The human gut microbiome is a key contributor to health, and its perturbations are linked to many diseases. Small-molecule xenobiotics such as drugs, chemical pollutants and food additives can alter the microbiota composition and are now recognized as one of the main factors underlying microbiome diversity. Mapping the effects of such compounds on the gut microbiome is challenging because of the complexity of the community, anaerobic growth requirements of individual species and the large number of interactions that need to be quantitatively assessed. High-throughput screening setups offer a promising solution for probing the direct inhibitory effects of hundreds of xenobiotics on tens of anaerobic gut bacteria. When automated, such assays enable the cost-effective investigation of a wide range of compound-microbe combinations. We have developed an experimental setup and protocol that enables testing of up to 5,000 compounds on a target gut species under strict anaerobic conditions within 5 d. In addition, with minor modifications to the protocol, drug effects can be tested on microbial communities either assembled from isolates or obtained from stool samples. Experience in working in an anaerobic chamber, especially in performing delicate work with thick chamber gloves, is required for implementing this protocol. We anticipate that this protocol will accelerate the study of interactions between small molecules and the gut microbiome and provide a deeper understanding of this microbial ecosystem, which is intimately intertwined with human health.

人类肠道微生物组是健康的关键因素，其扰动与许多疾病有关。药物、化学污染物和食品添加剂等小分子外源物质可以改变微生物群的组成，现在被认为是微生物组多样性的主要因素之一。由于群落的复杂性、单个物种的厌氧生长要求以及需要定量评估的大量相互作用，绘制此类化合物对肠道微生物组的影响具有挑战性。高通量筛选装置为探索数百种异生物质对数十种厌氧肠道细菌的直接抑制作用提供了一种有前途的解决方案。当自动化时，此类测定可以对各种化合物-微生物组合进行经济有效的研究。我们开发了一种实验装置和方案，能够在严格厌氧条件下在 5 天内对目标肠道物种进行多达 5,000 种化合物的测试。此外，通过对方案进行微小修改，可以在从分离株组装的微生物群落或从粪便样本中获得的微生物群落上测试药物效果。实施该协议需要在厌氧室中工作的经验，特别是使用厚室手套进行精细工作的经验。我们预计该协议将加速小分子与肠道微生物组之间相互作用的研究，并提供对与人类健康密切相关的微生物生态系统的更深入的了解。