The "dark matter" in metabolomics (unknowns) represents an exciting frontier with significant potential for discovery in relation to biochemistry, yet it also presents one of the largest challenges to overcome. This focussed review takes a close look at the current state-of-the-art and future challenges in tackling the unknowns with specific focus on the human gut microbiome and host-microbe interactions. Metabolomics, like metabolism itself, is a very dynamic discipline, with many workflows and methods under development, both in terms of chemical analysis and post-analysis data processing. Here, we look at developments in the mutli-omic analyses and the use of mass spectrometry to investigate the exchange of metabolites between the host and the microbiome as well as the environment within the microbiome. A case study using HuMiX, a microfluidics-based human-microbial co-culture system that enables the co-culture of human and microbial cells under controlled conditions, is used to highlight opportunities and current limitations. Common definitions, approaches, databases and elucidation techniques from both the environmental and metabolomics fields are covered, with perspectives on how to merge these, as the boundaries blur between the fields. While reflecting on the number of unknowns remaining to be conquered in typical complex samples measured with mass spectrometry (often orders of magnitude above the "knowns"), we provide an outlook on future perspectives and challenges in elucidating the relevant "dark matter".

中文翻译：

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宿主微生物组代谢组学中的暗物质：解决未知问题——综述

代谢组学（未知）中的“暗物质”代表了一个激动人心的前沿领域，在生物化学方面具有巨大的发现潜力，但它也是需要克服的最大挑战之一。这篇重点综述仔细研究了当前在解决未知问题方面的最新技术和未来挑战，特别关注人类肠道微生物组和宿主-微生物相互作用。代谢组学与代谢本身一样，是一门非常动态的学科，在化学分析和分析后数据处理方面有许多工作流程和方法正在开发中。在这里，我们着眼于多组学分析的发展以及使用质谱法研究宿主与微生物组以及微生物组内环境之间代谢物的交换。使用 HuMiX 的案例研究，一种基于微流体的人类-微生物共培养系统，可以在受控条件下实现人类和微生物细胞的共培养，用于强调机会和当前的局限性。涵盖了环境和代谢组学领域的常见定义、方法、数据库和阐明技术，并就如何合并这些领域提出了观点，因为这些领域之间的界限变得模糊。在反思用质谱法测量的典型复杂样品中仍有待克服的未知数（通常比“已知”高出几个数量级）的同时，我们展望了阐明相关“暗物质”的未来前景和挑战。用于突出机会和当前的局限性。涵盖了环境和代谢组学领域的常见定义、方法、数据库和阐明技术，并就如何合并这些领域提出了观点，因为这些领域之间的界限变得模糊。在反思用质谱法测量的典型复杂样品中仍有待克服的未知数（通常比“已知”高出几个数量级）的同时，我们展望了阐明相关“暗物质”的未来前景和挑战。用于突出机会和当前的局限性。涵盖了环境和代谢组学领域的常见定义、方法、数据库和阐明技术，并就如何合并这些领域提出了观点，因为这些领域之间的界限变得模糊。在反思用质谱法测量的典型复杂样品中仍有待克服的未知数（通常比“已知”高出几个数量级）的同时，我们对阐明相关“暗物质”的未来前景和挑战进行了展望。