Spatially Organized Bacterial Interaction Networks in the Gut Microbiota

总结 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是常驻物种稳定共存的基础，并排除了其他物种， 并没有很好的定义。肠腔是一个动荡的，半流体景观，其中微生物细胞和饮食 植物细胞壁碎片的分布具有高度的异质性，并且在秒的时间尺度上重新分布。 我们认为，细菌选择性地粘附在肠腔中的膳食颗粒上， 共同粘附的微生物伴侣决定它们是否持续存在。我们建立了人工食物的多重图书馆 颗粒（由聚糖包被的磁珠组成），用于测量体内肠道细菌粘附，以及 发现拟杆菌门的许多成员粘附在菌株中的膳食聚糖颗粒上- 特异性和聚糖特异性方式。我们将首先确定家庭的粘附蛋白所需的这些 使用转座子诱变和插入位点测序的结合表型。接下来，我们将确定 相互作用的菌株网络，共同粘附在饮食颗粒上。使用口服给药的 荧光标记的珠子，我们将绘制与菌株， 在同一个宿主体内共同进化最后，我们将建立一个突变选择策略， 允许在遗传上难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依赖的种间关系的潜在起源。 这些研究将揭示肠道微生物群的空间结构不明确。我们的技术 在这项建议中，开发有望作为有意定位微生物成员的一种手段， 预防或改善代谢、免疫和感染的物理配置中的社区 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.