The human microbiome is a complex system of many microbial communities inhabiting a diversity of environmental niches throughout the human body. With at least an order of magnitude more cells and even greater diversity of genetic potential these microbial communities continually interact with the human host cells in complex but controlled manner that lead to normal human health. Our knowledge of the structure and function of these communities and the interactions with the human host is limited because analyses of microbial physiology and genetics have been largely confined to isolates grown in laboratories. Recent acquisition of genomic data directly from natural samples has begun to reveal the genetic potential of communities (Tyson, Nature 2004) and environments (Venter, Science 2004). The ability to obtain whole or partial genome sequences from microbial community samples has opened up the door for other system level studies of microbial communities such as community proteomics or metaproteomics (Ram, Science 2005, Lo, Nature 2007; Wilmes, ISME 2008). The human gut contains a dense, complex, and diverse microbial community. A healthy gut microbiome is clearly key for human health, thus making this system one of the major target areas of the human microbiome project. Metagenomics has recently revealed the composition of genes in the gut microbiome (Gill, Science 2006), but provides no direct information about which genes are ex pressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about what genes were expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples from two normal adult twins. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production, and carbohydrate metabolism compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-target ed glimpse of the host response to the microbiota. Similar integrated genomic, transcriptomic and proteomic studies are on-going in germ free gnotobiotic mice. In this system the mice can be directly colonized with known sequenced human gut-derived type strains of B. thetaiotao micron or E. rectale or even more complex communities. Furthermore, in this mouse system, the cecum can be removed and the microbial communities directly assayed thus providing a perfect model system for the development of omic techniques for studying host-microbial interactions.
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