Nam Kee-Myoung, Li Changhao, Cockx Bastiaan J R, Nguyen Danh T, Li Ying, Kreft Jan-Ulrich, Yan Jing
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
Department of Biology, Pennsylvania State University, State College, PA, USA.
Curr Opin Solid State Mater Sci. 2025 Jul;37. doi: 10.1016/j.cossms.2025.101228. Epub 2025 May 31.
Biofilms are surface-attached bacterial communities encased within extracellular matrices (ECMs) of biopolymers that play many significant roles in health and society. Biofilms are versatile, living biomaterials that are resilient to a wide range of external perturbations, primarily due to the ECM, which consists of a complex network of polymeric macromolecules. Newly established platforms for live biofilm imaging at single-cell resolution have revealed a wealth of novel insights into the emergence of cellular organization within a developing biofilm. This has, in turn, necessitated the development of modeling approaches that can pinpoint the mechanistic origins of this organization. In this review, we discuss the use of agent-based models (ABMs) as a general framework for simulating the development of bacterial colonies and biofilms. We describe the ingredients that are typically included in an ABM, together with the biological entity or process that each such ingredient represents, and the assumptions that underlie its precise formulation within the model. We then discuss a selection of recent studies in which ABMs have been used to investigate the physical mechanisms that govern biofilm development, focusing on our recent work on orientational ordering within biofilms. Finally, we describe the numerous ways in which we foresee that ABMs can be leveraged to further our understanding of biofilm development.
生物膜是附着于表面的细菌群落，被包裹在生物聚合物的细胞外基质（ECM）中，在健康和社会中发挥着许多重要作用。生物膜是多功能的活体生物材料，对多种外部干扰具有抗性，这主要归因于由聚合大分子组成的复杂网络的细胞外基质。新建立的单细胞分辨率下活生物膜成像平台揭示了关于发育中生物膜内细胞组织形成的大量新见解。这反过来又需要开发能够精确确定这种组织形成机制起源的建模方法。在这篇综述中，我们讨论了基于主体的模型（ABM）作为模拟细菌菌落和生物膜发育的通用框架的应用。我们描述了ABM中通常包含的要素，以及每个要素所代表的生物实体或过程，以及其在模型中精确表述所依据的假设。然后，我们讨论了一系列近期研究，其中ABM被用于研究控制生物膜发育的物理机制，重点介绍了我们最近关于生物膜内取向有序化的研究工作。最后，我们描述了我们预见到的ABM可用于进一步加深我们对生物膜发育理解的多种方式。
