Physical Structure and Inter-Species Interactions in Gut Microbial Communities

在我们的每一个肠道内都居住着数以万亿计的微生物，代表着数百个物种。这些微生物相互竞争、合作和相互作用，并与我们的人体细胞和器官相互作用，从而影响正常的生理过程和各种具有挑战性的疾病。我们对肠道生态系统的结构，结构如何影响功能，以及结构和组成如何改变的理解仍然很少，部分原因是这些生态系统不容易在“培养皿”研究中重现。肠道微生物组在强大的物理约束下运行。物种以高密度共存，迫使它们靠近边界和竞争对手，并在肠道运输和处理食物时受到有力的流动。因此，了解肠道微生物组的结构需要对真实的肠道环境进行观察和定量表征，这是该奖项的动机。研究人员的实验室率先使用斑马鱼幼虫的三维显微镜来深入了解肠道微生物组的物理方面。斑马鱼与人类和其他脊椎动物有许多生理上的相似之处，使它们成为一种很好的动物模型。在年轻的时候，它们是相当透明的，最近开发的“光片荧光显微镜”技术能够在整个肠道的视野内进行快速的三维成像，分辨率能够辨别单个肠道细菌。过去的研究表明，许多肠道细菌物种形成聚集体：三维菌落，其群体从几个细胞到数万个成员。这些观察结果提出了关于肠道聚集的性质和后果的基本问题，该项目旨在回答这些问题。第一：细菌物种之间是否存在相互作用的结构特征？在制备的斑马鱼中，只有一种细菌物种驻留在肠道中，研究人员已经表明，聚集体大小的统计分布反映了聚结，碎片化和肠道运输的物理过程。此外，多物种群落共存的程度比预期的要高得多，原因仍然是神秘的。研究人员怀疑聚集体的特征，例如竞争物种的聚集体如何位于肠道景观中，以及物种如何改变其他物种的聚集行为，可以解释肠道细菌群落结构。 第二：聚集状态能预测对入侵的敏感性吗？肠道微生物不断受到新细菌的访问，但对入侵者的抗性或易感性的原因知之甚少。该项目的重点是能够改变肠道物理环境的细菌入侵者，即增强肠道机械收缩强度的菌株。研究人员假设聚集状态是入侵易感性的主要因素，因为大的聚集体很容易通过肠道的收缩被运输和排出。该奖项涉及在斑马鱼中构建由不同数量和类型的物种组成的肠道群落，将微生物组组织的观察结果与入侵结果联系起来。此外，选择抗入侵群落的实验可能对其他动物物种（包括人类）产生肠道弹性特别重要。除了上述实验和分析外，研究人员还将设计使用微生物组数据的教育活动，以说明生物成像和计算分析之间的交叉。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

Resident within each of our intestines are trillions of microbes representing hundreds of species. These microorganisms compete, cooperate, and interact with each other and with our human cells and organs, and in doing so influence both normal physiological processes and a wide range of challenging diseases. Our understanding of how intestinal ecosystems are structured, how structure influences function, and how structure and composition can be altered remain minimal, in part because these ecosystems are not easily recapitulated in in “petri dish” studies. The gut microbiome operates under strong physical constraints. Species coexist at high densities, forcing them close to boundaries as well as competitors, and are subject to vigorous flows as the gut transports and processes food. Understanding the structure of the gut microbiome therefore requires observation and quantitative characterization of real intestinal environments, motivating this award. The investigators’ labs have pioneered the use of three-dimensional microscopy of larval zebrafish to gain insights into physical aspects of the gut microbiome. Zebrafish share many physiological similarities with humans and other vertebrates, making them an excellent animal model. At young ages they are quite transparent, and the recently developed technique of “light sheet fluorescence microscopy” enables fast, three-dimensional imaging over fields of view spanning the entire intestine, with resolution capable of discerning individual gut bacteria. Past work has shown that many gut bacterial species form aggregates: three-dimensional colonies with populations ranging from a few cells to tens of thousands of members. These observations raise fundamental questions about the nature and consequences of intestinal aggregation that this project aims to answer. First: Are there structural signatures of interactions among bacterial species? In zebrafish prepared such that only a single bacterial species is resident in the gut, the investigators have shown that the statistical distribution of aggregate sizes reflects physical processes of coalescence, fragmentation, and intestinal transport. In addition, multi-species communities coexist to a much greater degree than would be expected, for reasons that remain mysterious. The investigators suspect that the characteristics of aggregates, for example how aggregates of competing species are situated in the intestinal landscape and how species alter other species’ aggregation behaviors, can explain gut bacterial community structure. Second: Can aggregation state predict susceptibility to invasion? Intestinal microbes are constantly visited by new bacteria, but the reasons for resistance or susceptibility to invaders are poorly understood. This project focuses on a bacterial invader capable of altering the physical environment of the gut, namely a strain that enhances the strength of gut mechanical contractions. The investigators hypothesize that aggregation state is a major factor in invasion susceptibility, as large aggregates are readily transported and expelled by the contractions of the gut. This award involves the construction of intestinal communities in zebrafish composed of different numbers and types of species, linking observations of microbiome organization with invasion outcomes. In addition, experiments that select for invasion-resistant communities may be of particular importance for generating intestinal resilience in other animal species, including humans.In addition to the experiments and analyses described above, the investigators will design educational activities that use microbiome data to illustrate the intersection between biological imaging and computational analysis. These will be implemented in a day camp that targets low socio-economic status high school students.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.