Spatially Organized Bacterial Interaction Networks in the Gut Microbiota

摘要 每个成年人的肠道中都有数百种细菌。然而，微生物的网络- 微生物之间的相互作用，削弱了常驻物种的稳定共存，并排除了额外的物种， 没有很好地定义。肠腔是一种混乱的、半流动的景观，微生物细胞和饮食 植物细胞壁碎片的分布具有高度的异质性，并在秒的时间尺度上重新分布。 我们认为细菌选择性地附着在肠道中的饮食颗粒上，并且与它们的相互作用 共同依附的微生物伙伴决定了它们是否持续存在。我们创造了人工食品的多元化图书馆 颗粒(由葡聚糖包覆的磁珠组成)以测量体内肠道细菌的粘附性，以及 发现拟杆菌门的许多成员在一株菌株中附着在饮食中的多糖颗粒上- 特定的和特定于多糖的方式。我们将首先确定这些所需的黏附蛋白家族 利用转座子突变和插入位点测序的结合表型。接下来，我们将确定 共同附着在饮食颗粒上的相互作用的菌株网络。使用口服给药的图书馆 荧光标记的珠子，我们将绘制共黏附网络在诺生菌小鼠定植的菌株 在单一的捐赠者宿主中共同进化。最后，我们将建立一种突变选择策略， 允许在遗传上难以处理的肠道微生物中同时产生不同的结合特异性。 对这些突变的分析将揭示粘附性依赖的物种间关系的潜在来源。 这些研究将阐明肠道微生物区系定义不清的空间结构。我们的技术 在这项提案中发展作为一种有意定位微生物成员的手段 防止或改善新陈代谢、免疫学和传染性的物理配置的社区 疾病。

SUMMARY Each adult human harbors hundreds of bacterial species in their intestine. However, the networks of microbe- microbe interactions that underly the stable co-existence of resident species, and exclude additional species, are not well defined. The intestinal lumen is a turbulent, semi-fluid landscape where microbial cells and dietary plant cell wall fragments are distributed with high heterogeneity, and redistributed on the time scale of seconds. We propose that bacteria selectively adhere to dietary particles in the gut lumen and that interactions with their co-adherent microbial partners dictate whether they persist. We created multiplex libraries of artificial food particles (consisting of glycan-coated magnetic beads) to measure gut bacterial adhesion in vivo, and discovered that many members of the phylum Bacteroidetes adhere to dietary glycan particles in a strain- specific and glycan-specific manner. We will first identify families of adhesion proteins required for these binding phenotypes using transposon mutagenesis and insertion site sequencing. Next, we will identify networks of interacting strains that co-adhere to dietary particles. Using orally administered libraries of fluorescently labeled beads, we will map co-adhesion networks in gnotobiotic mice colonized with strains that have evolved together in a single donor host. Finally, we will establish a mutational selection strategy that permits the simultaneous generation of different binding specificities in genetically intractable gut microbes. Analysis of these mutations will reveal the potential origins of adhesion-dependent interspecies relationships. These studies will shed light on the poorly defined spatial structure of the gut microbiota. The technologies we develop in this proposal hold promise as a means to intentionally position the members of microbial communities in physical configurations that prevent or ameliorate metabolic, immunologic, and infectious diseases.