Development of a New Bead Movement-Based Computational Framework Shows that Bacterial Amyloid Curli Reduces Bead Mobility in Biofilms.
Development of a New Bead Movement-Based Computational Framework Shows that Bacterial Amyloid Curli Reduces Bead Mobility in Biofilms.
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DOI：
10.1128/jb.00253-20
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发表时间：
2020-08-25
影响因子：
3.2
通讯作者：
Queisser G
中科院分区：
文献类型：
--
作者：
Malhotra K;Hunter T;Henry B;Ishmail Y;Gaddameedi P;Tursi S;Tükel Ç;Hoffer M;Buttaro BA;Queisser G
数学模型对于理解生物膜的材料组成如何影响其物理性质是必要的。在这里，我们开发了一个4D计算工具链，用于分析珠子轨迹，为建立生物膜中颗粒运动数学模型的关键参数奠定了基础。使用这种开源轨迹分析仪，我们确定细菌淀粉样蛋白卷曲的存在会改变生物膜的材料特性，使生物膜基质变硬。该软件是分析处理和环境引起的生物膜结构和生物膜中细胞运动变化的强大工具。该开源分析器是完全适应性和可扩展的模块化方式使用VRL-Studio进一步增强和扩展其功能。生物膜作为胃肠道菌群的一部分存在于包括肠道在内的复杂环境中。浮游细菌与生物膜的相互作用可以受到生物膜的材料性质的影响。在以前的共聚焦研究中，我们观察到含有淀粉样卷曲的沙门氏菌和大肠杆菌生物膜出现刚性。在这些研究中，缺乏卷曲样蛋白的粪肠球菌表现出更多的流体运动。为了更好地表征生物膜的材料性质，设计了一个四维（4D）模型，使用激光扫描共聚焦显微镜在约20 min内跟踪10- 20 μ m厚生物膜中1-μm乙醛酸珠的运动。开发了软件来分析微珠轨迹、它们可以遵循的时间量（轨迹寿命）、移动速度、覆盖的表面积（边界框）和每个微珠周围的细胞密度。微珠的运动主要是布朗运动。与大肠杆菌相比，含有卷曲的生物膜在整个生物膜的低密度和高密度区域中具有非常小的珠运动。faecalis和等基因curli突变体。含有卷曲的生物膜倾向于具有比缺乏卷曲的生物膜更稳定的珠相互作用（更长的轨迹寿命）。在缺乏卷曲的生物膜中，珠运动的速度和边界框体积都不严格依赖于细胞密度，这表明生物膜的其他材料性质影响珠的运动和材料的柔性。总之，这些研究提出了一种4D方法来分析珠在3D生物膜中随时间的移动，并表明curli赋予生物膜的细胞外基质刚性。重要性数学模型是必要的，以了解生物膜的材料组成如何影响其物理性质。在这里，我们开发了一个4D计算工具链，用于分析珠子轨迹，为建立生物膜中颗粒运动数学模型的关键参数奠定了基础。使用这种开源轨迹分析仪，我们确定细菌淀粉样蛋白卷曲的存在改变了生物膜的材料特性，使生物膜基质变硬。该软件是分析处理和环境引起的生物膜结构和生物膜中细胞运动变化的强大工具。该开源分析器是完全适应性和可扩展的模块化方式使用VRL-Studio进一步增强和扩展其功能。
Mathematical models are necessary to understand how the material composition of biofilms can influence their physical properties. Here, we developed a 4D computational toolchain for the analysis of bead trajectories, which laid the groundwork for establishing critical parameters for mathematical models of particle movement in biofilms. Using this open-source trajectory analyzer, we determined that the presence of bacterial amyloid curli changes the material properties of a biofilm, making the biofilm matrix rigid. This software is a powerful tool to analyze treatment- and environment-induced changes in biofilm structure and cell movement in biofilms. The open-source analyzer is fully adaptable and extendable in a modular fashion using VRL-Studio to further enhance and extend its functions. Biofilms exist in complex environments, including the intestinal tract, as a part of the gastrointestinal microbiota. The interaction of planktonic bacteria with biofilms can be influenced by material properties of the biofilm. During previous confocal studies, we observed that amyloid curli-containing Salmonella enterica serotype Typhimurium and Escherichia coli biofilms appeared rigid. In these studies, Enterococcus faecalis, which lacks curli-like protein, showed more fluid movement. To better characterize the material properties of the biofilms, a four-dimensional (4D) model was designed to track the movement of 1-μm glyoxylate beads in 10- to 20-μm-thick biofilms over approximately 20 min using laser-scanning confocal microscopy. Software was developed to analyze the bead trajectories, the amount of time they could be followed (trajectory life span), the velocity of movement, the surface area covered (bounding boxes), and cellular density around each bead. Bead movement was found to be predominantly Brownian motion. Curli-containing biofilms had very little bead movement throughout the low- and high-density regions of the biofilm compared to E. faecalis and isogenic curli mutants. Curli-containing biofilms tended to have more stable bead interactions (longer trajectory life spans) than biofilms lacking curli. In biofilms lacking curli, neither the velocity of bead movement nor the bounding box volume was strictly dependent on cell density, suggesting that other material properties of the biofilms were influencing the movement of the beads and flexibility of the material. Taken together, these studies present a 4D method to analyze bead movement over time in a 3D biofilm and suggest curli confers rigidity to the extracellular matrix of biofilms. IMPORTANCE Mathematical models are necessary to understand how the material composition of biofilms can influence their physical properties. Here, we developed a 4D computational toolchain for the analysis of bead trajectories, which laid the groundwork for establishing critical parameters for mathematical models of particle movement in biofilms. Using this open-source trajectory analyzer, we determined that the presence of bacterial amyloid curli changes the material properties of a biofilm, making the biofilm matrix rigid. This software is a powerful tool to analyze treatment- and environment-induced changes in biofilm structure and cell movement in biofilms. The open-source analyzer is fully adaptable and extendable in a modular fashion using VRL-Studio to further enhance and extend its functions.