Collaborative Research: Engineering host-associated synthetic consortia based on ecological modules.

养活不断增长的人口需要开发新技术，提高畜牧业的效率，减少病原体的有害影响。肠道相关微生物群落的工程设计可能是这些新技术发展的关键。虽然微生物组科学经常在人类健康的背景下进行讨论，但微生物对动物的影响要明显得多，特别是在水产养殖等高强度农业的背景下，而水产养殖是人类高质量蛋白质和脂肪的主要来源之一。鉴于水产养殖在许多国家的经济和营养方面具有巨大的相关性，必须制定控制微生物组组成和功能的战略，以便以可持续的方式保持和提高生产力。在本项目中，将构建合成微生物组，以提高盐水对虾（Artemia salina）的饲料效率，并防止细菌病原体副溶血性弧菌（Vibrio parahaolyticus）的感染。副溶血性弧菌是全球水产养殖中造成巨大疾病损失的罪魁祸首。此外，将建立一个由麻省理工学院和中佛罗里达大学与厄瓜多尔国家水产养殖和海洋研究中心（CENAIM）合作的双管齐下的桥梁项目。该桥梁项目将直接促进可持续水产养殖方法的发展，同时保护海洋生物多样性和生态系统，并将提供一个关键的转化途径，在大规模的现实环境中测试这项工作的结果。本科生和研究生将参与研究的各个方面。微生物组工程是一个新兴的领域，从分离物设计和构建多物种系统的能力目前是有限的。该项目利用对海洋细菌群落和环境病原体的研究，设计合成微生物群落，最大限度地提高饲料效率，防止病原体在水产养殖中定植，水产养殖是人类食用蛋白质的主要来源。该项目的最终目标是开发标准化的动物微生物组，通过协同控制饲料效率和病原体定植之间的相互作用，可用于提高动物产量和福祉。在这个项目的基础上，一个新的框架，基于生物的“生态模块”，可以混合和匹配以获得所需的功能，将用于设计合成财团。研究人员已经建立了两个关键的生态模块，它们在海洋中降解复杂有机物的群落中无处不在，并积累了具有广泛代谢能力的大型菌株集合。通过将不同的初级降解剂和次级消费者结合起来，利用一个由盐水虾、盐渍Artemia salina和副溶血性弧菌（一种对全球水产养殖产生巨大影响的细菌病原体）组成的模型系统来调节宿主饮食并阻止病原体定植，将从这些收集物中构建合成联合体。总的来说，这项研究将产生一个实验平台，使用从天然分离物组装的模块来设计合成群落，以达到所需的功能，并可能为微生物组的组装和形成提供见解。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。

Feeding a growing human population will require the development of new technologies that increase the efficiency of animal farming and reduce the detrimental impact of pathogens. The engineering of gut-associated microbial consortia can hold the key to the development of these new technologies. While microbiome science is often discussed in the context of human health, the impact of microorganisms on animals is much more pronounced, especially in the context of high-intensity farming such as aquaculture – one of the main sources of high-quality protein and fat for humans. Given the enormous relevance of aquaculture in the economy and nutrition of many nations, it is imperative to develop strategies to control microbiome composition and function, in order to maintain and increase productivity in a sustainable manner. In this project, synthetic microbiomes will be constructed to increase feed efficiency in the brine shrimp, Artemia salina, and prevent infection by a bacterial pathogen, Vibrio parahaemolyticus, which is responsible for great losses from disease in aquaculture worldwide. Furthermore, a two-pronged bridge program partnering Massachusetts Institute of Technology and University of Central Florida with Ecuador’s National Center for Aquaculture and Marine Research (CENAIM) will be created. The bridge program will directly further the development of sustainable aquaculture methods while protecting marine biodiversity and ecosystems and will provide a critical translational avenue to test the results of this work in large-scale, real-world settings. Undergraduate and graduate students will be involved in all aspects of the research. Microbiome engineering is an emerging field and the ability to design and construct multispecies systems from isolates is currently limited. This project leverages research on marine bacterial communities and environmental pathogens to design synthetic microbial consortia that maximize feed efficiency and prevent pathogen colonization in aquaculture – a major source of edible protein for humans. The ultimate goal of the project is to develop standardized animal microbiomes that could be used to increase animal production and well-being by synergistically controlling the interaction between feed efficiency and pathogen colonization. Underlying this project, a novel framework, based on “ecological modules” of organisms that could be mix-and-matched to obtain a desired functionality, will be used to design synthetic consortia. The investigators have already established two key ecological modules that are ubiquitous in communities that degrade complex organic matter in the ocean and have amassed a large strain collection with a wide range of metabolic capabilities. Synthetic consortia will be built from this collection by combining different primary degraders and secondary consumers to modulate host diet and deter pathogen colonization using a model system consisting of the brine shrimp, Artemia salina, and Vibrio parahaemolyticus, a bacterial pathogen of enormous impact in aquaculture worldwide. Overall, this research will generate an experimental platform to design synthetic communities using modules assembled from natural isolates for desired functionalities and may provide insight into microbiome assembly and formation.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.