The gut microbiota contributes to host physiology through the production of a myriad of metabolites. These metabolites exert their effects within the host as signalling molecules and substrates for metabolic reactions. Although the study of host–microbiota interactions remains challenging due to the high degree of crosstalk both within and between kingdoms, metabolite-focused research has identified multiple actionable microbial targets that are relevant for host health. Metabolites, as the functional output of combined host and microorganism interactions, provide a snapshot in time of an extraordinarily complex multi-organism system. Although substantial work remains towards understanding host–microbiota interactions and the underlying mechanisms, we review the current state of knowledge for each of the major classes of microbial metabolites with emphasis on clinical and translational research implications. We provide an overview of methodologies available for measurement of microbial metabolites, and in addition to discussion of key challenges, we provide a potential framework for integration of discovery-based metabolite studies with mechanistic work. Finally, we highlight examples in the literature where this approach has led to substantial progress in understanding host–microbiota interactions.

肠道微生物群通过产生无数代谢物来促进宿主生理机能。这些代谢物在宿主体内发挥作用，作为代谢反应的信号分子和底物。尽管由于界内和界之间的高度串扰，宿主-微生物群相互作用的研究仍然具有挑战性，但以代谢物为重点的研究已经确定了多个与宿主健康相关的可操作微生物目标。代谢物作为宿主和微生物相互作用的功能输出，提供了一个非常复杂的多生物系统的及时快照。尽管在理解宿主-微生物群相互作用及其潜在机制方面仍有大量工作要做，我们回顾了每个主要微生物代谢物类别的当前知识状态，重点是临床和转化研究的影响。我们概述了可用于测量微生物代谢物的方法，除了讨论关键挑战之外，我们还提供了一个潜在的框架，用于将基于发现的代谢物研究与机械工作相结合。最后，我们重点介绍了文献中的例子，其中这种方法在理解宿主-微生物群相互作用方面取得了实质性进展。我们提供了一个潜在的框架，将基于发现的代谢物研究与机械工作相结合。最后，我们重点介绍了文献中的例子，其中这种方法在理解宿主-微生物群相互作用方面取得了实质性进展。我们提供了一个潜在的框架，将基于发现的代谢物研究与机械工作相结合。最后，我们重点介绍了文献中的例子，其中这种方法在理解宿主-微生物群相互作用方面取得了实质性进展。