Jiang Xiaoteng, Zhang Yan, Wang Huiyu, Wang Zeyuan, Hu Shen, Cao Chengxi, Xiao Hua
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
Research (Wash D C). 2022 Oct 13;2022:9781578. doi: 10.34133/2022/9781578. eCollection 2022.
The human oral microbiome correlates with numerous diseases, including lung cancer. Identifying the functional changes by metaproteomics helps understand the disease-related dysbiosis, yet characterizing low-abundant bacteria is challenging. Here, we developed a free-flow isoelectric focusing electrophoresis-mass spectrometry- (FFIEF-MS-) based metaproteomics strategy to reduce host interferences and enrich low-abundant bacteria for in-depth interpretation of the oral microbiome. With our method, the number of interfering peptides decreased by 52.87%, whereas the bacterial peptides and species increased by 94.97% and 44.90%, respectively, compared to the conventional metaproteomics approach. We identified 3647 bacterial proteins, which is the most comprehensive oral metaproteomics study to date. Lung cancer-associated bacteria were validated among an independent cohort. The imbalanced and and their dysregulated functions in inhibiting immune response and maintaining cell redox homeostasis were revealed. The FFIEF-MS may serve as a valuable strategy to study the mechanisms between human diseases and microbiomes with broader applications.
人类口腔微生物群与包括肺癌在内的多种疾病相关。通过元蛋白质组学确定功能变化有助于理解疾病相关的生态失调，但表征低丰度细菌具有挑战性。在此，我们开发了一种基于自由流动等电聚焦电泳-质谱（FFIEF-MS）的元蛋白质组学策略，以减少宿主干扰并富集低丰度细菌，从而深入解读口腔微生物群。与传统的元蛋白质组学方法相比，我们的方法使干扰肽的数量减少了52.87%，而细菌肽和细菌种类分别增加了94.97%和44.90%。我们鉴定出3647种细菌蛋白，这是迄今为止最全面的口腔元蛋白质组学研究。在一个独立队列中验证了与肺癌相关的细菌。揭示了其失衡以及在抑制免疫反应和维持细胞氧化还原稳态方面的功能失调。FFIEF-MS可能是一种有价值的策略，可用于研究人类疾病与微生物群之间的机制，并具有更广泛的应用。
