It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted.

中文翻译：

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肠道代谢组与微生物组：理解宿主与微生物关系的方法论视角

众所周知，肠道微生物及其代谢产物调节宿主代谢。宿主与其肠道微生物群之间的相互作用是高度动态和复杂的。在这篇综述中，我们提出并讨论了研究肠道微生物生态系统的代谢组学策略。我们强调了研究粪便样本的代谢分析方法，旨在破译来自肠道微生物群的代谢产物。我们还讨论了代谢组学数据如何与来自肠道微生物群的宏基因组学数据相结合，以及这些方法如何更好地了解微生物功能。最后，强调了研究微生物共代谢和宿主-微生物相互作用的基因组规模代谢建模的新兴方法。