Collaborative Research: Mechanisms of community coalescence in synthetic microbiomes

不同的微生物群经常混合在自然和工程系统中。例如，陆地和水生微生物群落在河流中混合，土壤微生物群落在农业中相互入侵，当两个人握手时，人体皮肤微生物群会接触。这种跨微生物群的入侵统称为群落合并。这些混合事件如何影响微生物组的功能，以及具有新功能的新群落形成的频率仍不清楚。本研究项目使用发酵食品微生物群，包括酵母发酵剂、康普茶和发酵蔬菜，来确定微生物群在混合时如何重组，以及聚结如何影响微生物群的功能。这些实验可处理的发酵食品系统的发现确定了如何将群落聚结作为微生物组工程的工具，以及它在改善医学和工业相关微生物组操作方面的潜力。发酵食品系统的广泛吸引力也用于增加本科生研究的参与和扩大公众对微生物组的理解。该项目还通过MicrobialFoods.org上的科普文章和访谈更广泛地吸引公众参与。MicrobialFoods.org是一个科普网站，旨在为食品爱好者和教育工作者提供通俗易懂的内容，解释科学论文中复杂的生物学概念。管理跨社区入侵的机制仍然知之甚少。大多数研究都集中在自然系统中群落合并的后果上，而对潜在机制的确定是有限的。本项目操作了一套发酵食品模型系统，源自发酵食品微生物群，包括酵母发酵剂、康普茶和发酵蔬菜，进行群落聚合实验。这项研究揭示了聚结的后果，控制它的机制，以及它在微生物组工程中的潜在效用。通过使用共培养相互作用分析、代谢建模、rna测序和靶向代谢组学，该项目剖析了形成聚合结果的潜在相互作用机制。实验进化用于确定非生物和生物适应如何限制或促进交叉入侵结果。该项目提供了一种机制的理解，这是预测聚结结果和利用微生物群落在工业应用中的群落聚结所必需的。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。

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.