Metaproteomics technologies for microbiomes

微生物组一词于1988年引入，定义为“占据合理、明确的栖息地的一种特征微生物群落”。微生物群由细菌、真菌、古菌、原生生物和病毒组成。到目前为止，在所有研究的动植物身上都发现了微生物群，它们是寄主生物体的重要组成部分。有益和有害微生物区系水平的紊乱(生物失调)可能会导致寄主有机体出现系统性问题。随着微生物组在人类健康、农业、生物技术、净水、采矿等领域的应用，微生物组研究领域正在迅速发展。到目前为止，大多数微生物组研究依赖于元基因组学和偏转录组学。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。到目前为止，很少有文献涉及代谢蛋白质组学。这在一定程度上是由于处理不同物种的复杂混合物时的技术和生物信息学问题。 15年来，我的实验室一直在开发蛋白质和蛋白质组研究的分析技术。在过去的5年里，我们开发了研究微生物组的新技术。在这里，我们建议进一步开发利用代谢蛋白质组学研究微生物组和微生物组翻译后修饰的分析技术，最初的重点是蛋白质糖基化。 我们的短期目标(1-3年)是开发新的方法来识别和量化复杂微生物群中的蛋白质和糖基化。特别是，我们将1)开发微生物组的深度代谢蛋白质组分析方法，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)是开发自动化微流控技术，用于加工和通过质谱仪从微生物组中识别蛋白质糖基化，并证明它们在分析微生物组方面的兼容性。长期目标：(&>5年)。我们的长期目标是应用这些微流控技术来研究微生物组的动态性，使这些系统自动化，并扩大它们对其他蛋白质修饰的能力。持续的目标：我们目标的一个重要方面是为学生、PDF和来访的科学家提供关于微生物组分析的偏蛋白质组学和偏糖组学技术和质谱学的开发的培训。 这项研究的成果将是1)用于微生物组的新的微流控加工设备，2)通过代谢蛋白质组和偏糖组学更好地研究微生物组的能力，以及3)培训高素质的人员(HQP)。这些技术具有很好的多种应用和商业化潜力。

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.