MTM 1: Experimental framework for marine fish microbiomes through synthetic communities and multi-omic approaches

鱼类是全球重要的食物资源，是水生生态系统的重要组成部分，也是研究脊椎动物生物学的重要实验室模式生物。像所有动物一样，鱼在其外部身体表面（如皮肤）和内部（如肠道）都有丰富的共生微生物群落。这些微生物种群通过提供针对入侵病原体的保护，调节免疫功能以及环境和饮食化合物的分解，在宿主的健康和健身中发挥重要作用。该项目调查了与两种常见的海洋鱼类相关的微生物群，这两种鱼类具有截然不同的摄食生态，即肉食性太平洋鲭鱼和草食性猫眼鱼。将开发强大的培养系统，以在实验室中繁殖与鱼类相关的微生物，并使用高通量DNA测序和小分子检测方法进行分析。这些数据将被纳入计算模型，以分析和预测微生物组相互作用。因此，这项研究将提供一个实验框架，以了解微生物对鱼类生物学的贡献，并揭示鱼肠道微生物生态系统中微生物之间复杂的相互作用。这项工作对于了解促进海洋鱼类多样性和生态的微生物活动具有广泛的意义，并可以通过操纵鱼类微生物组来改善鱼类健康和水产养殖产量，从而为可持续水产养殖实践提供信息。对社会的其他好处包括培训本科生和研究生，以及开发探索海洋微生物组的STEM教育模块。 与海洋鱼类相关的微生物群代表了影响其宿主生理和生态的新型分解代谢和生物合成途径的未知来源。该项目将率先开发强大的体外生物反应器培养系统，以在实验室中复制和繁殖海鱼肠道微生物群，以评估和实验操纵鱼类微生物组的代谢输出。经典和高通量培养方法也将用于从天然样品和体外生物反应器中获得代表不同鱼肠道微生物组功能团的分离物。这些分离株将组装成可重复的和实验上易于处理的合成社区，以研究社区组织和微生物-微生物相互作用的新兴特性。将使用计算建模方法（神经网络统计方法）整合多组学数据集（宏基因组学，元转录组学和非靶向代谢组学），以发现高保真生物反应器系统中关键微生物类群，酶多样性，代谢产物生产和生物转化之间的联系。该项目将提供水生动物微生物组动力学的新视角，为未来微生物组宿主研究和微生物发现的新资源奠定基础。该项目由理解生命规则：微生物组理论和机制计划资助，作为NSF十大理念的一部分，通过生物科学理事会新兴前沿部门管理。共同资助由系统和合成生物学计划，分子和细胞生物科学部，生物科学理事会提供。该奖项反映了NSF的法定使命，并已被认为是值得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的支持。

Fish are recognized as a major global food resource, key ecological components of aquatic ecosystems, and have been valuable laboratory model organisms to study vertebrate biology. Like all animals, fish harbor rich communities of symbiotic microorganisms both upon their external body surfaces, such as the skin, and internally, such as the gut. These microbial populations play important roles in the health and fitness of their hosts by providing protection against invading pathogens, regulating immune functions, and the breakdown of environmental and dietary compounds. This project investigates the microbiota associated with two common marine fish species with contrasting feeding ecologies, the carnivorous Pacific chub mackerel and the herbivorous opaleye. Robust cultivation systems will be developed to propagate fish-associated microbes in the laboratory and analyzed using high-throughput DNA sequencing and small molecule detection methods. The data will be incorporated into a computational model to analyze and predict microbiome interactions. Thus, this research will provide an experimental framework to understand microbial contributions to fish biology and reveal the intricate interactions between microbes within the fish gut microbial ecosystem. This work has broad significance for understanding microbial activities that promote the diversity and ecology of marine fishes and can inform sustainable aquaculture practices by manipulating the fish microbiome to improve fish health and aquaculture yield. Additional benefits to society include the training of undergraduate and graduate students and the development of STEM education modules that explore the ocean microbiome. The microbiota associated with marine fish represent an uncharted source of novel catabolic and biosynthetic pathways that impact the physiology and ecology of their hosts. This project will pioneer the development of robust in vitro bioreactor cultivation systems to replicate and propagate marine fish gut microbiota in the laboratory to assess and experimentally manipulate metabolic outputs of the fish microbiome. Classical and high-throughput cultivation methods will also be used to obtain isolates representing different fish gut microbiome functional guilds from natural samples and in vitro bioreactors. These isolates will be assembled into reproducible and experimentally tractable synthetic communities to study emergent properties of community organization and microbe-microbe interactions. Multi-omic data sets (metagenomics, metatranscriptomics, and untargeted metabolomics) will be integrated using computational modeling approaches (neural network statistical methods) to discover linkages between key microbial taxa, their enzyme diversity, metabolite production, and biotransformations within the high-fidelity bioreactor systems. The project will deliver new perspectives on microbiome dynamics in aquatic animals, setting the foundation for future microbiome-host studies and novel resources for microbial discovery.This project is funded by the Understanding the Rules of Life: Microbiome Theory and Mechanisms Program, administered as part of NSF's Ten Big Ideas through the Division of Emerging Frontiers in the Directorate for Biological Sciences. Co-funding is provided by the Systems and Synthetic Biology Program, Division of Molecular and Cellular Biosciences, Directorate for Biological Sciences.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.