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

我们的微生物区系是一个复杂的群落，近年来，我们对其组成的了解有了显著的提高。炎症、饮食和恶性疾病与肠道微生物组成的数量变化有关。虽然这些数量差异是众所周知的，但人们对微生物区系的确切分布和空间组织的变化知之甚少。最近的工作表明，肠道细菌向肠上皮移位可能与饮食和炎症改变有关，但这种移位的确切条件和影响尚不清楚。我们假设肠道慢性病变的发生是由肠道细菌向肠上皮的病理性移位促进的。肠道细菌直接附着于隐窝中的特殊上皮肠上皮细胞，特别是隐窝底部的干细胞，可能会通过诱导严重的免疫反应而导致直接的上皮损伤和间接的损伤。我们将应用可视化技术和新的计算分析系统来研究健康肠道组织以及炎症性肠病和结直肠癌患者的样本中细菌与宿主上皮解剖的关系。为了揭示促进细菌向上皮细胞移位的条件，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鼠以及一种新的原代上皮细胞培养系统。在小鼠中，将研究炎症和饮食变化对微生物区系空间重组和由干细胞介导的反应的影响。此外，还将对具有能够附着在肠道上皮细胞上的特定细菌菌株的小鼠进行定居。利用体外培养的人和小鼠结肠上皮干细胞原代培养系统，我们将研究某些细菌及其毒力因子对包括长寿命干细胞在内的不同亚群上皮细胞的直接影响。该系统还将被调节，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.