Resource competition predicts assembly of gut bacterial communities in vitro.
Resource competition predicts assembly of gut bacterial communities in vitro.
复制标题
资源竞争预测体外肠道细菌群落的组装。
DOI：
10.1038/s41564-024-01625-w
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发表时间：
2024
影响因子：
28.3
通讯作者：
Huang,KerwynCasey
中科院分区：
文献类型：
--
作者：
Ho,Po-Yi;Nguyen,TaylorH;Sanchez,JuanM;DeFelice,BrianC;Huang,KerwynCasey
微生物群落动态通过物种间的相互作用产生，包括资源竞争，交叉喂养和pH调节。这些机制对社区结构的单独贡献很难解开。在这里，我们开发了一个框架，估计多物种生态位重叠相结合的代谢组学数据的个别物种，在用过的媒体和数学模型的增长测量。我们将我们的框架应用于体外模型系统，该系统包括复杂介质中的15个人类肠道菌群，并表明资源竞争的简单模型占大多数成对相互作用。接下来，我们通过对同一组物种消耗的代谢组学特征进行分组，建立了一个粗粒度的消费者-资源模型，并表明该模型以合理的准确度预测了2- 15成员社区的组成。此外，我们发现，纳入交叉喂养和pH值介导的相互作用改善了模型预测的物种共存。我们的理论模型和实验框架可以应用于表征细菌群落中的种间相互作用。
Microbial community dynamics arise through interspecies interactions, including resource competition, cross-feeding and pH modulation. The individual contributions of these mechanisms to community structure are challenging to untangle. Here we develop a framework to estimate multispecies niche overlaps by combining metabolomics data of individual species, growth measurements in spent media and mathematical models. We applied our framework to an in vitro model system comprising 15 human gut commensals in complex media and showed that a simple model of resource competition accounted for most pairwise interactions. Next, we built a coarse-grained consumer-resource model by grouping metabolomic features depleted by the same set of species and showed that this model predicted the composition of 2-member to 15-member communities with reasonable accuracy. Furthermore, we found that incorporation of cross-feeding and pH-mediated interactions improved model predictions of species coexistence. Our theoretical model and experimental framework can be applied to characterize interspecies interactions in bacterial communities in vitro.