NSF Postdoctoral Fellowship in Biology FY 2021: Bacterial spatial organization as a microscale mechanism of ecosystem resilience

2021 财年 NSF 生物学博士后奖学金：细菌空间组织作为生态系统恢复力的微观机制

• 批准号: 2109890
• 负责人: Jen Nguyen
• 金额: $ 13.8万
• 依托单位: Nguyen, Jen
• 依托单位国家: 美国
• 项目类别: Fellowship Award
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2109890&HistoricalAwards=false
• 关键词: NSF; Postdoctoral; Fellowship; Biology; FY

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2021, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. Ecosystems — from plant roots to animal guts to oceans — are sustained by their microbial communities: collections of microorganisms that can protect or promote disease, depending on the environmental conditions. These communities routinely experience and endure environmental change. Some environmental changes destabilize communities, leading to pronounced changes in the microbial species composing a community. How these changes persist, even long after normal environmental conditions return, is not yet understood. This project seeks to learn how the spatial organization of single bacterial cells can determine how the bacterial community within the mammalian gut responds to environmental perturbation. By combining sequence-based observation with biophysical insights, the Fellow seeks to provide the first causal mechanism to explain and visualize how some gut ecosystems recover from disturbance while others suffer lasting change. Students recruited from underrepresented groups in STEM disciplines will engage in these activities with the Fellow. This project will investigate how organization of intestinal communities maintains the homeostasis of their host’s gut ecosystem by changing the bacterial species residing in microscopic folds of the gut epithelium (crypts). Both crypt- and whole-gut species composition can be altered after diarrhea, a perturbation that increases the abundance of some bacterial species and causes the extinction of others. Diarrhea also alters mucus and fluid flow in the gut that might enable changes in bacterial spatial organization that favor or destabilize the presence of specific species in the gut. To test this, the Fellow will develop a microfluidic system to track bacterial movement in a structural mimic of the mucus and fluid flow in the gut. The Fellow will generate a spatio-temporal map of bacteria in pre- and post-diarrhea guts to link in situ spatial organization with whole community composition. These multiscale data will unveil bacterial behaviors currently masked by prevailing sequencing techniques. This dataset, and all tools developed to generate it, will be made available through public repositories to promote multiscale research across diverse ecosystems. The training objectives include developing new skills in bioinformatics and histology, enabling the Fellow to complement findings from these methods with existing expertise in microfluidics and bacterial growth.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.

该行动资助2021财年NSF生物学博士后研究奖学金，研究基因组，环境和表型之间相互作用的生命规则的综合研究。该奖学金支持将以创新方式为《生活规则》领域作出贡献的研究员的研究和培训。生态系统——从植物根部到动物肠道再到海洋——是由它们的微生物群落维持的：微生物的集合可以根据环境条件保护或促进疾病。这些社区经常经历和忍受环境变化。一些环境变化会破坏群落的稳定，导致组成群落的微生物物种发生显著变化。这些变化是如何持续的，甚至在正常环境条件恢复后很长一段时间，目前还不清楚。该项目旨在了解单个细菌细胞的空间组织如何决定哺乳动物肠道内的细菌群落如何对环境扰动作出反应。通过将基于序列的观察与生物物理见解相结合，该研究员试图提供第一个因果机制，以解释和可视化一些肠道生态系统如何从干扰中恢复，而另一些则遭受持久的变化。从STEM学科中代表性不足的群体中招募的学生将与研究员一起参与这些活动。该项目将研究肠道群落的组织如何通过改变居住在肠道上皮（隐窝）微观褶皱中的细菌种类来维持宿主肠道生态系统的稳态。腹泻后，隐窝和全肠的细菌组成都可能发生改变，这种扰动会增加某些细菌种类的丰度，并导致其他细菌种类的灭绝。腹泻还会改变肠道中的粘液和液体流动，这可能会改变细菌的空间组织，从而有利于或破坏肠道中特定物种的存在。为了验证这一点，研究员将开发一种微流体系统来跟踪细菌在肠道粘液和液体流动的结构模拟中的运动。该研究员将生成腹泻前和腹泻后肠道细菌的时空图，以将原位空间组织与整个群落组成联系起来。这些多尺度数据将揭示目前被主流测序技术所掩盖的细菌行为。该数据集以及为生成该数据集而开发的所有工具将通过公共存储库提供，以促进跨不同生态系统的多尺度研究。培训目标包括发展生物信息学和组织学方面的新技能，使研究员能够将这些方法的发现与微流体和细菌生长方面的现有专业知识相补充。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Cause or effect? The spatial organization of pathogens and the gut microbiota in disease

因还是果？

• DOI: 10.1016/j.micinf.2021.104815
• 发表时间: 2021
• 期刊: Microbes and Infection
• 影响因子: 5.8
• 作者: Nguyen, Jen;Pepin, Deanna M.;Tropini, Carolina
• 通讯作者: Tropini, Carolina