Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
Nat Commun. 2020 Nov 4;11(1):5589. doi: 10.1038/s41467-020-19368-7.
Conjugative plasmids can mediate the spread and maintenance of diverse traits and functions in microbial communities. This role depends on the plasmid's ability to persist in a population. However, for a community consisting of multiple populations transferring multiple plasmids, the conditions underlying plasmid persistence are poorly understood. Here, we describe a plasmid-centric framework that makes it computationally feasible to analyze gene flow in complex communities. Using this framework, we derive the 'persistence potential': a general, heuristic metric that predicts the persistence and abundance of any plasmids. We validate the metric with engineered microbial consortia transferring mobilizable plasmids and with quantitative data available in the literature. We believe that our framework and the resulting metric will facilitate a quantitative understanding of natural microbial communities and the engineering of microbial consortia.
可移动质粒可以介导微生物群落中多种特征和功能的传播和维持。这种作用取决于质粒在种群中持续存在的能力。然而,对于由多个转移多种质粒的种群组成的群落而言,质粒持续存在的条件还知之甚少。在这里,我们描述了一个以质粒为中心的框架,该框架使在复杂群落中分析基因流动在计算上成为可行。使用这个框架,我们推导出了“持久性潜力”:一种通用的启发式度量标准,可以预测任何质粒的持久性和丰度。我们用可转移质粒的工程微生物联合体和文献中可用的定量数据来验证该度量标准。我们相信,我们的框架和由此产生的度量标准将有助于对自然微生物群落进行定量理解,并有助于微生物联合体的工程设计。