Metaproteomics is the study of all protein samples recovered directly from environmental sources. Metaproteomics is used to classify experiments that deal with all the genes and proteins identified from complex communities, where individuals cannot be binned into species or organisms types. The metaproteomics approach is comparable to gene-centric environmental genomics, or metagenomics.
Origin of the term
The term "metaproteomics" was proposed by Francisco Rodríguez-Valera to describe the genes and/or proteins most abundantly expressed in environmental samples. The term was derived from "metagenome". Wilmes and Bond proposed the term "metaproteomics" for the large-scale characterization of the entireprotein complement of environmental microbiota at a given point in time. At the same time, the terms "microbial community proteomics" and "microbial community proteogenomics" are sometimes used interchangeably for different types of experiments and results.
The first proteomics experiment was conducted with the invention of two-dimensionalpolyacrylamide gel electrophoresis. The 1980s and 1990s saw the development of mass spectrometry and mass spectrometry based proteomics. The current proteomics of microbial community makes use of both gel-based and non-gel liquid chromatography based separation, where both rely on mass spectrometry based peptide identification. While proteomics is largely a discovery-based approach that is followed by other molecular or analytical techniques to provide a full picture of the subject system, it is not limited to simple cataloging of proteins present in a sample. With the combined capabilities of "top-down" and "bottom-up" approaches, proteomics can pursue inquiries ranging from quantitation of gene expression between growth conditions to protein structural information. A metaproteomics study of the human oral microbiome found 50 bacterial genera using shotgun proteomics. The results agreed with the Human Microbiome Project, a metagenomic based approach. Similarly, metaproteomics approaches have been used in larger clinical studies linking the bacterial proteome with human health. A recent paper used shotgun proteomics to characterize the vaginal microbiome, identifying 188 unique bacterial species in 688 women profiled. This study linked vaginal microbiome groups to the efficacy of topical antiretroviral drugs to prevent HIV acquisition in women, which was attributed to bacterial metabolism of the drug in vivo. In addition, metaproteomic approaches have been used to study other aspects of the vaginal microbiome, including the immunological and inflammatory consequences of vaginal microbial dysbiosis, as well as the influence of hormonal contraceptives on the vaginal microbiome.
