Ecological and evolutionary constraints on the design of synthetic microbiomes

人体，食物系统和自然生态系统都依赖于微生物群落的活动，通常称为微生物组。微生物学家已经确定了许多微生物组中部分（微生物物种）的多样性，但他们对这些部分如何组合在一起以及它们如何随时间变化的理解非常有限。如果没有一套微生物组的通用组装指令，就很难可预测地操纵这些系统。这项研究将使用从三种发酵食品（发酵茶、酸面团和奶酪）中分离的微生物来确定微生物群落如何进化以及这种进化对操纵和设计微生物生态系统的影响。这些食物微生物组是相对简单的系统（每个微生物组约2 - 10个物种），已在世界各地的不同环境中培养多年。通过确定进化如何影响这些模型系统的组装，这项研究将开始提供可用于医学，农业和工业的微生物组组装指令。这些模型系统的普及将被用来提高公众对科学的理解，并增加对微生物组研究的参与。通过公民合成生态网络（CSEN）的发展，数百名志愿者将提交将用于拟议研究的发酵食品微生物组。在你的厨房教育模块的演变将允许高中学生发酵食品微生物组的演变。PI的在线微生物外展平台www.example.com将传播有关微生物组科学，合成生态学和系统生物学基本概念的信息图表。 高通量测序调查迅速揭示了微生物多样性的模式，但控制微生物组组装的机制尚未确定。使用合成生态学框架，该项目将确定核心微生物组组分进化的原因和后果，以组装合成群落。该研究将确定核心微生物组物种如何在微生物群落中具有多样化的功能，以及这种功能差异如何导致可变的微生物相互作用网络和微生物组组装过程。来自全球分布的发酵食品微生物组的核心微生物组物种的基因组和功能多样性将通过基因组测序和体外群落测定来表征。实验进化将用于确定驱动核心微生物组成分多样化的机制。多样化的影响将通过评估合成群落的可持续性、可入侵性和稳定性来衡量。

Human bodies, food systems, and natural ecosystems are all dependent on the activities of microbial communities, commonly known as microbiomes. Microbiologists have identified the diversity of parts (microbial species) within many microbiomes, but they have a very limited understanding of how these parts fit together and how they change over time. Without a set of general assembly instructions for microbiomes, it is difficult to predictably manipulate these systems. This research will use microbes isolated from three fermented foods - fermented tea, sourdough, and cheese - to identify how communities of microbes evolve and the implications of this evolution for manipulating and designing microbial ecosystems. These food microbiomes are relatively simple systems (~2-10 species per microbiome) that have been cultivated for many years in different environments around the world. By identifying how evolution impacts the assembly of these model systems, this research will begin to provide microbiome assembly instructions that can be used in medicine, agriculture, and industry. The popularity of these model systems will be leveraged to improve public understanding of science and increase participation in microbiome research. Through the development of the Citizen Synthetic Ecology Network (CSEN), hundreds of volunteers will submit fermented food microbiomes that will be used in the proposed research. An Evolution in Your Kitchen education module will allow high school students to evolve fermented food microbiomes. The PI's online microbial outreach platform, MicrobialFoods.org, will disseminate infographics on basic concepts in microbiome science, synthetic ecology, and systems biology.   High-throughput sequencing surveys have rapidly unveiled patterns of microbial diversity, but the mechanisms that control the assembly of microbiomes have not been identified. Using a synthetic ecology framework, this project will determine the causes and consequences of the evolution of core microbiome components for the assembly of synthetic communities. The research will determine how core microbiome species have diversified functions across microbial communities and how this functional divergence leads to variable microbial interaction networks and microbiome assembly processes. The genomic and functional diversity of core microbiome species from globally distributed fermented food microbiomes will be characterized through genome sequencing and in vitro community assays. Experimental evolution will be used to determine the mechanisms that drive diversification of core microbiome components. Impacts of the diversification will be measured by assessing interchangeability, invasibility, and stability of synthetic communities.