Xian Feng, Brenek Malena, Krisp Christoph, Urbauer Elisabeth, Ravi Kumar Ranjith Kumar, Aguanno Doriane, Srikumar Tharan, Liu Qixin, Barry Allison M, Ma Bin, Krieger Jonathan, Haller Dirk, Schmidt Manuela, Gómez-Varela David
Center of Excellence for Metaproteomics and Systems Biology of Pain Laboratory, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
Bruker Daltonics GmbH & Co. KG, Bremen, Germany.
Nat Commun. 2025 Jul 18;16(1):6644. doi: 10.1038/s41467-025-61977-7.
The functional characterization of host-gut microbiome interactions remains limited by the sensitivity of current metaproteomic approaches. Here, we present uMetaP, an ultra-sensitive workflow combining advanced LC-MS technologies with an FDR-validated de novo sequencing strategy, novoMP. uMetaP markedly expands functional coverage and improves the taxonomic detection limit of the gut dark metaproteome by 5000-fold, enabling precise detection and quantification of low-abundance microbial and host proteins. Applied to a mouse model of intestinal injury, uMetaP revealed host-microbiome functional networks underlying tissue damage, beyond genomic findings. Orthogonal validation using transcriptomic data from Crohn's disease patients confirmed key host protein alterations. Furthermore, we introduce the concept of a druggable metaproteome, mapping functional targets within the host and microbiota. By redefining the sensitivity limits of metaproteomics, uMetaP provides a highly valuable framework for advancing microbiome research and developing therapeutic strategies for microbiome-related diseases.
宿主-肠道微生物组相互作用的功能表征仍然受到当前宏蛋白质组学方法灵敏度的限制。在此，我们展示了uMetaP，这是一种超灵敏的工作流程，它将先进的液相色谱-质谱技术与经过错误发现率（FDR）验证的从头测序策略novoMP相结合。uMetaP显著扩大了功能覆盖范围，并将肠道暗物质宏蛋白质组的分类检测限提高了5000倍，能够精确检测和定量低丰度微生物和宿主蛋白。应用于肠道损伤小鼠模型，uMetaP揭示了组织损伤背后的宿主-微生物组功能网络，这超出了基因组学研究结果。使用克罗恩病患者的转录组数据进行的正交验证证实了关键宿主蛋白的改变。此外，我们引入了可药物化宏蛋白质组的概念，绘制宿主和微生物群内的功能靶点。通过重新定义宏蛋白质组学的灵敏度极限，uMetaP为推进微生物组研究和开发微生物组相关疾病的治疗策略提供了一个非常有价值的框架。
