Predicting plasmid persistence in microbial communities by coarse-grained modeling,BioEssays

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Predicting plasmid persistence in microbial communities by coarse-grained modeling
BioEssays ( IF 3.2 ) Pub Date : 2021-07-18 , DOI: 10.1002/bies.202100084
Teng Wang ₁ , Andrea Weiss ₁ , Yuanchi Ha ₁ , Lingchong You _{1,

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Affiliation

Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid-centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model-guided predictions of plasmid fates can benefit from the development of new experimental tools and data-driven computational methods.

中文翻译：

通过粗粒度模型预测微生物群落中的质粒持久性

质粒是介导水平基因转移的主要类型的移动遗传元件（MGE）。质粒的稳定维持在微生物种群的功能和生存中起着至关重要的作用。然而，预测和控制复杂微生物群落中质粒的持久性和丰度仍然具有挑战性。在计算上，这一挑战源于与传统建模框架相关的组合爆炸。最近，已开发出以质粒为中心的框架 (PCF) 来克服这一计算瓶颈。该框架可以推导一个简单的度量标准，即持久性潜力，以预测质粒的持久性和丰度。在这里，我们讨论如何扩展 PCF 以解释质粒相互作用。

更新日期：2021-08-27

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