Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
Cell Syst. 2018 Sep 26;7(3):245-257.e7. doi: 10.1016/j.cels.2018.08.003. Epub 2018 Sep 5.
The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.
微生物群落中存在的物种多样性和数量为种间代谢相互作用创造了多种可能性。在这里，我们开发、应用并实验测试了一种推断与种间相互作用相关的代谢机制的框架。我们对来自模型鼠微生物组的菌株进行了成对的共培养生长和代谢组谱分析。然后，我们应用该框架来剖析共培养中出现的新兴代谢行为。基于该框架的一个推论，我们鉴定并探究了一种氨基酸交叉喂养相互作用，并验证了所提出的相互作用在体外导致了生长益处。我们的结果揭示了由肠道微生物组成的微生物群落中出现的代谢行为的类型和程度。我们关注的是调节生长的相互作用，但该框架也可以应用于调节微生物群落中任何感兴趣表型的种间相互作用。
