Physical Structure and Inter-Species Interactions in Gut Microbial Communities

肠道微生物群落的物理结构和种间相互作用

• 批准号: 2310570
• 负责人: Raghuveer Parthasarathy
• 金额: $ 60.11万
• 依托单位: University of Oregon Eugene
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2310570&HistoricalAwards=false
• 关键词: Physical; Structure; Inter; Species; Interactions

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.

我们的每个肠道内都栖息着代表数百个物种的数万亿微生物。这些微生物彼此之间以及与我们的人体细胞和器官竞争、合作和相互作用，从而影响正常的生理过程和一系列具有挑战性的疾病。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了解仍然很少，部分原因是这些生态系统不容易在“培养皿”研究中重现。肠道微生物组在强烈的物理限制下运行。物种以高密度共存，迫使它们与竞争对手一样接近边界，并且在肠道运输和加工食物时受到剧烈的流动。因此，了解肠道微生物组的结构需要对真实肠道环境进行观察和定量表征，这也是该奖项的动机。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相似之处，使它们成为优秀的动物模型。在年轻时，它们是相当透明的，最近开发的“光片荧光显微镜”技术可以在整个肠道的视野范围内进行快速三维成像，其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，其种群数量从几个细胞到数万个成员不等。这些观察结果提出了有关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？在斑马鱼肠道中仅存在单一细菌种类的情况下，研究人员表明，聚集体大小的统计分布反映了聚结、破碎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，其原因仍然是个谜。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：聚集状态可以预测入侵的易感性吗？肠道微生物不断受到新细菌的侵袭，但对入侵者产生抵抗力或易感性的原因却知之甚少。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，因为大聚集体很容易通过肠道收缩运输和排出。该奖项涉及由不同数量和类型的物种组成的斑马鱼肠道群落的构建，将微生物组组织的观察与入侵结果联系起来。此外，选择抗入侵群落的实验可能对于包括人类在内的其他动物物种产生肠道恢复能力特别重要。 除了上述实验和分析之外，研究人员还将设计教育活动，使用微生物组数据来说明生物成像和计算分析之间的交叉点。这些将在针对社会经济地位较低的高中生的日营中实施。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。