Collaborative Research: Mechanisms of community coalescence in synthetic microbiomes

Distinct microbiomes are often mixed in natural and engineered systems. For example, terrestrial and aquatic microbiomes mix in rivers, soil microbial communities invade one another in agriculture, and human skin microbiomes come into contact when two people shake hands. Such cross-microbiome invasions are collectively termed community coalescence. How these mixing events impact the function of microbiomes and how often new communities with novel functions form as a result remains unclear. This research project uses fermented food microbiomes, including sourdough starters, kombucha, and fermented vegetables, to determine how microbiomes reassemble when they mix and how coalescence impacts microbiome functions. Findings from these experimentally tractable fermented food systems identify how community coalescence can be used as a tool for microbiome engineering and its potential to improve the manipulation of medically and industrially relevant microbiomes. The broad appeal of fermented food systems is also used to increase participation in undergraduate research and broaden the public understanding of microbiomes. This project also engages the public more broadly through popular science articles and interviews on MicrobialFoods.org, a popular science venue developed to explain complex biological concepts in scientific papers in accessible content for food enthusiasts and educators. The mechanisms that govern cross-community invasions remain poorly understood. Most research has focused on the consequences of community coalescence in natural systems, while determination of underlying mechanisms is limited. This project manipulates a suite of fermented food model systems, derived from fermented food microbiomes, including sourdough starters, kombucha, and fermented vegetables, in conducting community coalescence experiments. The investigation sheds light on the consequences of coalescence, the mechanisms that govern it, and its potential utility for microbiome engineering. With the use of co-culture interaction assays, metabolic modeling, RNA-sequencing, and targeted metabolomics the project dissects the underlying interaction mechanisms that shape coalescence outcomes. Experimental evolution is used to determine how abiotic and biotic adaptation constrains or promotes cross-invasion outcomes. This project provides a mechanistic understanding that is required for predicting coalescence consequences and for leveraging community coalescence in industrial applications with microbial communities. 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.