BACKGROUND Human-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota. However, our understanding of such effects is limited due to a lack of rapid and scalable assay to comprehensively assess microbiome responses to drugs. Drugs and other compounds can drastically change the overall abundance, taxonomic composition, and functions of a gut microbiome. RESULTS Here, we developed an approach to screen compounds against individual microbiomes in vitro, using metaproteomics to both measure absolute bacterial abundances and to functionally profile the microbiome. Our approach was evaluated by testing 43 compounds (including 4 antibiotics) against 5 individual microbiomes. The method generated technically highly reproducible readouts, including changes of overall microbiome abundance, microbiome composition, and functional pathways. Results show that besides the antibiotics, the compounds berberine and ibuprofen inhibited the accumulation of biomass during in vitro growth of the microbiota. By comparing genus and species level-biomass contributions, selective antibacterial-like activities were found with 35 of the 39 non-antibiotic compounds. Seven of the compounds led to a global alteration of the metaproteome, with apparent compound-specific patterns of functional responses. The taxonomic distributions of altered proteins varied among drugs, i.e., different drugs affect functions of different members of the microbiome. We also showed that bacterial function can shift in response to drugs without a change in the abundance of the bacteria. CONCLUSIONS Current drug-microbiome interaction studies largely focus on relative microbiome composition and microbial drug metabolism. In contrast, our workflow enables multiple insights into microbiome absolute abundance and functional responses to drugs. The workflow is robust, reproducible, and quantitative and is scalable for personalized high-throughput drug screening applications.

中文翻译：

---

RapidAIM：基于培养和宏蛋白质组学的个体微生物组对药物反应的快速测定。

背景技术人类靶向药物可能会产生脱靶效应，或者可以重新调整肠道微生物群的用途。然而，由于缺乏快速且可扩展的分析方法来全面评估微生物组对药物的反应，我们对此类效应的理解有限。药物和其他化合物可以极大地改变肠道微生物组的总体丰度、分类组成和功能。结果在这里，我们开发了一种在体外筛选针对单个微生物组的化合物的方法，使用宏蛋白质组学来测量绝对细菌丰度并从功能上分析微生物组。我们的方法通过针对 5 个单独的微生物组测试 43 种化合物（包括 4 种抗生素）进行评估。该方法产生了技术上高度可重复的读数，包括总体微生物组丰度、微生物组组成和功能途径的变化。结果表明，除抗生素外，化合物小檗碱和布洛芬也抑制微生物群体外生长过程中生物量的积累。通过比较属和种水平的生物量贡献，发现 39 种非抗生素化合物中的 35 种具有选择性抗菌样活性。其中七种化合物导致了宏蛋白质组的整体改变，具有明显的化合物特异性功能反应模式。改变的蛋白质的分类分布因药物而异，即不同的药物影响微生物组不同成员的功能。我们还表明，细菌功能可以响应药物而发生变化，而细菌丰度不会发生变化。结论 目前的药物-微生物组相互作用研究主要集中在相关微生物组组成和微生物药物代谢上。相比之下，我们的工作流程可以对微生物组绝对丰度和对药物的功能反应进行多种深入了解。该工作流程稳健、可重复且定量，并且可针对个性化高通量药物筛选应用进行扩展。