title: Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease.
abstract: Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut. The advances in molecular separation methods coupled with mass spectrometry (e.g., LC-MS/MS) and proteome bioinformatics have been fundamental in these novel large-scale metaproteomic studies, which have further been performed in a wide range of samples including soil, plant and human environments. Metaproteomic studies will make major progress if a comprehensive database covering the genes and expresses proteins from all gut microbial species is developed. To this end, we here present some of the main limitations of metaproteomic studies in complex microbiota environments, such as the gut, also addressing the up-to-date pipelines in sample preparation prior to fractionation/separation and mass spectrometry analysis. In addition, a novel approach to the limitations of metagenomic databases is also discussed. Finally, prospects are addressed regarding the application of metaproteomic analysis using a unified host-microbiome gene database and other meta-OMICs platforms.
authors.affiliation: Department of Health, Molecular and Physiologic Adaptations to Exercise, Centro Universitário do Distrito Federal Brasília, Brazil.
authors.forename: Bernardo A
authors.initials: BA
authors.lastname: Petriz
authors.affiliation: S-Inova Biotech, Universidade Católica Dom Bosco Campo Grande, Brazil.
authors.forename: Octávio L
authors.initials: OL
authors.lastname: Franco
keywords: LC-MS/MS; OMICS; fecal metaproteome; gut microbiota; mass spectrometry based proteomics; metabolomics; microbiota genome catalog