鼠结肠上皮干细胞衍生的体外系统，我们将研究某些细菌及其毒力因子对不同上皮细胞亚群（包括长寿干细胞）的直接影响。该系统也将被调制，以研究特定的宿主因素如何影响肠粘膜屏障特性。

Our microbiota is a complex community and within the recent years, our understanding of its composition has dramatically improved. Inflammatory, dietary and malignant conditions are associated with quantitative changes of the microbial composition in the gut. While these quantitative differences are well established, little is known about the exact distribution and changes of the spatial organization of the microbiota. Recent work has demonstrated that dietary and inflammatory changes might be associated in translocation of luminal bacteria towards the gut epithelium but the exact conditions and the impact of this translocation are still not known.We hypothesize that development of chronic pathological conditions in the gut are promoted by pathological translocation of luminal bacteria towards the gut epithelium. Direct attachment of commensal luminal bacteria to specialized epithelial gut cells in the crypt and in particular to stem cells in the crypt base may result in direct epithelial damage as well as indirect injuries through induction of severe immunological responses.We will apply visualization technologies as well as new computational analysis systems to study the relation of the bacteria to the host epithelial anatomy in healthy intestinal tissue and in samples from patients with inflammatory bowel diseases and colorectal malignancies. To unravel the conditions that promote translocation of bacteria towards the epithelium and to study the impact of direct interaction of certain bacterial strains with the epithelial stem cells, we will use stem cell reporter mice as well as a new primary epithelial culture system. In mice, the impact of inflammation and dietary changes for spatial reorganization of the microbiota and responses, mediated specifically by the stem cells will be studied. Furthermore, colonization of mice with specific bacterial strains that have the ability to attach to the gut epithelium will be performed. Using primary epithelial human and murine colonic epithelial stem cell-derived in vitro systems, we will study direct effects of certain bacteria and their virulence factors on different subpopulations of epithelial cells including long-lived stem cells. This system will also be modulated to study how specific host factors affect the intestinal mucosal barrier properties.