Viral micro-epidemics and evolutionary dynamics in bacterial biofilms

细菌建立了称为生物膜的微观群落，就像人类群落一样，生物膜为细菌提供了稳定性和增强的弹性。生物膜可能是有益的，例如在工业废水处理系统中，或作为健康肠道微生物群的一部分。然而，生物膜也可能对各种工业和卫生系统造成损害，甚至导致可能致命的耐药感染。控制生物膜种群的一个重要的新方法是使用称为噬菌体的病毒寄生虫来攻击生物膜内的有害细菌。虽然生物膜和噬菌体在自然界中无处不在，但人们对生物膜与噬菌体的相互作用知之甚少。在这个项目中，研究人员将开发新的技术来时空跟踪生物膜菌落内噬菌体感染的实时传播。利用集成的计算模拟和实验平台，研究人员将研究噬菌体感染生物膜的机制，生物膜内细菌感染抗性的存在和进化，并探索利用控制微生物群落组成方面的知识的可能性。此外，作为该项目更广泛的教育影响的一部分，PI将为周边农村社区的K-12学生开发实践教学模块。生物膜是由细胞嵌入细胞外黏合剂分泌基质中的耐应力细菌群落。生物膜生长模式是常见的，存在于植物和动物生命表面的微生物群中。细菌生物膜的另一个普遍特征是暴露于噬菌体。虽然生活在生物膜上的细菌可能经常遇到噬菌体，但人们对生物膜内细胞尺度上的细菌-噬菌体相互作用知之甚少，而这对理解微生物的进化至关重要。这种理解上的差距部分是由于缺乏适当的理论和实验技术来询问噬菌体-生物膜的相互作用。为了解决这一差距，PI建议开发和使用基于个体的建模技术来模拟生物膜-噬菌体相互作用。研究人员还将开发一种新的实验系统来模拟生物膜-噬菌体感染。该系统将由大肠杆菌和噬菌体T7在微流控平台中共同培养组成，以便使用高通量共聚焦显微镜直接可视化噬菌体感染过程。研究人员将利用他们新颖的、集成的理论和实验平台来研究(1)噬菌体暴露对生物膜形成进化的影响，以及(2)生物膜结构对噬菌体耐药性进化的影响。本研究的预期结果将增加对生物膜内相对未量化的细菌-噬菌体相互作用动力学的理解。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。

Bacteria build microscopic communities, termed biofilms, and much like human communities, biofilms provide bacteria with stability and increased resilience. Biofilms can be beneficial, for instance in industrial wastewater treatment systems, or as part of a healthy gut microbiota. However, biofilms can also cause damage to various industrial and health systems, even resulting in potentially lethal drug-resistant infections. An important new approach in the control of biofilm populations is the prescriptive use of viral parasites, called phages, to attack harmful bacteria within the biofilms. Though biofilms and phages are ubiquitous in nature, little is known about biofilm-phage interactions. In this project, investigators will develop new techniques to spatio-temporally track the real-time spread of phage infections within biofilm colonies. Using an integrated computational simulation and experimental platform, researchers will investigate mechanisms by which phages infect biofilms, the existence and evolution of infection-resistance within biofilm-dwelling bacteria, and explore the possibility of leveraging the knowledge gained in the control of microbial community composition. In addition, as part of the educational broader impacts of the project, the PI will develop hands-on teaching modules for K-12 students in surrounding rural communities. Biofilms are stress-tolerant bacterial communities composed of cells embedded in a secreted matrix of extracellular adhesives. The biofilm mode of growth is commonplace, existing within the microbiomes of living surfaces of plants and animals. Another ubiquitous feature of bacterial biofilms is exposure to bacteriophages. While biofilm-dwelling bacteria presumably encounter phages often, very little is known about bacteria-phage interactions within biofilms on the cellular scales that are crucial for understanding microbial evolution. This gap in understanding is due in part to the absence of appropriate theoretical and experimental techniques for interrogating phage-biofilm interactions. To address this gap, the PI proposes to develop and use techniques from individual-based modeling to simulate biofilm-phage interactions. Investigators will also develop a new experimental system to mimic biofilm-phage infection. The system will consist of Escherichia coli and phage T7 co-cultured in a microfluidic platform to enable direct visualization of the phage infection process using high-throughput confocal microscopy. Investigators will leverage their novel, integrated theoretical and experimental platform to study (1) the influence of phage exposure on the evolution of biofilm formation, and (2) the influence of biofilm architecture on the evolution of phage resistance. Anticipated outcomes from this research will lead to an increased understanding of the relatively unquantified bacteria-phage interaction dynamics within biofilms.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.