Gut microbiota can either contribute to the host development and health, or lead to the pathogenesis of various diseases in the case of imbalance. Microbial metabolites can act as functional molecules in mediating microbiota-host cross-talk and modulating host phenotype. There is an increasing demand for metabolomics. This review firstly summarizes the general scheme and methods for identifying important gut microbiota derived metabolites related to health and disease by integrating metabolomics and gut microbiome. And then chromatography-mass spectrometry-based methods for microbiota related metabolite analysis are reviewed. Representative methods developed in the past decade are highlighted mainly with respect to targeted analysis and non-targeted analysis. The former deals with short chain fatty acids, bile acids, tryptophan-related metabolites, and methylamines, and the latter includes sample collection and preparation, separation, detection and metabolite structure annotation. Perspectives on the future directions and challenges of metabolomics in microbiota-related host health/disease studies are also presented.

肠道微生物群既可以促进宿主的发育和健康，也可以在失衡的情况下导致各种疾病的发病。微生物代谢物可以作为功能分子介导微生物群-宿主串扰和调节宿主表型。对代谢组学的需求不断增加。本综述首先总结了通过整合代谢组学和肠道微生物组来识别与健康和疾病相关的重要肠道微生物群衍生代谢物的一般方案和方法。然后回顾了基于色谱-质谱的微生物群相关代谢物分析方法。在过去十年中开发的代表性方法主要在靶向分析和非靶向分析方面得到强调。前者处理短链脂肪酸、胆汁酸、色氨酸相关代谢物、和甲胺，后者包括样品采集和制备、分离、检测和代谢物结构注释。还提出了对微生物群相关宿主健康/疾病研究中代谢组学的未来方向和挑战的展望。