Grant: Discovery Grants Program - Individual

This proposal outlines a research program to advance microbiome research through the development of innovative bioanalytical techniques for metaproteomics. The gut microbiome plays a crucial role in animal and human health. The function of the microbiome is performed predominantly by proteins. Metaproteomics study the ensemble of proteins from the microbiome, their interactions and functions. The gut microbiome is highly complex, consisting of hundreds of different microbes, and current metaproteomic methods can only measure proteins from the most abundant microbes. New bioanalytical technologies are needed to provide a deeper measurement of the metaproteome. This proposal does not involve Indigenous communities, societies or individuals. This proposal builds upon the research conducted by our laboratory over the past 15 years in the development of bioanalytical techniques for metaproteomics, introducing innovative ideas to further advance this field. The objectives are in the short term (1-3 years), to develop new bioanalytical techniques for metaproteomics, focusing on the "dark field" of the metaproteome, which includes proteins, and post-translational modifications (PTMs) not currently detectable by metaproteomics. In the medium term (2-5 years), we will multiplex these techniques. In the long term (over 5 years), we will apply these technologies to study the dynamic nature of the microbiome and develop automate systems for higher throughputs. Continuous objectives: Fundamental principles of our laboratory are open knowledge sharing, nurturing expertise and Equity, Diversity and Inclusion. As such, we are committed to: Providing extensive training opportunities for students, postdoctoral fellows, and visiting scientists from around the world in the development and application of metaproteomics technologies, software, and mass spectrometry methodologies for microbiome analyses in a safe, inclusive and equitable environment. The proposed methodologies include deep multiplex metaproteomics, involving size-based fractionation, enrichment-based approaches, and depletion-based methods, combined with mass spectrometry techniques. Additionally, the project aims to develop bioanalytical techniques to study the roles of protein modifications in the microbiome using in vitro microbiome assays (RapidAIM) coupled with affinity enrichment and mass spectrometry. The impact of this research is substantial, as it will result in the development of new bioanalytical techniques for deeper metaproteomics, providing enhanced insights into the microbiome functions and the age and sex-related effects on microbiome functions as well as the training of highly qualified personnel. Previous lab-developed bioanalytical techniques and software have been licensed to industry, are applied in clinical trials for precision microbiome interventions, and are at the basis of an international consortium for precision microbiome development.