Metaproteomics technologies for microbiomes

微生物组一词于 1988 年引入，被定义为“占据合理明确栖息地的特征微生物群落”。微生物组由细菌、真菌、古细菌、原生生物和病毒组成。迄今为止，微生物组已在所有研究的植物和动物中被发现，并且是宿主生物体的重要贡献者。有益和有害微生物群水平的紊乱（生态失调）可能会导致宿主生物体出现系统性问题。微生物组研究领域正在迅速发展，并在人类健康、农业、生物技术、水净化、采矿等领域得到应用。迄今为止，大多数微生物组研究都依赖于宏基因组学和宏转录组学。这些信息本身不足以理解微生物组中正在进行的生物过程。迄今为止，很少有出版物涉及宏蛋白质组学。这部分是由于处理不同物种的复杂混合物时的技术和生物信息问题。 我的实验室 15 年来一直致力于开发用于蛋白质和蛋白质组研究的分析技术。在过去 5 年中，我们开发了用于微生物组研究的新技术。在这里，我们建议进一步开发通过宏蛋白质组学研究微生物组的分析技术以及微生物组翻译后修饰的研究，最初的重点是蛋白质糖基化。 我们的短期目标（1-3 年）是开发新方法来识别和量化复杂微生物组中的蛋白质和糖基化。具体来说，我们将 1) 开发微生物组的深度宏蛋白质组学分析方法，2) 开发微生物组糖蛋白的多重快速分析技术；中期目标：我们的中期目标（2-5 年）是开发自动化微流体技术，用于通过质谱法处理和鉴定微生物组中的蛋白质糖基化，并证明其在分析微生物组时的兼容性。长期目标：（> 5 年）。我们的长期目标是应用这些微流体技术来研究微生物组的动态，使这些系统自动化，并扩展其其他蛋白质修饰的能力。持续目标：我们目标的一个重要方面是为学生、PDF 和访问科学家提供关于宏蛋白质组学和宏糖组学技术以及微生物组分析质谱技术开发的培训。 这项研究的成果将是：1）用于微生物组的新型微流体处理装置，2）通过宏蛋白质组学和宏糖组学更好地研究微生物组的能力，以及3）高素质人员（HQP）的培训。这些技术具有多种应用和商业化的巨大潜力。

The term microbiome was introduced in 1988 and was defined “as a characteristic microbial community occupying a reasonable well-defined habitat”. Microbiomes are composed of bacteria, fungi, archaea, protists and viruses. To date microbiomes have been found on/in all plants and animal studied and are important contributors to the host organism. A disturbance of the levels of beneficial and detrimental microbiota (dysbiosis) can lead to systemic problems for the host organism. The field of microbiome study is growing rapidly with applications in human health, agriculture, biotechnology, water purification, mining, etc. Most of the microbiome studies to date rely on metagenomics and metatranscriptomics. This information in itself is not sufficient to understand the biological processes that are ongoing in a microbiome. Few publications to date have dealt with metaproteomics. This is in part due to technological and bioinformatic issues when dealing with a complex mixture of different species. My laboratory has been developing analytical technologies for the study of proteins and proteomes for over 15 years. In the last 5 years, we developed new technologies for the study of the microbiome. Here, we propose to further develop analytical technologies for the study of microbiome by metaproteomics and the study of post-translational modifications in microbiome with an initial focus on protein glycosylations. Our short term objectives (1-3 years) are to develop new approaches to identify and quantify proteins and glycosylations from complex microbiomes. In particular, we will 1) Develop methods for deep metaproteomic analyses of microbiome, and 2) develop technologies for multiplexed and rapid analyses of the microbiome glycoproteins; Medium term objectives: Our medium term objectives (2-5 years) are to develop automated microfluidic technologies for the processing, and identification of protein glycosylation from microbiomes by mass spectrometry and to demonstrate their compatibility for analyzing microbiomes. Long term objectives: (> 5years). Our long term objectives are to apply these microfluidic technologies to study the dynamicity of the microbiome, to automate these systems, and to expand their capabilities for other protein modifications. Continuous objectives: An important aspect of our objectives is to provide training for students, PDFs, and visiting scientists on the development of metaproteomics and metaglycomics technologies and mass spectrometry for microbiome analyses. The outcomes of this research will be 1) new microfluidic processing devices for microbiomes, 2) ability to better study the microbiome by metaproteomics and metaglycomics, and 3) training of highly qualified personnel (HQPs). The technologies have excellent potential for multiple applications and commercialization.