Hong Juken, Xue Wenzhi, Wang Teng
Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
Elife. 2025 Mar 3;13:RP99593. doi: 10.7554/eLife.99593.
Microbial communities living in the same environment often display alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health, and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous studies, on the stability landscape of microbial populations. Combining mathematical modeling and numerical simulations, we demonstrate that, when mobile genetic elements (MGEs) only affect bacterial growth rates, increasing HGT rate in general promotes multistability of complex microbiota. We further extend our analysis to scenarios where HGT changes interspecies interactions, microbial communities are subjected to strong environmental selections and microbes live in metacommunities consisting of multiple local habitats. We also discuss the role of different mechanisms, including interspecies interaction strength, the growth rate effects of MGEs, MGE epistasis and microbial death rates in shaping the multistability of microbial communities undergoing HGT. These results reveal how different dynamic processes collectively shape community multistability and diversity. Our results provide key insights for the predictive control and engineering of complex microbiota.
生活在同一环境中的微生物群落通常表现出替代稳定状态，每种状态都以独特的物种组成为特征。了解微生物群落多稳定性的起源和决定因素在环境、人类健康和微生物群落工程方面具有广泛的意义。然而，尽管其概念上很重要，但复杂群落中多稳定性是如何出现的在很大程度上仍然未知。在这里，我们聚焦于水平基因转移（HGT）的作用，这是一个在以往研究中大多被忽视的重要方面，对微生物种群的稳定性格局的影响。通过结合数学建模和数值模拟，我们证明，当移动遗传元件（MGEs）仅影响细菌生长速率时，一般来说增加HGT速率会促进复杂微生物群的多稳定性。我们进一步将分析扩展到HGT改变物种间相互作用、微生物群落受到强烈环境选择以及微生物生活在由多个局部栖息地组成的集合群落的情景。我们还讨论了不同机制的作用，包括物种间相互作用强度、MGEs的生长速率效应、MGE上位性和微生物死亡率在塑造经历HGT的微生物群落多稳定性方面的作用。这些结果揭示了不同的动态过程如何共同塑造群落多稳定性和多样性。我们的结果为复杂微生物群的预测控制和工程提供了关键见解。
