Metaproteomics technologies for microbiomes

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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.