Taormina Michael J, Jemielita Matthew, Stephens W Zac, Burns Adam R, Troll Joshua V, Parthasarathy Raghuveer, Guillemin Karen
Department of Physics, University of Oregon, Eugene, Oregon 97403, USA.
Biol Bull. 2012 Aug;223(1):7-20. doi: 10.1086/BBLv223n1p7.
Microbial colonization of the digestive tract is a crucial event in vertebrate development, required for maturation of host immunity and establishment of normal digestive physiology. Advances in genomic, proteomic, and metabolomic technologies are providing a more detailed picture of the constituents of the intestinal habitat, but these approaches lack the spatial and temporal resolution needed to characterize the assembly and dynamics of microbial communities in this complex environment. We report the use of light sheet microscopy to provide high-resolution imaging of bacterial colonization of the intestine of Danio rerio, the zebrafish. The method allows us to characterize bacterial population dynamics across the entire organ and the behaviors of individual bacterial and host cells throughout the colonization process. The large four-dimensional data sets generated by these imaging approaches require new strategies for image analysis. When integrated with other "omics" data sets, information about the spatial and temporal dynamics of microbial cells within the vertebrate intestine will provide new mechanistic insights into how microbial communities assemble and function within hosts.
消化道的微生物定殖是脊椎动物发育中的一个关键事件，是宿主免疫系统成熟和建立正常消化生理所必需的。基因组学、蛋白质组学和代谢组学技术的进步正在为肠道栖息地的组成提供更详细的图景，但这些方法缺乏表征这个复杂环境中微生物群落组装和动态所需的空间和时间分辨率。我们报告了使用光片显微镜对斑马鱼肠道细菌定殖进行高分辨率成像。该方法使我们能够表征整个器官的细菌种群动态以及整个定殖过程中单个细菌和宿主细胞的行为。这些成像方法生成的大型四维数据集需要新的图像分析策略。当与其他“组学”数据集整合时，关于脊椎动物肠道内微生物细胞空间和时间动态的信息将为微生物群落在宿主体内如何组装和发挥功能提供新的机制见解。
