Syntrophic exchange in synthetic microbial communities
Syntrophic exchange in synthetic microbial communities
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DOI：
10.1073/pnas.1405641111
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发表时间：
2014-05-20
影响因子：
11.1
通讯作者：
Wang, Harris H.
中科院分区：
文献类型：
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作者：
Mee, Michael T.;Collins, James J.;Wang, Harris H.
代谢互食是一个重要的过程，可以广泛地塑造微生物群落。然而，很少有人知道具体的交叉喂养的原则，推动形成和维持的个人在一个混合的人口。在这里，我们设计了一系列的合成互养社区，以探索复杂的相互作用的氨基酸代谢交换。我们实验分析了多成员，多维社区日益复杂的大肠杆菌，以评估协同交叉喂养的结果。我们发现，生物合成昂贵的氨基酸，包括蛋氨酸，赖氨酸，异亮氨酸，精氨酸和芳香族，往往促进更强的合作相互作用比氨基酸，更便宜的生产。此外，沿着沿着分支途径共享共同中间体的细胞产生更多的协同生长，但是当这些相互作用扩展到更高维度时，表现出许多正上位性和负上位性的情况。在更复杂的社区中，我们发现某些成员表现出关键物种般的行为，极大地影响了社区动态。基于对来自不同环境的6,000多个测序细菌的比较基因组分析，我们提出的证据表明，氨基酸生物合成已被广泛优化，以减少个体代谢负担，有利于增强交叉喂养，以支持整个生物圈的协同生长。这些结果提高了我们对微生物共养的基本理解，同时也突出了当前建模方法在描述微生物生态系统动态复杂性方面的实用性和局限性。这项工作为未来解决微生物生态学和进化中的关键问题奠定了基础，并为工业生物技术开发更好，更强大的工程合成社区提供了平台。
Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we devised a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions scaled to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology.