Metaproteomics technologies for microbiomes

微生物组一词于1988年被引入，并被定义为“占据合理的明确栖息地的特征微生物群落”。微生物组由细菌、真菌、古生菌、原生生物和病毒组成。迄今为止，在所有被研究的植物和动物身上都发现了微生物群，它们是宿主生物的重要贡献者。有益和有害微生物群水平的紊乱（生态失调）可导致宿主生物体的系统性问题。微生物组研究在人类健康、农业、生物技术、水净化、采矿等领域的应用迅速发展。迄今为止，大多数微生物组研究都依赖于宏基因组学和亚转录组学。这些信息本身并不足以理解微生物群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学问题。

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.