Engineering bacterial behaviors to control microbiota invasion resistance

项目总结/摘要（项目1） 人类和其他动物的胃肠道微生物群，由大量单个细胞组成 代表许多不同的物种，作为一个虚拟的器官，有助于广泛的生理 流程.与大多数器官相比，它更容易受到强烈和频繁的扰动，因为它与 外部世界和物种间的竞争，这是它作为一个多物种财团的本质所固有的。这些 扰动可以是化学的，例如来自抗生素药物，或生物的，例如来自新物种的入侵，和 可能与微生物的物理特性如运动性和空间分布有关。很可能 人类微生物组组成的巨大变异性，无论是在个体内，随着时间的推移， 在群体中的个体，部分是由于对外部驱动刺激的变化的反应。尽管如此， 我们对特定扰动如何影响肠道微生物群落的理解， 功能可能统一不同的反应，仍然是最小的。我们提出了一系列的实验， 这是用斑马鱼幼虫作为宿主-微生物系统的模型。斑马鱼幼鱼对细菌的适应性 操纵使得能够用大的重复群体进行受控实验，并且它们的光学透明度 允许对微生物丰度、空间分布和动态进行基于成像的定量。我们专注 两类重要的扰动：新物种的入侵和抗生素的暴露。的 新物种的引入是肠道环境的一个恒定特征， 和趋化性可能发挥重要作用之间的相互作用的居民和入侵微生物。建筑 关于合成生物学的进展，我们将设计基因开关来报告和控制这些行为， 原位，使用由gnotobiotic斑马鱼提供的控制来操纵肠道群落。抗生素的使用是 从宏基因组学研究中已知，即使在低（亚- 致命剂量，原因尚待发现。基于初步数据，我们假设，即使 弱抗生素干扰可以显著改变细菌的行为、空间分布和持久性 在肠道内，改变物种丰度和传播到新的主机。我们提出的实验将 提供了关于常见扰动如何影响肠道微生物群动力学的新见解， 为了解健康和疾病期间人体微生物组的动态奠定基础。

PROJECT SUMMARY/ABSTRACT (PROJECT 1) The gastrointestinal microbiota of humans and other animals, composed of vast numbers of individual cells representing many different species, serves as a virtual organ contributing to a wide range of physiological processes. More than most organs, it is subject to strong and frequent perturbations due to its connectedness to the outside world and the inter-species competition inherent in its nature as a multi-species consortium. These perturbations may be chemical, e.g. from antibiotic drugs, or biological, e.g. from invasion by new species, and may couple to physical characteristics of microbes such as motility and spatial distribution. It is likely that the large variability in human microbiome composition, both within individuals over time and between individuals in populations, is due in part to responses to variations in externally driven stimuli. Despite this, our understanding of how specific perturbations influence gut microbial communities, and whether generic features might unify diverse responses, remains minimal. We propose a series of experiments that will address this, using larval zebrafish as a model host-microbe system. The amenability of larval zebrafish to gnotobiotic manipulation enables controlled experiments with large replicate populations, and their optical transparency allows imaging-based quantifications of microbial abundances, spatial distributions, and dynamics. We focus on two important classes of perturbations: invasion by new species and exposure to antibiotics. The introduction of new species is a constant feature of the intestinal environment, and behaviors such as motility and chemotaxis likely play important roles in interactions between resident and invasive microbes. Building on advances in synthetic biology, we will engineer genetic switches to report on and control these behaviors in situ, using the control afforded by gnotobiotic zebrafish to manipulate intestinal communities. Antibiotic use is known from metagenomic studies to dramatically affect the gastrointestinal microbiota, even at low (sub- lethal) doses, for reasons that remain to be discovered. Building on preliminary data, we hypothesize that even weak antibiotic perturbations can dramatically alter bacterial behaviors, spatial distributions, and persistence within the gut, altering both species abundances and dispersal to new hosts. Our proposed experiments will provide new insights into how common perturbations influence intestinal microbiota dynamics and will establish a foundation for understanding the dynamics of human microbiomes during both health and disease.