Microbiome spectra serve as critical clues to elucidate the evolutionary biology pathways, potential pathologies, and even behavioral patterns of the host organisms. Furthermore, exotic sources of microbiota represent an unexplored niche to discover microbial secondary metabolites. However, establishing the bacterial functionality is complicated by an intricate web of interactions inside the microbiome. Here we apply an ultrahigh-throughput (uHT) microfluidic droplet platform for activity profiling of the entire oral microbial community of the Siberian bear to isolate Bacillus strains demonstrating antimicrobial activity against Staphylococcus aureus. Genome mining allowed us to identify antibiotic amicoumacin A (Ami) as responsible for inhibiting the growth of S. aureus. Proteomics and metabolomics revealed a unique mechanism of Bacillus self-resistance to Ami, based on a subtle equilibrium of its deactivation and activation by kinase AmiN and phosphatase AmiO, respectively. We developed uHT quantitative single-cell analysis to estimate antibiotic efficacy toward different microbiomes and used it to determine the activity spectra of Ami toward human and Siberian bear microbiota. Thus, uHT microfluidic droplet platform activity profiling is a powerful tool for discovering antibiotics and quantifying external influences on a microbiome.

微生物组光谱是阐明宿主生物的进化生物学途径，潜在病理甚至行为模式的关键线索。此外，微生物群的外来来源代表了发现微生物次生代谢产物的未开发的生态位。但是，建立微生物功能的过程由于微生物组内部复杂的相互作用网络而变得复杂。在这里，我们为西伯利亚熊整个口腔微生物群落的活性分析应用超高通量（uHT）微流体液滴平台，以分离出表现出对金黄色葡萄球菌具有抗菌活性的芽孢杆菌菌株。基因组挖掘使我们能够鉴定出抗生素金古霉素A（Ami）可以抑制金黄色葡萄球菌的生长。蛋白质组学和代谢组学揭示了芽孢杆菌对Ami的自我抗性的独特机制，基于其失活和分别被激酶AmiN和磷酸酶AmiO激活的微妙平衡。我们开发了uHT定量单细胞分析来评估抗生素对不同微生物群的功效，并用于确定Ami对人和西伯利亚熊微生物群的活性谱。因此，uHT微流控液滴平台活性分析是发现抗生素并量化对微生物组的外部影响的有力工具。