Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activities and interactions of these microbial systems at a comprehensive level never before possible. Such information not only provides details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked and exploited under certain environmental conditions. Since bacteria naturally exist in complex ecosystems, it is imperative to develop and utilize analytical approaches that can provide molecular level details on systems consisting of mixed microbial membership. This is the realm of metaproteomics — the characterization of the complement of proteins expressed by a microbial community in an environmental sample.

► Multi-dimensional LC-MS provides deep metaproteome measurements. ► High throughput and mass accuracy capabilities for MS are critical for metaproteome measurements. ► Metaproteomics provides functional information for bioremediation of soils or sludge water. ► Metaproteomics provides information about host and microbial proteins in plant and human samples.