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复杂细菌殖民地形态的生物物理代谢建模

Ilija Dukovski¹, Lauren Golden², Jing Zhang³

¹Bioinformatics Program, Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA; Center for Advanced Interdisciplinary Research, Ss. Cyril and Methodius University, Skopje, North Macedonia.

|August 9, 2025

概括

这项研究整合了微生物代谢和生物质传播,以实现现实的大肠杆菌殖民地模拟. 新模型准确地预测了殖民地形态和遗传多样性,推进了预测性微生物生态系统建模.

科学领域:

微生物生态学微生物生态学
计算生物学计算生物学
系统生物学系统生物学

背景情况:

微生物殖民地生长受到生物质传播,营养扩散和环境代谢反应的影响.
现有的模型往往缺乏对生物质传播和代谢过程的全面整合.
了解这些综合动态对于预测微生物生态系统行为至关重要.

研究的目的:

开发一个计算框架,将新陈代谢的动态流量平衡建模与集体生物质传播和人口波动相结合.
模拟和分析大肠杆菌 (E. coli) 殖民地生长动态和形态.
为微生物生态系统行为提供更细致和更具预测性的模型.

主要方法:

利用了微生物生态系统在时间和空间中的计算 (COMETS) 框架.
组合动态流量平衡建模 (dFBA) 与集体生物质传播模型.
纳入人口的波动来模拟大肠杆菌殖民地发展.

主要成果:

模拟生成了与实验观测一致的现实的殖民地形态.
标志着平滑和的殖民地结构之间的过渡.
在模拟殖民地内观察到遗传多样性的衰减.
鉴定了由于生物质积累而形成的"代谢环",与咖啡污点环不同.

结论:

综合建模方法为预测性微生物生态系统建模提供了重大进展.
该模型成功地捕捉了微生物殖民地发展的关键方面,包括形态和多样性.
这些发现为微生物社区结构的物理和代谢驱动因素提供了新的见解.

关键词:

委员会提出的建议细菌殖民地细菌殖民地咖啡染色效应的咖啡染色效应.殖民地形态学殖民地形态学动态流量平衡分析遗传性脱混合遗传性脱混合基因组规模的代谢建模增长不稳定不稳定的增长代谢维护是指代谢维护.代谢环的代谢环.

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