Valiei Amin, Dickson Andrew, Aminian-Dehkordi Javad, Mofrad Mohammad R K
Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, 94720, USA.
Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
NPJ Biofilms Microbiomes. 2024 Oct 2;10(1):99. doi: 10.1038/s41522-024-00572-y.
The gut microbiome plays a major role in human health; however, little is known about the structural arrangement of microbes and factors governing their distribution. In this work, we present an in silico agent-based model (ABM) to conceptually simulate the dynamics of gut mucosal bacterial communities. We explored how various types of metabolic interactions, including competition, neutralism, commensalism, and mutualism, affect community structure, through nutrient consumption and metabolite exchange. Results showed that, across scenarios with different initial species abundances, cross-feeding promotes species coexistence. Morphologically, competition and neutralism resulted in segregation, while mutualism and commensalism fostered high intermixing. In addition, cooperative relations resulted in community properties with little sensitivity to the selective uptake of metabolites produced by the host. Moreover, metabolic interactions strongly influenced colonization success following the invasion of newcomer species. These results provide important insights into the utility of ABM in deciphering complex microbiome patterns.
肠道微生物群在人类健康中起着重要作用；然而，对于微生物的结构排列以及控制其分布的因素，我们却知之甚少。在这项研究中，我们提出了一种基于计算机模拟的个体模型（ABM），用以从概念上模拟肠道黏膜细菌群落的动态变化。我们通过营养物质消耗和代谢物交换，探索了包括竞争、中立、共生和互利共生在内的各种类型的代谢相互作用如何影响群落结构。结果表明，在不同初始物种丰度的情况下，交叉喂养促进了物种共存。从形态学角度来看，竞争和中立导致了隔离，而互利共生和共生则促进了高度混合。此外，合作关系导致群落特性对宿主产生的代谢物的选择性摄取几乎不敏感。而且，代谢相互作用强烈影响新物种入侵后的定殖成功。这些结果为ABM在解读复杂微生物群落模式方面的效用提供了重要见解。
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