ORNL - Jansson Study on Characterization
of the Human Gut Microbial Metaproteome
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Characterization of the Human Gut Microbial Metaproteome

Over the period of evolution, we human beings have co-evolved an intricate symbiosis with microorganisms that inhabit our gastrointestinal tract. These microorganisms are responsible for maintaining a healthy gut environment, they aid in digestion of our food and our immune system and they guard us against invading pathogens. In addition, some diseases, such as Crohn's disease, are somehow correlated to the composition of the gut microbiota and this is an area we and others are currently exploring. Although we are dependent on microorganisms for normal gut functioning, much remains to be learned about microbial processes in the gut that are carried out by this huge community of largely unexplored microbial cells that can amount to numbers as great as 1011 per gram of feces. Recently, we have been aided by the development of molecular tools that enable us to determine the composition of microorganisms inhabiting the intestine without having to cultivate them. In addition to the increasing amounts of information about the identities of microorganisms in the gut from our own studies and others, there have been a limited number of studies of the functional genes in the entire gut microbial metagenome, using sequencing based metagenomics approaches. A next step is to determine what genes are actually expressed and the function of the gut microbiota in different states of health and disease. This is therefore the basis of our study of the human gut microbial metaproteome described in this website. We used a shotgun proteomics approach to determine what proteins were expressed in fecal samples from a pair of healthy Swedish female identical twins. The results of this study were groundbreaking in demonstrating that first of all it was possible to get high quality protein identifications by screening metagenome sequence data collected from completely different individuals than the Swedish twins. The databases that were screened included the two metagenome sequences available at the time (Gill et al. 2006. Science. 312, 1355-1359), in addition to human proteins, the rice genome, and a series of microbial genomes representing beneficial and pathogenic human isolates, as well as environmental microbial isolates that one would not expect to find in the gut as distracters. Using this approach we were able to identify thousands of proteins in the gut. The majority of the proteins were classified into COG categories for translation, energy generation and carbohydrate metabolism. Many of the proteins could not be placed into COG functional categories and some of these "hypothetical" proteins were screened more thoroughly using advanced bioinformatics approaches. As a result some novel proteins representing previously undescribed pathways were found that were highly represented in the gut environment. These studies further pave the way for use of community proteomics approaches, or "metaproteomics" to explore other complex environmental communities.