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,, 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.

National Science Foundation (NSF)
Division of Molecular and Cellular Biosciences (MCB)
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David Rockcliffe
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Tufts University
United States
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