Viral micro-epidemics and evolutionary dynamics in bacterial biofilms

细菌建立微观社区，称为生物膜，就像人类社区一样，生物膜为细菌提供稳定性和增加的弹性。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，生物膜也会对各种工业和卫生系统造成损害，甚至导致潜在致命的耐药感染。控制生物膜种群的一种重要的新方法是规定性地使用病毒寄生虫（称为细菌）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普遍存在，但对生物膜-噬菌体相互作用知之甚少。在该项目中，研究人员将开发新技术来时空跟踪噬菌体感染在生物膜菌落内的实时传播。利用集成的计算模拟和实验平台，研究人员将研究细菌感染生物膜的机制，生物膜内细菌抗感染性的存在和演变，并探索利用在控制微生物群落组成方面获得的知识的可能性。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。生物膜是由包埋在分泌的细胞外粘附基质中的细胞组成的耐胁迫细菌群落。生物膜生长模式是常见的，存在于植物和动物的活表面的微生物组内。细菌生物膜的另一个普遍存在的特征是暴露于噬菌体。虽然居住在生物膜中的细菌可能经常遇到细菌，但对细胞尺度上生物膜内的细菌-噬菌体相互作用知之甚少，这对于理解微生物进化至关重要。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在微流体平台中共培养组成，以使用高通量共聚焦显微镜直接观察噬菌体感染过程。研究人员将利用他们新颖的综合理论和实验平台来研究（1）噬菌体暴露对生物膜形成演变的影响，以及（2）生物膜结构对噬菌体抗性演变的影响。这项研究的预期结果将导致对生物膜内相对未量化的细菌-噬菌体相互作用动力学的更多理解。该奖项反映了NSF的法定使命，并被认为值得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来支持。

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.