The interaction between microbial communities and their environment, such as the human gastrointestinal tract, has been an area of microbiology rapidly advanced, by developments in sequencing technology. However, these techniques are largely limited to the detection of the taxonomic composition of a microbial community and/or its genetic functional capacity. Here, we discuss a range of mass spectrometry-based approaches which researchers can employ to explore the host-microbiome interactions at the metabolic level. Traditional approaches to mass spectrometry are detailed, alongside new developments in the field, namely ambient ionisation mass spectrometry and imaging mass spectrometry, which we believe will prove to be important to future work in this field. We further discuss considerations for experimental workflows, data analysis options and propose a methodology for the establishment of causal relationships between functional host-microbiome interactions with regards to health and disease in the human gastrointestinal tract.

随着测序技术的发展，微生物群落及其环境（例如人体胃肠道）之间的相互作用已成为微生物学快速发展的领域。但是，这些技术在很大程度上限于检测微生物群落的生物分类组成和/或其遗传功能。在这里，我们讨论了一系列基于质谱的方法，研究人员可以利用这些方法在代谢水平上探索宿主-微生物组的相互作用。详细介绍了传统的质谱方法，以及该领域的新发展，即环境电离质谱和成像质谱，我们认为这对将来在该领域的工作将具有重要意义。我们将进一步讨论实验性工作流程的注意事项，