Yuan Jinhui, Sun Boyan, Li Murong, Yang Congyi, Zhang Lingqiang, Chen Ning, Chen Feng, Li Leyuan
State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 102206, Beijing, China.
Central Laboratory, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, 100081, Beijing, China.
NPJ Biofilms Microbiomes. 2025 Apr 23;11(1):63. doi: 10.1038/s41522-025-00692-z.
The human oral microbiome has been associated with multiple inflammatory conditions including inflammatory bowel disease (IBD). Identifying functional changes in oral microbiome by metaproteomics helps understanding the factors driving dysbiosis related to intestinal diseases. However, enriching bacterial cells from oral samples (such as saliva and mouth rinse) rich in host proteins is challenging. Here, we present an Optimized Salivary MetaProteomic sample analysis workflow (OSaMPle) to enrich salivary bacteria and reduce host-derived interferences for in-depth analysis of the oral metaproteome. Compared to a conventional approach, OSaMPle improved the identification of bacterial peptides and proteins by 3.2 folds and 1.7 folds, respectively. Furthermore, applying OSaMPle to analyze mouth rinse samples from IBD patients revealed significant alterations in bacterial protein expressions under disease conditions. Specifically, proteins involved in the fatty acid elongation pathway in Peptostreptococcus were significantly less abundant in IBD patients, whereas proteins associated with the TCA cycle in Neisseria were significantly more abundant. The OSaMPle workflow is capable of processing small-volume oral samples and adaptable to high-throughput automation. It holds promise as a strategy for investigating the functional responses of oral microbiomes under disease conditions and identifying disease-associated microbes with their proteins, providing critical insights for detecting disease-related biomarkers within the oral microbiome.
人类口腔微生物群与多种炎症性疾病相关，包括炎症性肠病（IBD）。通过元蛋白质组学确定口腔微生物群的功能变化有助于理解驱动与肠道疾病相关的微生物群落失调的因素。然而，从富含宿主蛋白质的口腔样本（如唾液和漱口水）中富集细菌细胞具有挑战性。在这里，我们提出了一种优化的唾液元蛋白质组学样本分析工作流程（OSaMPle），以富集唾液细菌并减少宿主来源的干扰，从而深入分析口腔元蛋白质组。与传统方法相比，OSaMPle分别将细菌肽和蛋白质的鉴定率提高了3.2倍和1.7倍。此外，应用OSaMPle分析IBD患者的漱口水样本发现，疾病状态下细菌蛋白质表达存在显著变化。具体而言，消化链球菌中参与脂肪酸延长途径的蛋白质在IBD患者中显著减少，而奈瑟菌中与三羧酸循环相关的蛋白质则显著增加。OSaMPle工作流程能够处理小体积口腔样本，并适用于高通量自动化。它有望作为一种策略，用于研究疾病状态下口腔微生物群的功能反应，并通过其蛋白质鉴定与疾病相关的微生物，为检测口腔微生物群中与疾病相关的生物标志物提供关键见解。
