URoL:MTM2: Defining the ecological and genomic properties that underlie microbiome sensitivity and resilience

微生物群是生活在植物和动物身上和体内的一个生物群落，对宿主的健康起着重要作用。然而，科学家目前对微生物组如何应对变化以及这些变化如何改变其宿主的健康轨迹的潜在过程知之甚少。该项目将实施一个新的概念和方法框架，以实质性地推进这些过程的发现。为了改变对干扰如何影响植物和动物微生物组的理解，将对三种重要的水生生物：海草，珊瑚和斑马鱼进行一系列实验。中心目标是定义微生物组对环境变化的敏感性和恢复力的统一原则和特性。此外，该项目将确定微生物组的敏感性和弹性如何解释其宿主健康的减少或改善。这种普遍特性的识别有可能改变微生物组的研究和创新，特别是当它适用于健康和自然资源管理时。为了进一步提高科学家定义改变微生物群-宿主相互作用机制的能力，从事该项目的研究人员将开发新颖且免费的数据分析工具和软件。还将制定有效的培训、推广和评估计划，以增加各种背景的微生物组科学家的参与和促进未来的职业发展。最后，在这个项目中，努力可能会产生理论框架，预测宿主-微生物组相互作用如何响应环境变化，这对如何优化野生动物、牲畜、农业和人类健康管理具有重要意义。该项目旨在定义宿主相关微生物组的普遍特性，使其能够抵抗或从干扰中恢复。为此，将进行实验，正式测试微生物组的先天特性是否会影响其对干扰的反应和恢复。为了揭示这些特性，珊瑚、海草和斑马鱼这三种模式和系统发育多样的水生宿主系统的微生物组将受到三种外源性和环境相关的压力源的挑战——抗生素、变暖的海水和病原体感染。然后将开发建模方法，以解决影响应激反应的微生物组的普遍特性，而不考虑群落的具体扰动或生态环境。这些与系统无关的微生物组测量，或“samm”，将包括常见的生态指标，以及使用人工智能算法开发的新指标，这些算法以系统独立的方式将微生物特征背景化。宿主特性也将被测量，以模拟宿主-微生物组在干扰之前，期间和之后的相互作用，以了解这些特性如何与宿主生理学相关。该项目的独特之处在于，它测量了宿主-微生物组系统如何随着时间的推移对干扰做出反应并从中恢复，考虑了多种生态相关干扰之间的相互作用，并整合了跨系统的结果，以揭示可推广的趋势。最后，这项工作有望为人类活动如何通过微生物群影响野生动物提供基础见解。最终，预计这些努力将有助于未来微生物组被管理或操纵，以缓冲其宿主免受人类世的影响。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。

The microbiome is a community of organisms that lives on and within plants and animals, playing a fundamental role in the health of their hosts. However, scientists currently have limited knowledge about the processes underlying how microbiomes respond to change and how such changes may alter the health trajectories of their hosts. This project will implement a novel conceptual and methodological framework to substantially advance discovery of these processes. To transform understanding of how disturbances impact plant and animal microbiomes, a series of experiments with three important aquatic organisms: seagrasses, corals, and zebrafish, will be performed. The central aim is to define the unifying principles and properties that define a microbiome’s sensitivity and resilience to environmental changes. Moreover, this project will determine how the microbiome’s sensitivity and resilience explains reductions or improvements in their host’s health. The identification of such universal properties holds potential to transform microbiome research and innovation, particularly as it applies to health and natural resource management. To further advance the ability of scientists to define the mechanisms that alter microbiome-host interactions, researchers working on this project will develop novel and freely available data analytic tools and software. Effective training, outreach, and assessment programs that increase participation and advance the future careers of microbiome scientists of all backgrounds will also be developed. Lastly, during this project, efforts will likely yield theoretical frameworks for predicting how host-microbiome interactions respond to environmental variation, which holds implications for how optimally wildlife, livestock, agricultural, and human health are managed.This project seeks to define universal properties of host-associated microbiomes that enable their ability to resist or recover from disturbances. To do so, experiments to formally test whether innate properties of the microbiome influence its response to and recovery from a disturbance will be conducted. To uncover such properties, microbiomes of three model and phylogenetically diverse aquatic host systems - corals, seagrass, and zebrafish – will be challenged with three exogenous and environmentally relevant stressors – antibiotics, warming waters, and pathogen infection. Modeling approaches will then be developed to resolve universal properties of the microbiome that influence stress responses, irrespective of the specific perturbation or ecological context of the community. These System Agnostic Microbiome Measures, or ‘SAMMs’, will include common ecological metrics as well as novel metrics developed using AI algorithms that contextualize microbial features in a system-independent way. Host traits will also be measured to model host-microbiome interactions before, during, and after disturbance to understand how these properties relate to host physiology. This project is distinctive in that it measures how host-microbiome systems both respond to and recover from disturbances over time, considers interactions between multiple ecologically relevant disturbances, and integrates the results across systems to uncover generalizable trends. Lastly this work is expected to develop foundational insights into how human activity impacts wildlife through their microbiomes. Ultimately, it is anticipated that these efforts will contribute to a future wherein microbiomes are managed or manipulated to buffer their hosts from the impacts of the Anthropocene.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.