Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease.
Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease.
复制标题
元蛋白质组学是健康和疾病中肠道菌群的互补方法。
DOI：
10.3389/fchem.2017.00004
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发表时间：
2017
影响因子：
5.5
通讯作者：
Franco OL
中科院分区：
文献类型：
--
作者：
Petriz BA;Franco OL
经典的系统型图谱研究仅限于微生物成分的鉴定，缺乏关于这些细菌群落与宿主基因组的分子相互作用以及宿主生物学中可能的结果的信息。一系列组学方法提供了巨大的进展，将微生物区系与健康和疾病联系起来。然而，通过基于蛋白质组质谱的工具对这一背景的研究仍在改进中。因此，元蛋白质组学或社区蛋白质组学作为元基因组数据的补充方法出现，成为蛋白质组学中的一个领域，旨在对来自环境微生物区系(如人类肠道)的蛋白质进行大规模表征。分子分离方法结合质谱学(例如LC-MS/MS)和蛋白质组生物信息学的进展是这些新的大规模元蛋白质组研究的基础，这些研究已经在广泛的样品中进行，包括土壤、植物和人类环境。如果建立一个涵盖所有肠道微生物物种的基因和表达蛋白质的全面数据库，则代谢蛋白质组学研究将取得重大进展。为此，我们在这里介绍了在复杂的微生物区系环境中，如肠道，代谢蛋白质组研究的一些主要限制，还讨论了在分离/分离和质谱分析之前样品制备的最新管道。此外，还讨论了一种解决元基因组数据库局限性的新方法。最后，展望了利用统一的宿主微生物组基因数据库和其他元组学平台进行元蛋白质组分析的应用前景。
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut. The advances in molecular separation methods coupled with mass spectrometry (e.g., LC-MS/MS) and proteome bioinformatics have been fundamental in these novel large-scale metaproteomic studies, which have further been performed in a wide range of samples including soil, plant and human environments. Metaproteomic studies will make major progress if a comprehensive database covering the genes and expresses proteins from all gut microbial species is developed. To this end, we here present some of the main limitations of metaproteomic studies in complex microbiota environments, such as the gut, also addressing the up-to-date pipelines in sample preparation prior to fractionation/separation and mass spectrometry analysis. In addition, a novel approach to the limitations of metagenomic databases is also discussed. Finally, prospects are addressed regarding the application of metaproteomic analysis using a unified host-microbiome gene database and other meta-OMICs platforms.